AnatomyOrganismsChemicals and DrugsAnalytical, Diagnostic and Therapeutic Techniques and EquipmentPhenomena and ProcessesDisciplines and OccupationsAnthropology, Education, Sociology and Social PhenomenaTechnology, Industry, AgricultureInformation ScienceHealth Care
Molecular Dynamics SimulationComputer SimulationModels, MolecularWaterHydrogen BondingThermodynamicsProtein ConformationMolecular ConformationModels, ChemicalProtein Structure, SecondaryStatic ElectricityMotionLipid BilayersSolventsBiophysicsProtein Structure, TertiaryBinding SitesCrystallography, X-RayHydrophobic and Hydrophilic InteractionsProtein BindingProtein FoldingBiophysical PhenomenaSolutionsNuclear Magnetic Resonance, BiomolecularDimyristoylphosphatidylcholine1,2-DipalmitoylphosphatidylcholineAmino Acid SequenceQuantum TheoryEntropyMolecular Docking SimulationMagnetic Resonance SpectroscopyMolecular Sequence DataNucleic Acid ConformationLigandsIonsMembrane FluidityCatalytic DomainPeptidesTemperatureProtein StabilityMolecular StructureProtein UnfoldingProteinsProtein MultimerizationAlamethicinAlgorithmsDiffusionKineticsPorosityProtonsSoftwarePhosphatidylcholinesProtein Structure, QuaternaryCrystallographyBase PairingMutationModels, BiologicalPhase TransitionGramicidinDNA, B-FormProtein DenaturationSurface PropertiesStructure-Activity RelationshipDNATime FactorsMyoglobinDimerizationMonte Carlo MethodModels, StatisticalMechanicsModels, TheoreticalEnergy TransferNeutron DiffractionPliabilityStructural Homology, ProteinAmino Acid SubstitutionMembranes, ArtificialNanoporesCatalysisComputational BiologyMutant ProteinsPrincipal Component AnalysisOctanesBacterial ProteinsElasticityKv1.2 Potassium ChannelBiocatalysisSaltsIon ChannelsSubstrate SpecificityProtein Interaction Domains and MotifsCell MembraneStress, MechanicalHexanesTryptophanIon Channel GatingMicroscopy, Atomic ForceRotationAmyloidX-Ray Diffraction
Molecular Dynamics Simulation
A computer simulation developed to study the motion of molecules over a period of time.
Computer Simulation
Computer-based representation of physical systems and phenomena such as chemical processes.
Models, Molecular
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
Water
A clear, odorless, tasteless liquid that is essential for most animal and plant life and is an excellent solvent for many substances. The chemical formula is hydrogen oxide (H2O). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Hydrogen Bonding
A low-energy attractive force between hydrogen and another element. It plays a major role in determining the properties of water, proteins, and other compounds.
Thermodynamics
A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)
Protein Conformation
The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).
Molecular Conformation
The characteristic three-dimensional shape of a molecule.
Models, Chemical
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
Protein Structure, Secondary
The level of protein structure in which regular hydrogen-bond interactions within contiguous stretches of polypeptide chain give rise to alpha helices, beta strands (which align to form beta sheets) or other types of coils. This is the first folding level of protein conformation.
Static Electricity
The accumulation of an electric charge on a object
Motion
Physical motion, i.e., a change in position of a body or subject as a result of an external force. It is distinguished from MOVEMENT, a process resulting from biological activity.
Lipid Bilayers
Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.
Solvents
Liquids that dissolve other substances (solutes), generally solids, without any change in chemical composition, as, water containing sugar. (Grant & Hackh's Chemical Dictionary, 5th ed)
Biophysics
The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.
Protein Structure, Tertiary
The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.
Binding Sites
The parts of a macromolecule that directly participate in its specific combination with another molecule.
Crystallography, X-Ray
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Hydrophobic and Hydrophilic Interactions
The thermodynamic interaction between a substance and WATER.
Protein Binding
The process in which substances, either endogenous or exogenous, bind to proteins, peptides, enzymes, protein precursors, or allied compounds. Specific protein-binding measures are often used as assays in diagnostic assessments.
Protein Folding
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
Biophysical Phenomena
The physical characteristics and processes of biological systems.
Solutions
The homogeneous mixtures formed by the mixing of a solid, liquid, or gaseous substance (solute) with a liquid (the solvent), from which the dissolved substances can be recovered by physical processes. (From Grant & Hackh's Chemical Dictionary, 5th ed)
Nuclear Magnetic Resonance, Biomolecular
NMR spectroscopy on small- to medium-size biological macromolecules. This is often used for structural investigation of proteins and nucleic acids, and often involves more than one isotope.
Dimyristoylphosphatidylcholine
A synthetic phospholipid used in liposomes and lipid bilayers for the study of biological membranes.
1,2-Dipalmitoylphosphatidylcholine
Synthetic phospholipid used in liposomes and lipid bilayers to study biological membranes. It is also a major constituent of PULMONARY SURFACTANTS.
Amino Acid Sequence
The order of amino acids as they occur in a polypeptide chain. This is referred to as the primary structure of proteins. It is of fundamental importance in determining PROTEIN CONFORMATION.
Quantum Theory
The theory that the radiation and absorption of energy take place in definite quantities called quanta (E) which vary in size and are defined by the equation E=hv in which h is Planck's constant and v is the frequency of the radiation.
Entropy
The measure of that part of the heat or energy of a system which is not available to perform work. Entropy increases in all natural (spontaneous and irreversible) processes. (From Dorland, 28th ed)
Molecular Docking Simulation
A computer simulation technique that is used to model the interaction between two molecules. Typically the docking simulation measures the interactions of a small molecule or ligand with a part of a larger molecule such as a protein.
Magnetic Resonance Spectroscopy
Spectroscopic method of measuring the magnetic moment of elementary particles such as atomic nuclei, protons or electrons. It is employed in clinical applications such as NMR Tomography (MAGNETIC RESONANCE IMAGING).
Molecular Sequence Data
Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.
Nucleic Acid Conformation
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
Ligands
A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)
Ions
An atom or group of atoms that have a positive or negative electric charge due to a gain (negative charge) or loss (positive charge) of one or more electrons. Atoms with a positive charge are known as CATIONS; those with a negative charge are ANIONS.
Membrane Fluidity
The motion of phospholipid molecules within the lipid bilayer, dependent on the classes of phospholipids present, their fatty acid composition and degree of unsaturation of the acyl chains, the cholesterol concentration, and temperature.
Catalytic Domain
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
Peptides
Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.
Temperature
The property of objects that determines the direction of heat flow when they are placed in direct thermal contact. The temperature is the energy of microscopic motions (vibrational and translational) of the particles of atoms.
Protein Stability
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
Molecular Structure
The location of the atoms, groups or ions relative to one another in a molecule, as well as the number, type and location of covalent bonds.
Protein Unfolding
Conformational transitions of the shape of a protein to various unfolded states.
Proteins
Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Protein Multimerization
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
Alamethicin
A cyclic nonadecapeptide antibiotic that can act as an ionophore and is produced by strains of Trichoderma viride. (From Singleton & Sainsbury, Dictionary of Microbiology and Molecular Biology, 2d ed)
Algorithms
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
Diffusion
The tendency of a gas or solute to pass from a point of higher pressure or concentration to a point of lower pressure or concentration and to distribute itself throughout the available space. Diffusion, especially FACILITATED DIFFUSION, is a major mechanism of BIOLOGICAL TRANSPORT.
Kinetics
The rate dynamics in chemical or physical systems.
Porosity
Condition of having pores or open spaces. This often refers to bones, bone implants, or bone cements, but can refer to the porous state of any solid substance.
Protons
Stable elementary particles having the smallest known positive charge, found in the nuclei of all elements. The proton mass is less than that of a neutron. A proton is the nucleus of the light hydrogen atom, i.e., the hydrogen ion.
Software
Sequential operating programs and data which instruct the functioning of a digital computer.
Phosphatidylcholines
Derivatives of phosphatidic acids in which the phosphoric acid is bound in ester linkage to a choline moiety. Complete hydrolysis yields 1 mole of glycerol, phosphoric acid and choline and 2 moles of fatty acids.
Protein Structure, Quaternary
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
Crystallography
The branch of science that deals with the geometric description of crystals and their internal arrangement. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Base Pairing
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
Mutation
Any detectable and heritable change in the genetic material that causes a change in the GENOTYPE and which is transmitted to daughter cells and to succeeding generations.
Models, Biological
Theoretical representations that simulate the behavior or activity of biological processes or diseases. For disease models in living animals, DISEASE MODELS, ANIMAL is available. Biological models include the use of mathematical equations, computers, and other electronic equipment.
Phase Transition
A change of a substance from one form or state to another.
Gramicidin
A group of peptide antibiotics from BACILLUS brevis. Gramicidin C or S is a cyclic, ten-amino acid polypeptide and gramicidins A, B, D are linear. Gramicidin is one of the two principal components of TYROTHRICIN.
DNA, B-Form
The most common form of DNA found in nature. It is a right-handed helix with 10 base pairs per turn, a pitch of 0.338 nm per base pair and a helical diameter of 1.9 nm.
Protein Denaturation
Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.
Surface Properties
Characteristics or attributes of the outer boundaries of objects, including molecules.
Structure-Activity Relationship
The relationship between the chemical structure of a compound and its biological or pharmacological activity. Compounds are often classed together because they have structural characteristics in common including shape, size, stereochemical arrangement, and distribution of functional groups.
DNA
A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).
Time Factors
Elements of limited time intervals, contributing to particular results or situations.
Myoglobin
A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.
Dimerization
The process by which two molecules of the same chemical composition form a condensation product or polymer.
Monte Carlo Method
In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)
Models, Statistical
Statistical formulations or analyses which, when applied to data and found to fit the data, are then used to verify the assumptions and parameters used in the analysis. Examples of statistical models are the linear model, binomial model, polynomial model, two-parameter model, etc.
Mechanics
The branch of physics which deals with the motions of material bodies, including kinematics, dynamics, and statics. When the laws of mechanics are applied to living structures, as to the locomotor system, it is referred to as BIOMECHANICAL PHENOMENA. (From Dorland, 28th ed)
Models, Theoretical
Theoretical representations that simulate the behavior or activity of systems, processes, or phenomena. They include the use of mathematical equations, computers, and other electronic equipment.
Energy Transfer
The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.
Neutron Diffraction
The scattering of NEUTRONS by matter, especially crystals, with accompanying variation in intensity due to interference effects. It is useful in CRYSTALLOGRAPHY and POWDER DIFFRACTION.
Pliability
The quality or state of being able to be bent or creased repeatedly. (From Webster, 3d ed)
Structural Homology, Protein
The degree of 3-dimensional shape similarity between proteins. It can be an indication of distant AMINO ACID SEQUENCE HOMOLOGY and used for rational DRUG DESIGN.
Amino Acid Substitution
The naturally occurring or experimentally induced replacement of one or more AMINO ACIDS in a protein with another. If a functionally equivalent amino acid is substituted, the protein may retain wild-type activity. Substitution may also diminish, enhance, or eliminate protein function. Experimentally induced substitution is often used to study enzyme activities and binding site properties.
Membranes, Artificial
Artificially produced membranes, such as semipermeable membranes used in artificial kidney dialysis (RENAL DIALYSIS), monomolecular and bimolecular membranes used as models to simulate biological CELL MEMBRANES. These membranes are also used in the process of GUIDED TISSUE REGENERATION.
Nanopores
Small holes of nanometer dimensions in a membrane, that can be used as single molecule detectors. The pores can be biological or synthetic.
Catalysis
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
Computational Biology
A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.
Mutant Proteins
Proteins produced from GENES that have acquired MUTATIONS.
Principal Component Analysis
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Octanes
Eight-carbon saturated hydrocarbon group of the methane series. Include isomers and derivatives.
Bacterial Proteins
Proteins found in any species of bacterium.
Elasticity
Resistance and recovery from distortion of shape.
Kv1.2 Potassium Channel
A delayed rectifier subtype of shaker potassium channels that is selectively inhibited by a variety of SCORPION VENOMS.
Biocatalysis
The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.
Salts
Substances produced from the reaction between acids and bases; compounds consisting of a metal (positive) and nonmetal (negative) radical. (Grant & Hackh's Chemical Dictionary, 5th ed)
Ion Channels
Gated, ion-selective glycoproteins that traverse membranes. The stimulus for ION CHANNEL GATING can be due to a variety of stimuli such as LIGANDS, a TRANSMEMBRANE POTENTIAL DIFFERENCE, mechanical deformation or through INTRACELLULAR SIGNALING PEPTIDES AND PROTEINS.
Substrate Specificity
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
Protein Interaction Domains and Motifs
Protein modules with conserved ligand-binding surfaces which mediate specific interaction functions in SIGNAL TRANSDUCTION PATHWAYS and the specific BINDING SITES of their cognate protein LIGANDS.
Cell Membrane
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
Stress, Mechanical
A purely physical condition which exists within any material because of strain or deformation by external forces or by non-uniform thermal expansion; expressed quantitatively in units of force per unit area.
Hexanes
Six-carbon saturated hydrocarbon group of the methane series. Include isomers and derivatives. Various polyneuropathies are caused by hexane poisoning.
Tryptophan
An essential amino acid that is necessary for normal growth in infants and for NITROGEN balance in adults. It is a precursor of INDOLE ALKALOIDS in plants. It is a precursor of SEROTONIN (hence its use as an antidepressant and sleep aid). It can be a precursor to NIACIN, albeit inefficiently, in mammals.
Ion Channel Gating
The opening and closing of ion channels due to a stimulus. The stimulus can be a change in membrane potential (voltage-gated), drugs or chemical transmitters (ligand-gated), or a mechanical deformation. Gating is thought to involve conformational changes of the ion channel which alters selective permeability.
Microscopy, Atomic Force
A type of scanning probe microscopy in which a probe systematically rides across the surface of a sample being scanned in a raster pattern. The vertical position is recorded as a spring attached to the probe rises and falls in response to peaks and valleys on the surface. These deflections produce a topographic map of the sample.
Rotation
Motion of an object in which either one or more points on a line are fixed. It is also the motion of a particle about a fixed point. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Amyloid
A fibrous protein complex that consists of proteins folded into a specific cross beta-pleated sheet structure. This fibrillar structure has been found as an alternative folding pattern for a variety of functional proteins. Deposits of amyloid in the form of AMYLOID PLAQUES are associated with a variety of degenerative diseases. The amyloid structure has also been found in a number of functional proteins that are unrelated to disease.
X-Ray Diffraction
The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Electrons
Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.
Melitten
Basic polypeptide from the venom of the honey bee (Apis mellifera). It contains 26 amino acids, has cytolytic properties, causes contracture of muscle, releases histamine, and disrupts surface tension, probably due to lysis of cell and mitochondrial membranes.
Amino Acid Motifs
Commonly observed structural components of proteins formed by simple combinations of adjacent secondary structures. A commonly observed structure may be composed of a CONSERVED SEQUENCE which can be represented by a CONSENSUS SEQUENCE.
Pressure
A type of stress exerted uniformly in all directions. Its measure is the force exerted per unit area. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Circular Dichroism
A change from planar to elliptic polarization when an initially plane-polarized light wave traverses an optically active medium. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Mutagenesis, Site-Directed
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
Micelles
Particles consisting of aggregates of molecules held loosely together by secondary bonds. The surface of micelles are usually comprised of amphiphatic compounds that are oriented in a way that minimizes the energy of interaction between the micelle and its environment. Liquids that contain large numbers of suspended micelles are referred to as EMULSIONS.
Crystallization
The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Muramidase
A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.
Macromolecular Substances
Compounds and molecular complexes that consist of very large numbers of atoms and are generally over 500 kDa in size. In biological systems macromolecular substances usually can be visualized using ELECTRON MICROSCOPY and are distinguished from ORGANELLES by the lack of a membrane structure.
Alanine
A non-essential amino acid that occurs in high levels in its free state in plasma. It is produced from pyruvate by transamination. It is involved in sugar and acid metabolism, increases IMMUNITY, and provides energy for muscle tissue, BRAIN, and the CENTRAL NERVOUS SYSTEM.
Nanostructures
Materials which have structured components with at least one dimension in the range of 1 to 100 nanometers. These include NANOCOMPOSITES; NANOPARTICLES; NANOTUBES; and NANOWIRES.
Neutrons
Electrically neutral elementary particles found in all atomic nuclei except light hydrogen; the mass is equal to that of the proton and electron combined and they are unstable when isolated from the nucleus, undergoing beta decay. Slow, thermal, epithermal, and fast neutrons refer to the energy levels with which the neutrons are ejected from heavier nuclei during their decay.
Hydrogen
The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.
Enzyme Stability
The extent to which an enzyme retains its structural conformation or its activity when subjected to storage, isolation, and purification or various other physical or chemical manipulations, including proteolytic enzymes and heat.
Allosteric Regulation
The modification of the reactivity of ENZYMES by the binding of effectors to sites (ALLOSTERIC SITES) on the enzymes other than the substrate BINDING SITES.
Apoproteins
The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).
Spectrophotometry, Infrared
Spectrophotometry in the infrared region, usually for the purpose of chemical analysis through measurement of absorption spectra associated with rotational and vibrational energy levels of molecules. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Protein Subunits
Single chains of amino acids that are the units of multimeric PROTEINS. Multimeric proteins can be composed of identical or non-identical subunits. One or more monomeric subunits may compose a protomer which itself is a subunit structure of a larger assembly.
Hydrodynamics
The motion of fluids, especially noncompressible liquids, under the influence of internal and external forces.
Drug Design
The molecular designing of drugs for specific purposes (such as DNA-binding, enzyme inhibition, anti-cancer efficacy, etc.) based on knowledge of molecular properties such as activity of functional groups, molecular geometry, and electronic structure, and also on information cataloged on analogous molecules. Drug design is generally computer-assisted molecular modeling and does not include pharmacokinetics, dosage analysis, or drug administration analysis.
Scattering, Small Angle
Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale.
Calorimetry
The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
Escherichia coli Proteins
Proteins obtained from ESCHERICHIA COLI.
Allosteric Site
A site on an enzyme which upon binding of a modulator, causes the enzyme to undergo a conformational change that may alter its catalytic or binding properties.
Carbohydrate Conformation
The characteristic 3-dimensional shape of a carbohydrate.
Sequence Homology, Amino Acid
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
Amino Acids
Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
Escherichia coli
A species of gram-negative, facultatively anaerobic, rod-shaped bacteria (GRAM-NEGATIVE FACULTATIVELY ANAEROBIC RODS) commonly found in the lower part of the intestine of warm-blooded animals. It is usually nonpathogenic, but some strains are known to produce DIARRHEA and pyogenic infections. Pathogenic strains (virotypes) are classified by their specific pathogenic mechanisms such as toxins (ENTEROTOXIGENIC ESCHERICHIA COLI), etc.
Peptide Fragments
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
Hydrogen-Ion Concentration
The normality of a solution with respect to HYDROGEN ions; H+. It is related to acidity measurements in most cases by pH = log 1/2[1/(H+)], where (H+) is the hydrogen ion concentration in gram equivalents per liter of solution. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Amyloid beta-Peptides
Peptides generated from AMYLOID BETA-PEPTIDES PRECURSOR. An amyloid fibrillar form of these peptides is the major component of amyloid plaques found in individuals with Alzheimer's disease and in aged individuals with trisomy 21 (DOWN SYNDROME). The peptide is found predominantly in the nervous system, but there have been reports of its presence in non-neural tissue.
Truncated Hemoglobins
A family of hemoglobin-like proteins found in BACTERIA; PLANTS; and unicellular eukaryotes. Truncated hemoglobins are distantly related to vertebrate hemoglobins and are typically shorter than vertebrate hemoglobins by 20-40 residues.
Camphor 5-Monooxygenase
A soluble cytochrome P-450 enzyme that catalyzes camphor monooxygenation in the presence of putidaredoxin, putidaredoxin reductase, and molecular oxygen. This enzyme, encoded by the CAMC gene also known as CYP101, has been crystallized from bacteria and the structure is well defined. Under anaerobic conditions, this enzyme reduces the polyhalogenated compounds bound at the camphor-binding site.
Sperm Whale
The species Physeter catodon (also called Physeter macrocephalus), in the family Physeteridae. The common name is derived from the milky wax substance in its head (spermaceti). The species also produces an intestinal secretion AMBERGRIS, which was previously used in perfumes. The sperm whale is the largest toothed MAMMAL in the world.
Membrane Lipids
Lipids, predominantly phospholipids, cholesterol and small amounts of glycolipids found in membranes including cellular and intracellular membranes. These lipids may be arranged in bilayers in the membranes with integral proteins between the layers and peripheral proteins attached to the outside. Membrane lipids are required for active transport, several enzymatic activities and membrane formation.
Multiprotein Complexes
Macromolecular complexes formed from the association of defined protein subunits.
Nucleotides
The monomeric units from which DNA or RNA polymers are constructed. They consist of a purine or pyrimidine base, a pentose sugar, and a phosphate group. (From King & Stansfield, A Dictionary of Genetics, 4th ed)
Surface Tension
The force acting on the surface of a liquid, tending to minimize the area of the surface. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Ribonuclease, Pancreatic
An enzyme that catalyzes the endonucleolytic cleavage of pancreatic ribonucleic acids to 3'-phosphomono- and oligonucleotides ending in cytidylic or uridylic acids with 2',3'-cyclic phosphate intermediates. EC 3.1.27.5.
Whales
Large marine mammals of the order CETACEA. In the past, they were commercially valued for whale oil, for their flesh as human food and in ANIMAL FEED and FERTILIZERS, and for baleen. Today, there is a moratorium on most commercial whaling, as all species are either listed as endangered or threatened.
Phospholipids
Lipids containing one or more phosphate groups, particularly those derived from either glycerol (phosphoglycerides see GLYCEROPHOSPHOLIPIDS) or sphingosine (SPHINGOLIPIDS). They are polar lipids that are of great importance for the structure and function of cell membranes and are the most abundant of membrane lipids, although not stored in large amounts in the system.
Fullerenes
A polyhedral CARBON structure composed of around 60-80 carbon atoms in pentagon and hexagon configuration. They are named after Buckminster Fuller because of structural resemblance to geodesic domes. Fullerenes can be made in high temperature such as arc discharge in an inert atmosphere.
Heme
The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.
Stochastic Processes
Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.
Carbon
A nonmetallic element with atomic symbol C, atomic number 6, and atomic weight [12.0096; 12.0116]. It may occur as several different allotropes including DIAMOND; CHARCOAL; and GRAPHITE; and as SOOT from incompletely burned fuel.
Chemistry, Physical
The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.
Stereoisomerism
The phenomenon whereby compounds whose molecules have the same number and kind of atoms and the same atomic arrangement, but differ in their spatial relationships. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)
Electrochemistry
The study of chemical changes resulting from electrical action and electrical activity resulting from chemical changes.
Oligopeptides
Peptides composed of between two and twelve amino acids.
Connectin
A giant elastic protein of molecular mass ranging from 2,993 kDa (cardiac), 3,300 kDa (psoas), to 3,700 kDa (soleus) having a kinase domain. The amino- terminal is involved in a Z line binding, and the carboxy-terminal region is bound to the myosin filament with an overlap between the counter-connectin filaments at the M line.
Permeability
Property of membranes and other structures to permit passage of light, heat, gases, liquids, metabolites, and mineral ions.
Aprotinin
A single-chain polypeptide derived from bovine tissues consisting of 58 amino-acid residues. It is an inhibitor of proteolytic enzymes including CHYMOTRYPSIN; KALLIKREIN; PLASMIN; and TRYPSIN. It is used in the treatment of HEMORRHAGE associated with raised plasma concentrations of plasmin. It is also used to reduce blood loss and transfusion requirements in patients at high risk of major blood loss during and following open heart surgery with EXTRACORPOREAL CIRCULATION. (Reynolds JEF(Ed): Martindale: The Extra Pharmacopoeia (electronic version). Micromedex, Inc, Englewood, CO, 1995)
Sequence Alignment
The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.
Nanotechnology
The development and use of techniques to study physical phenomena and construct structures in the nanoscale size range or smaller.
Nanotubes, Carbon
Nanometer-sized tubes composed mainly of CARBON. Such nanotubes are used as probes for high-resolution structural and chemical imaging of biomolecules with ATOMIC FORCE MICROSCOPY.
Histidine
An essential amino acid that is required for the production of HISTAMINE.
Sodium
A member of the alkali group of metals. It has the atomic symbol Na, atomic number 11, and atomic weight 23.
Membrane Proteins
Proteins which are found in membranes including cellular and intracellular membranes. They consist of two types, peripheral and integral proteins. They include most membrane-associated enzymes, antigenic proteins, transport proteins, and drug, hormone, and lectin receptors.
Cations
Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.
Biomechanical Phenomena
The properties, processes, and behavior of biological systems under the action of mechanical forces.
Bacteriorhodopsins
Rhodopsins found in the PURPLE MEMBRANE of halophilic archaea such as HALOBACTERIUM HALOBIUM. Bacteriorhodopsins function as an energy transducers, converting light energy into electrochemical energy via PROTON PUMPS.
Physical Processes
The forces and principles of action of matter and energy.
G-Quadruplexes
Higher-order DNA and RNA structures formed from guanine-rich sequences. They are formed around a core of at least 2 stacked tetrads of hydrogen-bonded GUANINE bases. They can be formed from one two or four separate strands of DNA (or RNA) and can display a wide variety of topologies, which are a consequence of various combinations of strand direction, length, and sequence. (From Nucleic Acids Res. 2006;34(19):5402-15)
Spectroscopy, Fourier Transform Infrared
A spectroscopic technique in which a range of wavelengths is presented simultaneously with an interferometer and the spectrum is mathematically derived from the pattern thus obtained.
Base Sequence
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Protein Refolding
Conformational transitions of a protein from unfolded states to a more folded state.
Databases, Protein
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
Phosphoric Triester Hydrolases
A class of enzymes that catalyze the hydrolysis of one of the three ester bonds in a phosphotriester-containing compound.
Movement
The act, process, or result of passing from one place or position to another. It differs from LOCOMOTION in that locomotion is restricted to the passing of the whole body from one place to another, while movement encompasses both locomotion but also a change of the position of the whole body or any of its parts. Movement may be used with reference to humans, vertebrate and invertebrate animals, and microorganisms. Differentiate also from MOTOR ACTIVITY, movement associated with behavior.
Phosphatidylethanolamines
Derivatives of phosphatidic acids in which the phosphoric acid is bound in ester linkage to an ethanolamine moiety. Complete hydrolysis yields 1 mole of glycerol, phosphoric acid and ethanolamine and 2 moles of fatty acids.
Lysine
An essential amino acid. It is often added to animal feed.
Liquid Crystals
Materials in intermediate state between solid and liquid.
Spin Labels
Molecules which contain an atom or a group of atoms exhibiting an unpaired electron spin that can be detected by electron spin resonance spectroscopy and can be bonded to another molecule. (McGraw-Hill Dictionary of Chemical and Technical Terms, 4th ed)
Retinaldehyde
A carotenoid constituent of visual pigments. It is the oxidized form of retinol which functions as the active component of the visual cycle. It is bound to the protein opsin forming the complex rhodopsin. When stimulated by visible light, the retinal component of the rhodopsin complex undergoes isomerization at the 11-position of the double bond to the cis-form; this is reversed in "dark" reactions to return to the native trans-configuration.
Aspartic Acid
One of the non-essential amino acids commonly occurring in the L-form. It is found in animals and plants, especially in sugar cane and sugar beets. It may be a neurotransmitter.
Ribosome Subunits, Large, Archaeal
The large subunit of the archaeal 70s ribosome. It is composed of the 23S RIBOSOMAL RNA, the 5S RIBOSOMAL RNA, and about 40 different RIBOSOMAL PROTEINS.
Phosphatidylglycerols
A nitrogen-free class of lipids present in animal and particularly plant tissues and composed of one mole of glycerol and 1 or 2 moles of phosphatidic acid. Members of this group differ from one another in the nature of the fatty acids released on hydrolysis.
Isomerism
The phenomenon whereby certain chemical compounds have structures that are different although the compounds possess the same elemental composition. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 5th ed)
HIV Protease
Enzyme of the human immunodeficiency virus that is required for post-translational cleavage of gag and gag-pol precursor polyproteins into functional products needed for viral assembly. HIV protease is an aspartic protease encoded by the amino terminus of the pol gene.
Spectrometry, Fluorescence
Measurement of the intensity and quality of fluorescence.
Streptomyces lividans
An actinomycete used for production of commercial ANTIBIOTICS and as a host for gene cloning.
Aquaporins
A class of porins that allow the passage of WATER and other small molecules across CELL MEMBRANES.
Scattering, Radiation
The diversion of RADIATION (thermal, electromagnetic, or nuclear) from its original path as a result of interactions or collisions with atoms, molecules, or larger particles in the atmosphere or other media. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Mechanical Processes
The behaviors of materials under force.
Transition Temperature
The temperature at which a substance changes from one state or conformation of matter to another.
Spectrum Analysis
The measurement of the amplitude of the components of a complex waveform throughout the frequency range of the waveform. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Population Dynamics
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
Adenine
A purine base and a fundamental unit of ADENINE NUCLEOTIDES.
Acetylcholinesterase
An enzyme that catalyzes the hydrolysis of ACETYLCHOLINE to CHOLINE and acetate. In the CNS, this enzyme plays a role in the function of peripheral neuromuscular junctions. EC 3.1.1.7.
Reproducibility of Results
The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.
Carbon Monoxide
Carbon monoxide (CO). A poisonous colorless, odorless, tasteless gas. It combines with hemoglobin to form carboxyhemoglobin, which has no oxygen carrying capacity. The resultant oxygen deprivation causes headache, dizziness, decreased pulse and respiratory rates, unconsciousness, and death. (From Merck Index, 11th ed)
Arginine
An essential amino acid that is physiologically active in the L-form.
Rhodopsin
A purplish-red, light-sensitive pigment found in RETINAL ROD CELLS of most vertebrates. It is a complex consisting of a molecule of ROD OPSIN and a molecule of 11-cis retinal (RETINALDEHYDE). Rhodopsin exhibits peak absorption wavelength at about 500 nm.
Vibration
A continuing periodic change in displacement with respect to a fixed reference. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
Lipids
A generic term for fats and lipoids, the alcohol-ether-soluble constituents of protoplasm, which are insoluble in water. They comprise the fats, fatty oils, essential oils, waxes, phospholipids, glycolipids, sulfolipids, aminolipids, chromolipids (lipochromes), and fatty acids. (Grant & Hackh's Chemical Dictionary, 5th ed)
Asparagine
A non-essential amino acid that is involved in the metabolic control of cell functions in nerve and brain tissue. It is biosynthesized from ASPARTIC ACID and AMMONIA by asparagine synthetase. (From Concise Encyclopedia Biochemistry and Molecular Biology, 3rd ed)
Haloarcula marismortui
A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.
RNA
A polynucleotide consisting essentially of chains with a repeating backbone of phosphate and ribose units to which nitrogenous bases are attached. RNA is unique among biological macromolecules in that it can encode genetic information, serve as an abundant structural component of cells, and also possesses catalytic activity. (Rieger et al., Glossary of Genetics: Classical and Molecular, 5th ed)
Deuterium
Deuterium. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.
Methanol
A colorless, flammable liquid used in the manufacture of FORMALDEHYDE and ACETIC ACID, in chemical synthesis, antifreeze, and as a solvent. Ingestion of methanol is toxic and may cause blindness.
Anisotropy
A physical property showing different values in relation to the direction in or along which the measurement is made. The physical property may be with regard to thermal or electric conductivity or light refraction. In crystallography, it describes crystals whose index of refraction varies with the direction of the incident light. It is also called acolotropy and colotropy. The opposite of anisotropy is isotropy wherein the same values characterize the object when measured along axes in all directions.

From atomic to mesoscopic descriptions of the internal dynamics of DNA. (1/3649)

An analysis of four 1-ns molecular dynamics trajectories for two different 15-bp oligonucleotides is presented. Our aim is to show which groups of atoms can be treated as rigid bodies within a bead representation of DNA, independently of the base sequence and for any conformations belonging to the A/B family. Five models with moderate intragroup deformations are proposed in which the groups are formed of atoms belonging to a single nucleotide or to a complementary nucleotide pair. The influence of group deformation in two of these models is studied using canonical correlation analysis, and it is shown that the internal DNA dynamics is indeed dominated by the rigid motion of the defined atom groups. Finally, using one of the models within a bead representation of duplex DNA makes it possible to obtain stretching, torsional, and bending rigidities in reasonable agreement with experiment but points to strongly correlated stretching motions.  (+info)

Molecular dynamics of synthetic leucine-serine ion channels in a phospholipid membrane. (2/3649)

Molecular dynamics calculations were carried out on models of two synthetic leucine-serine ion channels: a tetrameric bundle with sequence (LSLLLSL)(3)NH(2) and a hexameric bundle with sequence (LSSLLSL)(3)NH(2). Each protein bundle is inserted in a palmitoyloleoylphosphatidylcholine bilayer membrane and solvated by simple point charge water molecules inside the pore and at both mouths. Both systems appear to be stable in the absence of an electric field during the 4 ns of molecular dynamics simulation. The water motion in the narrow pore of the four-helix bundle is highly restricted and may provide suitable conditions for proton transfer via a water wire mechanism. In the wider hexameric pore, the water diffuses much more slowly than in bulk but is still mobile. This, along with the dimensions of the pore, supports the observation that this peptide is selective for monovalent cations. Reasonable agreement of predicted conductances with experimentally determined values lends support to the validity of the simulations.  (+info)

Combined Monte Carlo and molecular dynamics simulation of fully hydrated dioleyl and palmitoyl-oleyl phosphatidylcholine lipid bilayers. (3/3649)

We have applied a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer to hydrated bilayers of dioleyl-phosphatidylcholine (DOPC) and palmitoyl-oleyl phosphatidylcholine (POPC). The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer in a constant volume and temperature ensemble. The procedure is applied to bilayers of 128 molecules of POPC with 4628 water molecules, and 128 molecules of DOPC with 4825 water molecules. Progress toward equilibration is almost three times as fast in central processing unit (CPU) time compared with a purely molecular dynamics (MD) simulation. Equilibration is complete, as judged by the lack of energy drift in 200-ps runs of continuous MD. After the equilibrium state was reached, as determined by agreement between the simulation volume per lipid molecule with experiment, continuous MD was run in an ensemble in which the lateral area was restrained to fluctuate about a mean value and a pressure of 1 atm applied normal to the bilayer surface. Three separate continuous MD runs, 200 ps in duration each, separated by 10,000 CBMC steps, were carried out for each system. Properties of the systems were calculated and averaged over the three separate runs. Results of the simulations are presented and compared with experimental data and with other recent simulations of POPC and DOPC. Analysis of the hydration environment in the headgroups supports a mechanism by which unsaturation contributes to reduced transition temperatures. In this view, the relatively horizontal orientation of the unsaturated bond increases the area per lipid, resulting in increased water penetration between the headgroups. As a result the headgroup-headgroup interactions are attenuated and shielded, and this contributes to the lowered transition temperature.  (+info)

Molecular dynamics study of the KcsA potassium channel. (4/3649)

The structural, dynamical, and thermodynamic properties of a model potassium channel are studied using molecular dynamics simulations. We use the recently unveiled protein structure for the KcsA potassium channel from Streptomyces lividans. Total and free energy profiles of potassium and sodium ions reveal a considerable preference for the larger potassium ions. The selectivity of the channel arises from its ability to completely solvate the potassium ions, but not the smaller sodium ions. Self-diffusion of water within the narrow selectivity filter is found to be reduced by an order of magnitude from bulk levels, whereas the wider hydrophobic section of the pore maintains near-bulk self-diffusion. Simulations examining multiple ion configurations suggest a two-ion channel. Ion diffusion is found to be reduced to approximately 1/3 of bulk diffusion within the selectivity filter. The reduced ion mobility does not hinder the passage of ions, as permeation appears to be driven by Coulomb repulsion within this multiple ion channel.  (+info)

Permeation of ions across the potassium channel: Brownian dynamics studies. (5/3649)

The physical mechanisms underlying the transport of ions across a model potassium channel are described. The shape of the model channel corresponds closely to that deduced from crystallography. From electrostatic calculations, we show that an ion permeating the channel, in the absence of any residual charges, encounters an insurmountable energy barrier arising from induced surface charges. Carbonyl groups along the selectivity filter, helix dipoles near the oval chamber, and mouth dipoles near the channel entrances together transform the energy barrier into a deep energy well. Two ions are attracted to this well, and their presence in the channel permits ions to diffuse across it under the influence of an electric field. Using Brownian dynamics simulations, we determine the magnitude of currents flowing across the channel under various conditions. The conductance increases with increasing dipole strength and reaches its maximum rapidly; a further increase in dipole strength causes a steady decrease in the channel conductance. The current also decreases systematically when the effective dielectric constant of the channel is lowered. The conductance with the optimal choice of dipoles reproduces the experimental value when the dielectric constant of the channel is assumed to be 60. The current-voltage relationship obtained with symmetrical solutions is linear when the applied potential is less than approximately 100 mV but deviates from Ohm's law at a higher applied potential. The reversal potentials obtained with asymmetrical solutions are in agreement with those predicted by the Nernst equation. The conductance exhibits the saturation property observed experimentally. We discuss the implications of these findings for the transport of ions across the potassium channels and membrane channels in general.  (+info)

Molecular dynamics of retinoic acid-induced craniofacial malformations: implications for the origin of gnathostome jaws. (6/3649)

BACKGROUND: Intake of retinoic acid (RA) or of its precursor, vitamin A, during early pregnancy is associated with increased incidence of craniofacial lesions. The origin of these teratogenic effects remains enigmatic as in cranial neural crest cells (CNCCs), which largely contribute to craniofacial structures, the RA-transduction pathway is not active. Recent results suggest that RA could act on the endoderm of the first pharyngeal arch (1stPA), through a RARbeta-dependent mechanism. METHODOLOGY/PRINCIPAL FINDINGS: Here we show that RA provokes dramatically different craniofacial malformations when administered at slightly different developmental times within a narrow temporal interval corresponding to the colonization of the 1(st) PA by CNCCs. We provide evidence showing that RA acts on the signalling epithelium of the 1(st) PA, gradually reducing the expression of endothelin-1 and Fgf8. These two molecular signals are instrumental in activating Dlx genes in incoming CNCCs, thereby triggering the morphogenetic programs, which specify different jaw elements. CONCLUSIONS/SIGNIFICANCE: The anatomical series induced by RA-treatments at different developmental times parallels, at least in some instances, the supposed origin of modern jaws (e.g., the fate of the incus). Our results might provide a conceptual framework for the rise of jaw morphotypes characteristic of gnathostomes.  (+info)

Computer-aided lead optimization: improved small-molecule inhibitor of the zinc endopeptidase of botulinum neurotoxin serotype A. (7/3649)

Optimization of a serotype-selective, small-molecule inhibitor of botulinum neurotoxin serotype A (BoNTA) endopeptidase is a formidable challenge because the enzyme-substrate interface is unusually large and the endopeptidase itself is a large, zinc-binding protein with a complex fold that is difficult to simulate computationally. We conducted multiple molecular dynamics simulations of the endopeptidase in complex with a previously described inhibitor (K(i) (app) of 7+/-2.4 microM) using the cationic dummy atom approach. Based on our computational results, we hypothesized that introducing a hydroxyl group to the inhibitor could improve its potency. Synthesis and testing of the hydroxyl-containing analog as a BoNTA endopeptidase inhibitor showed a twofold improvement in inhibitory potency (K(i) (app) of 3.8+/-0.8 microM) with a relatively small increase in molecular weight (16 Da). The results offer an improved template for further optimization of BoNTA endopeptidase inhibitors and demonstrate the effectiveness of the cationic dummy atom approach in the design and optimization of zinc protease inhibitors.  (+info)

Automated builder and database of protein/membrane complexes for molecular dynamics simulations. (8/3649)

Molecular dynamics simulations of membrane proteins have provided deeper insights into their functions and interactions with surrounding environments at the atomic level. However, compared to solvation of globular proteins, building a realistic protein/membrane complex is still challenging and requires considerable experience with simulation software. Membrane Builder in the CHARMM-GUI website (http://www.charmm-gui.org) helps users to build such a complex system using a web browser with a graphical user interface. Through a generalized and automated building process including system size determination as well as generation of lipid bilayer, pore water, bulk water, and ions, a realistic membrane system with virtually any kinds and shapes of membrane proteins can be generated in 5 minutes to 2 hours depending on the system size. Default values that were elaborated and tested extensively are given in each step to provide reasonable options and starting points for both non-expert and expert users. The efficacy of Membrane Builder is illustrated by its applications to 12 transmembrane and 3 interfacial membrane proteins, whose fully equilibrated systems with three different types of lipid molecules (DMPC, DPPC, and POPC) and two types of system shapes (rectangular and hexagonal) are freely available on the CHARMM-GUI website. One of the most significant advantages of using the web environment is that, if a problem is found, users can go back and re-generate the whole system again before quitting the browser. Therefore, Membrane Builder provides the intuitive and easy way to build and simulate the biologically important membrane system.  (+info)

Uranyl adsorption at muscovite surface through molecular dynamics simulation: Interfacial structure and adsorption free energy...
N. Loganathan, Andrey G. Kalinichev. Uranyl adsorption at muscovite surface through molecular dynamics simulation: Interfacial structure and adsorption free energy profiles. 51st Annual Meeting of The Clay Minerals Society, Clay Minerals Society, May 2014, College Station, TX, United States. ⟨in2p3-01577710⟩ ...
http://hal.in2p3.fr/in2p3-01577710
Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation -...Origins of biological function in DNA and RNA hairpin loop motifs from replica exchange molecular dynamics simulation -...
Deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) have remarkably similar chemical structures, but despite this, they play significantly different roles in modern biology. In this article, we explore the possible conformations of DNA and RNA hairpins to better understand the fundamental differences in structur Complex molecular systems: supramolecules, biomolecules and interfaces
http://pubs.rsc.org/en/content/articlelanding/2018/cp/c7cp06355e
Coarse-grained molecular dynamics simulations of the energetics of helix insertion into a lipid bilayer. - Oxford Neuroscience
Experimental and computational studies have indicated that hydrophobicity plays a key role in driving the insertion of transmembrane alpha-helices into lipid bilayers. Molecular dynamics simulations allow exploration of the nature of the interactions of transmembrane alpha-helices with their lipid bilayer environment. In particular, coarse-grained simulations have considerable potential for studying many aspects of membrane proteins, ranging from their self-assembly to the relation between their structure and function. However, there is a need to evaluate the accuracy of coarse-grained estimates of the energetics of transmembrane helix insertion. Here, three levels of complexity of model system have been explored to enable such an evaluation. First, calculated free energies of partitioning of amino acid side chains between water and alkane yielded an excellent correlation with experiment. Second, free energy profiles for transfer of amino acid side chains along the normal to a phosphatidylcholine
https://www.neuroscience.ox.ac.uk/publications/100612
Dynamics of micelle-nanoparticle systems undergoing shear: a coarse-grained molecular dynamics approach - Soft Matter (RSC...Dynamics of micelle-nanoparticle systems undergoing shear: a coarse-grained molecular dynamics approach - Soft Matter (RSC...
Recent work has shown that polymeric micelles can template nanoparticles via interstitial sites in shear-ordered micelle solutions. In this work, we report results based on a coarse-grained molecular dynamics (CGMD) model of a solvent/polymer/nanoparticle system. Our results demonstrate the importance of pol
http://pubs.rsc.org/en/Content/ArticleLanding/2013/SM/c3sm52194j
Structure and dynamics of the full-length lipid-modified H-ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer -...Structure and dynamics of the full-length lipid-modified H-ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer -...
Ras proteins regulate signal transduction processes that control cell growth and proliferation. Their disregulation is a common cause of human tumors. Atomic level structural and dynamical information in a membrane environment is crucial for understanding signaling specificity among Ras isoforms and for the design of selective anti-cancer agents. Here, the structure of the full-length H-Ras protein in complex with a 1,2-dimyristoylglycero-3-phosphocholine (DMPC) bilayer obtained from modeling and all-atom explicit solvent molecular dynamics simulations, as well as experimental validation of the main results, are presented. We find that, in addition to the lipid anchor, H-Ras membrane binding involves direct interaction of residues in the catalytic domain with DMPC phosphates. Two modes of binding (possibly modulated by GTP/GDP exchange) differing in the orientation and bilayer contact of the soluble domain as well as in the participation of the flexible linker in membrane binding are proposed. ...
http://research.abo.fi/converis/portal/Publication/1388943?auxfun=&lang=en_GB
Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with...
TY - JOUR. T1 - Prediction of hydration free energies for aliphatic and aromatic chloro derivatives using molecular dynamics simulations with the OPLS-AA force field. AU - Beckstein, Oliver. AU - Iorga, Bogdan I.. PY - 2012/5. Y1 - 2012/5. N2 - All-atom molecular dynamics computer simulations were used to blindly predict the hydration free energies of a range of chloro-organic compounds as part of the SAMPL3 challenge. All compounds were parameterized within the framework of the OPLS-AA force field, using an established protocol to compute the absolute hydration free energy via a windowed free energy perturbation approach and thermodynamic integration. Three different approaches to deriving partial charge parameters were pursued: (1) using existing OPLS-AA atom types and charges with minor adjustments of partial charges on equivalent connecting atoms; (2) calculation of quantum mechanical charges via geometry optimization, followed by electrostatic potential (ESP) fitting, using Jaguar at the ...
https://asu.pure.elsevier.com/en/publications/prediction-of-hydration-free-energies-for-aliphatic-and-aromatic-
A molecular dynamics approach for the association of apolipoproteinb-100 and chondroitin-6-sulfate - Fingerprint - Aalto...
Dive into the research topics of A molecular dynamics approach for the association of apolipoproteinb-100 and chondroitin-6-sulfate. Together they form a unique fingerprint. ...
https://research.aalto.fi/en/publications/a-molecular-dynamics-approach-for-the-association-of-apolipoprote/fingerprints/
CGDB: a database of membrane protein/lipid interactions by coarse-grained molecular dynamics simulations. - Oxford Neuroscience
Membrane protein function and stability has been shown to be dependent on the lipid environment. Recently, we developed a high-throughput computational approach for the prediction of membrane protein/lipid interactions. In the current study, we enhanced this approach with the addition of a new measure of the distortion caused by membrane proteins on a lipid bilayer. This is illustrated by considering the effect of lipid tail length and headgroup charge on the distortion caused by the integral membrane proteins MscS and FLAP, and by the voltage sensing domain from the channel KvAP. Changing the chain length of lipids alters the extent but not the pattern of distortion caused by MscS and FLAP; lipid headgroups distort in order to interact with very similar but not identical regions in these proteins for all bilayer widths investigated. Introducing anionic lipids into a DPPC bilayer containing the KvAP voltage sensor does not affect the extent of bilayer distortion.
https://www.neuroscience.ox.ac.uk/publications/100785
Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray...Structure of poly(propyl ether imine) dendrimer from fully atomistic molecular dynamics simulation and by small angle x-ray...
We study the structure of carboxylic acid terminated neutral poly(propyl ether imine)(PETIM) dendrimer from generations 1-6(G1-G6)in a good solvent (water)by fully atomistic molecular dynamics (MD)simulations. We determine as a function of generation the structural properties such as radius of gyration, shape tensor, asphericity, fractal dimension, monomer density distribution, and end-group distribution functions. The sizes obtained from the MD simulations have been validated by small angle x-ray scattering experiment on dendrimer of generations 2-4(G2-G4) A good agreement between the experimental and theoretical value of radius of gyration has been observed.We find a linear increase in radius of gyration with the generation. In contrast, $R_g$ scales as $\sim N^x$ with the number of monomers. We find two distinct exponents depending on the generations, x=0.47 for G1-G3 and x=0.28 for G3-G6, which reveal their nonspace filling nature. In comparison with the amine terminated ...
http://eprints.iisc.ac.in/8954/
Accelerating molecular dynamics simulations with population annealing<...
TY - JOUR. T1 - Accelerating molecular dynamics simulations with population annealing. AU - Christiansen, Henrik. AU - Weigel, Martin. AU - Janke, Wolfhard. PY - 2019/2/15. Y1 - 2019/2/15. N2 - Population annealing is a powerful tool for large-scale Monte Carlo simulations. We adapt this method to molecular dynamics simulations and demonstrate its excellent accelerating effect by simulating the folding of a short peptide commonly used to gauge the performance of algorithms. The method is compared to the well established parallel tempering approach and is found to yield similar performance for the same computational resources. In contrast to other methods, however, population annealing scales to a nearly arbitrary number of parallel processors, and it is thus a unique tool that enables molecular dynamics to tap into the massively parallel computing power available in supercomputers that is so much needed for a range of difficult computational problems.. AB - Population annealing is a powerful ...
https://pureportal.coventry.ac.uk/en/publications/accelerating-molecular-dynamics-simulations-with-population-annea
Binding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations - SeRCBinding sites for luminescent amyloid biomarkers from non-biased molecular dynamics simulations - SeRC
A visual analytics environment VIA-MD(visual interactive analysis of molecular dynamics) tailored for large-scale spatio-temporal molecular dynamics simulation data has been developed. A key concept of the environment is to link interactive 3D exploration of geometry and statistical analysis. Semantic property editor support the specification of complex molecular properties for filtering and aggregation. Thus it is possible to interactively and effectively find spatial, temporal and statistical patterns hidden in large data volumes [1]. One example is the identification of binding sites for the interaction between a pentameric oligothiophene and an amyloid-b(1-42) fibril from molecular dynamics simulations [2]. In this site, the probe is locked in an all-trans conformation due to the interactions between the anionic carboxyl groups of the probe and the cationic e-amino groups in the lysine side chain. The identification of interaction hotspots has been achieved with the use ofcombined filter ...
https://e-science.se/2019/09/binding-sites-for-luminescent-amyloid-biomarkers-from-non-biased-molecular-dynamics-simulations/
Molecular dynamics simulations reveal mechanisms by which metal nanowires deform or break under strainMolecular dynamics simulations reveal mechanisms by which metal nanowires deform or break under strain
Experimentalists searching for strong structural materials have established that nanocrystalline metals, which have average grain sizes smaller than 100 nanometers, are stronger, harder and more resistant to fatigue than coarser-grained metals. Despite this strength, nanocrystalline metals undergo problematic deformations in response to loading or heating. To date, researchers have struggled to verify the complex interplay of processes that lead to these deformations.
https://phys.org/news/2014-01-molecular-dynamics-simulations-reveal-mechanisms.html
Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data. -...Probing the Structure and Dynamics of Proteins by Combining Molecular Dynamics Simulations and Experimental NMR Data. -...
NMR experiments provide detailed structural information about biological macromolecules in solution. However, the amount of information obtained is usually much less than the number of degrees of freedom of the macromolecule. Moreover, the relationships between experimental observables and structural information, such as interatomic distances or dihedral angle values, may be multiple-valued and may rely on empirical parameters and approximations. The extraction of structural information from experimental data is further complicated by the time- and ensemble-averaged nature of NMR observables. Combining NMR data with molecular dynamics simulations can elucidate and alleviate some of these problems, as well as allow inconsistencies in the NMR data to be identified. Here, we use a number of examples from our work to highlight the power of molecular dynamics simulations in providing a structural interpretation of solution NMR data.
https://www.semanticscholar.org/paper/Probing-the-Structure-and-Dynamics-of-Proteins-by-Allison-Hertig/57319f2d384ea4c1b118dda4db0eab48eb309e53
Molecular dynamics simulation of folding of a short helical peptide with many charged residues<...Molecular dynamics simulation of folding of a short helical peptide with many charged residues<...
TY - JOUR. T1 - Molecular dynamics simulation of folding of a short helical peptide with many charged residues. AU - Wei, Chung Cheng. AU - Ho, Ming Hsun. AU - Wang, Wen Hung. AU - Sun, Ying Chieh. PY - 2005/10/27. Y1 - 2005/10/27. N2 - A molecular dynamics simulation of the folding of conantokin-T (con-T), a short helical peptide with 5 helical turns of 21 amino acids with 10 charged residues, was carried out to examine folding pathways for this peptide and to predict the folding rate. In the 18 trajectories run at 300 K, 16 trajectories folded, with an averaged folding time of ∼50 ns. Two trajectories did not fold in up to 200 ns simulation. The folded structure in folded trajectories is in good agreement with experimental structure (Skjærbæk; et al. J. Biol. Chem. 1997, 272, 2291. Lin; et al. FEBS Lett. 1997, 407, 243). An analysis of the trajectories showed that, at the beginning of a few nanoseconds, helix formation started from residues 5-9 with assistance of a hydrophobic clustering ...
https://scholar.lib.ntnu.edu.tw/en/publications/molecular-dynamics-simulation-of-folding-of-a-short-helical-pepti
A molecular dynamics approach to the structural characterization of amyloid aggregation | Caflisch - UZH
A novel computational approach to the structural analysis of ordered β-aggregation is presented and validated on three known amyloidogenic polypeptides. The strategy is based on the decomposition of the sequence into overlapping stretches and equilibrium implicit solvent molecular dynamics (MD) simulations of an oligomeric system for each stretch. The structural stability of the in-register parallel aggregates sampled in the implicit solvent runs is further evaluated using explicit water simulations for a subset of the stretches. The beta-aggregation propensity along the sequence of the Alzheimers amyloid-β peptide (Aβ42) is found to be highly heterogeneous with a maximum in the segment V12HHQKLVFFAE22 and minima at S8G9, G25S26, G29A30, and G38V39, which are turn-like segments. The simulation results suggest that these sites may play a crucial role in determining the aggregation tendency and the fibrillar structure of Aβ42. Similar findings are obtained for the human amylin, a 37-residue ...
http://www.biochem-caflisch.uzh.ch/publist/0076
Nanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation StudyNanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation Study
Mechanical and Aerospace Engineering, ICMAE2011: Nanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation Study
https://www.scientific.net/AMM.110-116.3888
Serval - Molecular dynamics simulations show how the FMRP Ile304Asn mutation destabilizes the KH2 domain structure and affects...Serval - Molecular dynamics simulations show how the FMRP Ile304Asn mutation destabilizes the KH2 domain structure and affects...
Mutations or deletions of FMRP, involved in the regulation of mRNA metabolism in brain, lead to the Fragile X syndrome (FXS), the most frequent form of inherited intellectual disability. A severe manifestation of the disease has been associated with the Ile304Asn mutation, located on the KH2 domain of the protein. Several hypotheses have been proposed to explain the possible molecular mechanism responsible for the drastic effect of this mutation in humans. Here, we performed a molecular dynamics simulation and show that the Ile304Asn mutation destabilizes the hydrophobic core producing a partial unfolding of two α-helices and a displacement of a third one. The affected regions show increased residue flexibility and motion. Molecular docking analysis revealed strongly reduced binding to a model single-stranded nucleic acid in agreement with known data that the two partially unfolded helices form the RNA-binding surface. The third helix, which we show here to be also affected, is involve
https://serval.unil.ch/en/notice/serval:BIB_E7AAE90F7978
Publications | Laboratoire de Biochimie ThéoriquePublications | Laboratoire de Biochimie Théorique
Liang C, Derreumaux P, Mousseau N, Wei G. 2008. The beta-strand-loop-beta-strand conformation is marginally populated in beta(2)-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations. Biophys. J.. 95:510-517. ...
http://www-lbt.ibpc.fr/publications?page=4&%3Bs=year&%3Bf%5Bag%5D=H&%3Bo=desc&f%5Bauthor%5D=228
Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation studyHydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study
The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. The radial distribution functions and coordination numbers around water molecules have been found to be strongly dependent on the number of hydrogen bonds formed by each molecule, revealing also the existence of local structural heterogeneities in the structure of the liquid. The results obtained have also revealed the strong effect of the local hydrogen-bonding network on the local tetrahedral structure and entropy. The investigation of the dynamics of the local hydrogen-bonding network in liquid water has shown that this network is very labile, and the hydrogen bonds break and reform very rapidly. Nevertheless, it has been found that the hydrogen-bonding states associated with the formation of four hydrogen bonds by a water molecule exhibit the largest survival probability and corresponding lifetime. The reorientational motions of water ...
http://upcommons.upc.edu/handle/2117/76835
Simbios: Bringing Biomedical Simulation to Your Fingertips | Biomedical Computation Review
le GPU platforms-and have made these algorithms available to everybody. In early tests, OpenMM achieved speedups of as much as 700-fold compared with traditional CPU implementations. Since GPUs are available on desktops and laptops, this means that scientists can now do fast molecular dynamics using a computer they have under their desk, Pande says. The preview version of OpenMM was released in September 2008 and the software has already been downloaded 2000 times.. Since the initial release, weve been rapidly adding functionality, Pande says. One of the most exciting additions, released in May, is the ability to support explicit solvent models (where water is modeled as individual atoms rather than as a continuous fluid). For many people molecular simulation means explicit solvent, Pande says. So this advance gives the software much, much broader applicability, he says. Its turning out to be the fastest single GPU code to do explicit solvent molecular dynamics, he adds.. Pandes team ...
http://www.bcr.org/content/simbios-bringing-biomedical-simulation-your-fingertips
Studies on Molecular Dynamics Simulation and Solvent Stability analysis of Collagen Mimetic Peptide GFO with Cyclodextrin ? An...Studies on Molecular Dynamics Simulation and Solvent Stability analysis of Collagen Mimetic Peptide GFO with Cyclodextrin ? An...
Collagen mimetic peptides (CMPs) and collagen-like proteins (CLPs) that mimic either structural or functional characteristics of natural collagens hav..
http://www.alliedacademies.org/abstract/studies-on-molecular-dynamics-simulation-and-solvent-stability-analysis-of-collagen-mimetic-peptide-gfo-with-cyclodextrin--an-insi-4325.html
Index Catalog // Deep Blue DataIndex Catalog // Deep Blue Data
We provide the parameters used in Umbrella Sampling simulations reported in our study Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method, namely the set positions and spring constants for each window in simulations. Two tables are provided. Table 1 lists the names of the peptides and their corresponding sequences. Table 2 lists the parameters. The abstract of our work is the following: We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with Weighted Histogram Analysis Method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse-grained (CG) force field (MARTINI) is less prone to significant error induced by biased-sampling than using an atomistic force field (AMBER). We ...
https://deepblue.lib.umich.edu/data/catalog?locale=en&page=27&per_page=10&sort=score+desc%2C+system_create_dtsi+desc
Index Catalog // Deep Blue DataIndex Catalog // Deep Blue Data
We provide the parameters used in Umbrella Sampling simulations reported in our study Efficient Estimation of Binding Free Energies between Peptides and an MHC Class II Molecule Using Coarse-Grained Molecular Dynamics Simulations with a Weighted Histogram Analysis Method, namely the set positions and spring constants for each window in simulations. Two tables are provided. Table 1 lists the names of the peptides and their corresponding sequences. Table 2 lists the parameters. The abstract of our work is the following: We estimate the binding free energy between peptides and an MHC class II molecule using molecular dynamics (MD) simulations with Weighted Histogram Analysis Method (WHAM). We show that, owing to its more thorough sampling in the available computational time, the binding free energy obtained by pulling the whole peptide using a coarse-grained (CG) force field (MARTINI) is less prone to significant error induced by biased-sampling than using an atomistic force field (AMBER). We ...
https://deepblue.lib.umich.edu/data/catalog?f%5Bcreator_sim%5D%5B%5D=Wen%2C+Fei&f%5Bcreator_sim%5D%5B%5D=Larson%2C+Ronald+G.&f%5Bcreator_sim%5D%5B%5D=Huang%2C+Ming&f%5Blanguage_sim%5D%5B%5D=English&locale=en&per_page=10&sort=system_modified_dtsi+asc
Biology | Free Full-Text | Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation | NotesBiology | Free Full-Text | Free Energy Profile of APOBEC3G Protein Calculated by a Molecular Dynamics Simulation | Notes
The human APOBEC3G protein (A3G) is a single-stranded DNA deaminase that inhibits the replication of retrotransposons and retroviruses, including HIV-1. Atomic details of A3Gs catalytic mechanism have started to emerge, as the structure of its catalytic domain (A3Gctd) has been revealed by NMR and X-ray crystallography. The NMR and crystal structures are similar overall; however, differences are apparent for β2 strand (β2) and loops close to the catalytic site. To add some insight into these differences and to better characterize A3Gctd dynamics, we calculated its free energy profile by using the Generalized-Born surface area (GBSA) method accompanied with a molecular dynamics simulation. The GBSA method yielded an enthalpy term for A3Gctds free energy, and we developed a new method that takes into account the distribution of the proteins dihedral angles to calculate its entropy term. The structure solved by NMR was found to have a lower energy than that of the crystal structure, suggesting that
http://www.mdpi.com/2079-7737/1/2/245/notes
Structural rearrangement in fcc metals under shear deformation. Molecular dynamics simulation<...
TY - JOUR. T1 - Structural rearrangement in fcc metals under shear deformation. Molecular dynamics simulation. AU - Psakhie, S. G.. AU - Zolnikov, K. P.. AU - Dmitriev, A. I.. AU - Kryzhevich, D. S.. AU - Nikonov, A. Y.. PY - 2010/12/1. Y1 - 2010/12/1. N2 - The features of fcc metals atomic lattice structural reorganization under shift deformation are investigated. Mechanisms of deformation both for ideal crystalline and for a crystal containing various structural defects are analyzed. Investigations are carried out on the basis of computer simulations by mean of molecular dynamics method. It is shown that the beginning of structural reorganization of crystalline at plastic deformation is connected with atomic volume redistribution. In fcc lattice of metals it is possible to allocate local formations having hcp configuration and being some kind of precursor of irreversible structural changes in the atomic lattice. It was show also, that a nonuniform distribution of stress fields in the loaded ...
https://tpu.pure.elsevier.com/en/publications/structural-rearrangement-in-fcc-metals-under-shear-deformation-mo
Effect of adsorption on the surface structure of sodium alumino-silicate glasses: a molecular dynamics simulation<...
TY - JOUR. T1 - Effect of adsorption on the surface structure of sodium alumino-silicate glasses. T2 - a molecular dynamics simulation. AU - Athanasopoulos, D. C.. AU - Garofalini, S. H.. N1 - Funding Information: The authors gratefully acknowledges upport from the US Department of Energy, Office of Basic Energy Sciences,D E-FG05-88ER45368.. PY - 1992/6/15. Y1 - 1992/6/15. N2 - Classical molecular dynamics (MD) computer simulations were used to study adsorption of model metals onto sodium alumino-silicate glasses and the effect these adsorbates have on the surface structure of the glass substrates. Multibody potentials were used to describe the substrate-substrate interactions; Lennard-Jones potentials were used to describe the adsorbate-adsorbate and adsorbate-substrate interactions. Lennard-Jones parameters and adsorbate mass were chosen to model Pt as the adsorbate. The adsorbate atoms penetrated 5-6Å into the glass, with multilayer coverage eventually occurring during deposition. The ...
https://sofi-northwestern.pure.elsevier.com/en/publications/effect-of-adsorption-on-the-surface-structure-of-sodium-alumino-s
Diffusion Maps in Molecular Dynamics Analysis · John DetlefsDiffusion Maps in Molecular Dynamics Analysis · John Detlefs
Fine! Back to the matter at hand, dimension reduction is an invaluable tool in modern computational chemistry because of the massive dimensionality of molecular dynamics simulations. To my knowledge, the biggest things being studied by MD currently are on the scale of the HIV-1 Capsid at 64 million atoms! Of course, these studies are being done on supercomputers, and for the most part studies are running on a much smaller number of atoms. For a thorough explanation of how MD simulations work, my Summer of Code colleague Fiona Naughton has an excellent and cat-filled post explaining MD and Umbrella Sampling. Why do we care about dynamics? As Dr. Cecilia Clementi mentions in her slides, Crystallography gives structures, but function requires dynamics!. A molecular dynamics simulation can be thought of as a diffusion process subject to drag (from the interactions of molecules) and random forces, (brownian motion). This means that the time evolution of the probability density of a molecule ...
http://jdetle.com/2016/06/15/diffusion_maps/
Laboratoire Chrono-environnement - UMR 6249 CNRS-UFC - RAMSEYER ChristopheLaboratoire Chrono-environnement - UMR 6249 CNRS-UFC - RAMSEYER Christophe
FOLEY-MEYER Sarah, RAMSEYER Christophe, ENESCU Mironel - 2019 - Fate of cisplatin and its main hydrolysed forms in the presence of thiolates: a comprehensive computational and experimental study. - Metallomics. Article RAMSEYER Christophe, Yesylevskyy Semen, Savenko Mariia, Mura Simona, Couvreur Patrick - 2018 - Low density lipoproteins and human serum albumin as the carriers of squalenoylated drugs: insights from molecular simulations. - Molecular Pharmaceutics. Article Yesylevskyy Semen, RIVEL Timothée, RAMSEYER Christophe - 2017 - The influence of curvature on the properties of the plasma membrane. Insights from atomistic molecular dynamics simulations. - Scientific Reports. Article Yesylevskyy Semen, RIVEL Timothée, RAMSEYER Christophe, Yesylevskyy Semen O. - 2017 - Structures of single, double and triple layers of lipids adsorbed on graphene: Insights from all-atom molecular dynamics simulations. - Carbon. Article Sobot Dunja, Mura Simona, Yesylevskyy Semen O., Dalbin Laura, Cayre Fanny, ...
https://chrono-environnement.univ-fcomte.fr/spip.php?page=perso&nom=RAMSEYER&prenom=Christophe&lang=fr
Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations | MIT...Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations | MIT...
We use molecular dynamics simulations to study the crystallization of spherical nucleic-acid (SNA) gold nanoparticle conjugates, guided by sequence-specific DNA hybridization events. Binary mixtures of SNA gold nanoparticle conjugates (inorganic core diameter in the 8-15 nm range) are shown to assemble into BCC, CsCl, AlB2, and Cr3Si crystalline structures, depending upon particle stoichiometry, number of immobilized strands of DNA per particle, DNA sequence length, and hydrodynamic size ratio of the conjugates involved in crystallization. These data have been used to construct phase diagrams that are in excellent agreement with experimental data from wet-laboratory studies.. ...
http://dmse.mit.edu/publications/modeling-crystallization-spherical-nucleic-acid-nanoparticle-conjugates-molecular
Ligand Field Molecular Dynamics Simulation of Pt(II)-Phenanthroline Binding to N-Terminal Fragment of Amyloid-beta Peptide ...Ligand Field Molecular Dynamics Simulation of Pt(II)-Phenanthroline Binding to N-Terminal Fragment of Amyloid-beta Peptide ...
Rhestr o setiau data » Ligand Field Molecular Dynamics Simulation of Pt(II)-Phenanthroline Binding to N-Terminal Fragment of Amyloid-beta Peptide [Data set] - Platts J, Turner M, Mutter ST, et al. (2017). Cardiff University. 10.5281/zenodo.1050388. Alzheimers Disease Molecular dynamics ...
https://research.cardiff.ac.uk/converis/portal/detail/Dataset/46306049?auxfun=&lang=cy_CY
Publications - Institute for Bioengineering of Catalonia (IBEC)Publications - Institute for Bioengineering of Catalonia (IBEC)
Bio-catalytic micro- and nanomotors self-propel by the enzymatic conversion of substrates into products. Despite the advances in the field, the fundamental aspects underlying enzyme-powered self-propulsion have rarely been studied. In this work, we select four enzymes (urease, acetylcholinesterase, glucose oxidase, and aldolase) to be attached on silica microcapsules and study how their turnover number and conformational dynamics affect the self-propulsion, combining both an experimental and molecular dynamics simulations approach. Urease and acetylcholinesterase, the enzymes with higher catalytic rates, are the only enzymes capable of producing active motion. Molecular dynamics simulations reveal that urease and acetylcholinesterase display the highest degree of flexibility near the active site, which could play a role on the catalytic process. We experimentally assess this hypothesis for urease micromotors through competitive inhibition (acetohydroxamic acid) and increasing enzyme rigidity ...
http://www.ibecbarcelona.eu/for-researchers/publications/Biocatalysis/
Extracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case | ChemAxonExtracting Conformational Ensembles of Small Molecules from Molecular Dynamics Simulations: Ampicillin as a Test Case | ChemAxon
Abstract. The accurate and exhaustive description of the conformational ensemble sampled by small molecules in solution, possibly at different physiological conditions, is of primary interest in many fields of medicinal chemistry and computational biology. Recently, we have built an on-line database of compounds with antimicrobial properties, where we provide all-atom force-field parameters and a set of molecular properties, including representative structures extracted from cluster analysis over μs-long molecular dynamics (MD) trajectories. In the present work, we used a medium-sized antibiotic from our sample, namely ampicillin, to assess the quality of the conformational ensemble. To this aim, we compared the conformational landscape extracted from previous unbiased MD simulations to those obtained by means of Replica Exchange MD (REMD) and those originating from three freely-available conformer generation tools widely adopted in computer-aided drug-design. In addition, for different ...
https://chemaxon.com/publication/extracting-conformational-ensembles-of-small-molecules-from-molecular-dynamics-simulations-ampicillin-as-a-test-case
An efficient local molecular dynamics polymerization simulation combined with an ab initio MO method<...
TY - JOUR. T1 - An efficient local molecular dynamics polymerization simulation combined with an ab initio MO method. AU - Xie, Peng. AU - Orimoto, Yuuichi. AU - Aoki, Yuriko. PY - 2013. Y1 - 2013. N2 - A new local ab initio molecular dynamics method, namely elongation molecular dynamics (ELG-MD) is proposed for highly efficient simulations of aperiodic polymer systems. ELG-MD combines the elongation method (ELG) with the Gear predictor corrector (GPC) algorithm of molecular dynamics simulation. In this method, the local gradients acting on the atoms nucleus in the active region are calculated by the ELG method while the equations of the nucleuss motion are solved by the GPC algorithm. In this work, the first application of this ELG-MD method is described to investigate the stable conformation of polyglycine with surrounding water molecules. The water effects on the structure of polyglycine are examined. The ELG-MD simulations show that the formation of the polyglycine helix is strongly ...
https://kyushu-u.pure.elsevier.com/en/publications/an-efficient-local-molecular-dynamics-polymerization-simulation-c
Evidence from molecular dynamics simulations for non-metallic behaviour of solid hydrogen above 160 GPa | NatureEvidence from molecular dynamics simulations for non-metallic behaviour of solid hydrogen above 160 GPa | Nature
THE behaviour of molecular hydrogen at high pressures has implications for the interiors of the giant planets, which consist mainly of hydrogen. In particular, the question of whether solid hydrogen becomes metallic under these conditions has been much debated1-9, in part because the structure that molecular hydrogen adopts at high pressure is not known. Here we report the results of first-principles molecular dynamics simulations of solid hydrogen at pressures up to 270 GPa. We find that at 77 K, hydrogen exists as a stable, orientationally disordered phase up to 60 GPa, consistent with experimental results1,10. As the presssure is raised, a gradual transformation to an ordered orthorhombic structure begins at 160 GPa, and by 260 GPa the solid becomes semi-conducting, with an indirect band gap of 1.4eV. The calculated vibrational density of states of this phase is consistent with infrared and Raman spectra measured up to 160 GPa (ref. 11). Although limitations on the simulation time and size may result
https://www.nature.com/articles/378595a0?error=cookies_not_supported&code=eb4f7453-97e8-47f0-a883-23b59f82a6b7
Molecular dynamics simulations of a phospholipid-detergent mixture. An improved empirical potential energy function for...Molecular dynamics simulations of a phospholipid-detergent mixture. An improved empirical potential energy function for...
Molecular dynamics simulations of a phospholipid-detergent mixture. An improved empirical potential energy function for molecular simulations of phospholipids
http://www.readabstracts.com/Chemicals-plastics-and-rubber-industries/Molecular-dynamics-simulations-of-a-phospholipid-detergent-mixture.html
Molecular Dynamics Simulations of Small Peptides : Can One Derive Conformational Preferences from ROESY Spectra?Molecular Dynamics Simulations of Small Peptides : Can One Derive Conformational Preferences from ROESY Spectra?
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https://kops.uni-konstanz.de/handle/123456789/40242
Dynamical Simulations of Virus Wrapping and Budding - Department of Theoretical Condensed Matter PhysicsDynamical Simulations of Virus Wrapping and Budding - Department of Theoretical Condensed Matter Physics
We explore this process through modeling the wrapping of a spherical particle by a model bilayer membrane, using coarse-grained molecular dynamics simulations and a theoretical elastic model. Specifically, we study the kinetics and morphologies of wrapping as a function of the relevant system parameters, including the particle radius, the strength of the membrane-particle interaction, and the membrane bending rigidity. The theoretical model predicts a phase diagram as a function of the system parameters, which is compared to results of the dynamics simulations ...
https://dep.ftmc.uam.es/dynamical-simulations-of-virus-wrapping-and-budding/
Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation | Nanoscale...Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation | Nanoscale...
Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the
https://nanoscalereslett.springeropen.com/articles/10.1186/s11671-016-1616-1/figures/3
Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation | Nanoscale...Rolling Resistance and Mechanical Properties of Grinded Copper Surfaces Using Molecular Dynamics Simulation | Nanoscale...
Mechanical properties of copper (Cu) film under grinding process were accomplished by molecular dynamics simulation. A numerical calculation was carried out to understand the distributions of atomic and slip vector inside the Cu films. In this study, the roller rotation velocity, temperature, and roller rotation direction change are investigated to clarify their effect on the deformation mechanism. The simulation results showed that the destruction of materials was increased proportionally to the roller rotation velocity. The machining process at higher temperature results in larger kinetic energy of atoms than lower temperature during the grinding process of the Cu films. The result also shows that the roller rotation in the counterclockwise direction had the better stability than the roller rotation in the clockwise direction due to significantly increased backfill atoms in the groove of the Cu film surface. Additionally, the effects of the rolling resistances on the Cu film surfaces during the
https://nanoscalereslett.springeropen.com/articles/10.1186/s11671-016-1616-1/figures/8
IJMS | Free Full-Text | Dimerization of Protegrin-1 in Different EnvironmentsIJMS | Free Full-Text | Dimerization of Protegrin-1 in Different Environments
The dimerization of the cationic β-hairpin antimicrobial peptide protegrin-1 (PG1) is investigated in three different environments: water, the surface of a lipid bilayer membrane, and the core of the membrane. PG1 is known to kill bacteria by forming oligomeric membrane pores, which permeabilize the cells. PG1 dimers are found in two distinct, parallel and antiparallel, conformations, known as important intermediate structural units of the active pore oligomers. What is not clear is the sequence of events from PG1 monomers in solution to pores inside membranes. The step we focus on in this work is the dimerization of PG1. In particular, we are interested in determining where PG1 dimerization is most favorable. We use extensive molecular dynamics simulations to determine the potential of mean force as a function of distance between two PG1 monomers in the aqueous subphase, the surface of model lipid bilayers and the interior of these bilayers. We investigate the two known distinct modes of dimerization
http://www.mdpi.com/1422-0067/11/9/3177
Ammonia channeling in bacterial glucosamine-6-phosphate synthase (Glms): molecular dynamics simulations and kinetic studies of...
Ammonia transfer from the glutamine site to the fructose-6P site of bacterial glucosamine-6-phosphate synthase was studied by molecular dynamics simulations. The studies suggest a key role for Trp74, in the sealing of the hydrophobic channel connecting the two binding sites, as well as for the two Ala602 and Val605 residues, which form a narrow passage whose opening/closing constitutes an essential event in ammonia transfer. Kinetic analyses of the corresponding protein mutants confirmed our predictions. The efficiency of ammonia transfer which was close to zero in the W74A mutant was partially restored by increasing the size of the corresponding side-chain; the simulations performed on the W74A mutant suggested the formation of a hole in the channel. In the case of A602L and V605L mutants, the efficiency of ammonia transfer decreased to 50% of the value of the native protein. None of the mutants were, however, able to use exogenous ammonia as a substrate.
https://hal.inria.fr/inria-00188598
Binding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulationsBinding energy calculations for hevein-carbohydrate interactions using expanded ensemble molecular dynamics simulations
Accurate estimation of protein-carbohydrate binding energies using computational methods is a challenging task. Here we report the use of expanded ensemble molecular dynamics (EEMD) simulation with double decoupling for estimation of binding energies of hevein, a plant lectin with its monosaccharide and disaccharide ligands GlcNAc and (GlcNAc)(2), respectively. In addition to the binding energies, enthalpy and entropy components of the binding energy are also calculated. The estimated binding energies for the hevein-carbohydrate interactions are within the range of +/- 0.5 kcal of the previously reported experimental binding data. For comparison, binding energies were also estimated using thermodynamic integration, molecular dynamics end point calculations (MM/GBSA) and the expanded ensemble methodology is seen to be more accurate. To our knowledge, the method of EEMD simulations has not been previously reported for estimating biomolecular binding energies.. ...
http://su.diva-portal.org/smash/record.jsf?pid=diva2:786743
USF :: Department of PhysicsUSF :: Department of Physics
My groups research in computational and theoretical materials physics focuses on discovery of new materials with unique electronic, vibrational, thermal, mechanical, optical, transport and superconducting properties using a combination of first-principles quantum mechanical, and atomistic molecular dynamics simulation tools. Working closely with experimental collaborators, we predict new materials and study their properties before their synthesis is attempted in a laboratory. The current focus is on the search of novel high-nitrogen content energetic materials, superhard materials, novel superconductors and 2D materials for energy applications.. Another key research effort is to study behavior of materials at extreme conditions of high pressure, high temperature and high strain rates. Large-scale molecular dynamics simulations are performed to uncover fundamental mechanisms of shock-induced plasticity, phase transitions, and the fundamental atomic-scale mechanisms of condensed-phase ...
http://physics.usf.edu/faculty/ioleynik/
The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations<...
TY - JOUR. T1 - The NMR structure of [Xd(C2)]4 investigated by molecular dynamics simulations. AU - Malliavin, Thérèse E.. AU - Snoussi, Karim. AU - Leroy, Jean Louis. PY - 2003/1/1. Y1 - 2003/1/1. N2 - The i-motif tetrameric structure is built up from two parallel duplexes intercalated in a head-to-tail orientation, and held together by hemiprotonated cytosine pairs. Two topologies exist for the i-motif structure, one with outermost 3′ extremities and the other with outermost 5′ extremities, called the 3′E and 5′E topology, respectively. Since the comparison of sugar and phosphate group interactions between the two topologies is independent of the length of the intercalation motif, the relative stability of the 3′E and 5′E topologies therefore should not depend on this length. Nevertheless, it has been shown that the 3′E topology of the [d(C2)]4 is much more stable than the 5′E topology, and that the former is the only species observed in solution. In order to understand the ...
https://jhu.pure.elsevier.com/en/publications/the-nmr-structure-of-xdc24-investigated-by-molecular-dynamics-sim-4
Molecular dynamics simulations of an oligosaccharide using a force field modified for carbohydratesMolecular dynamics simulations of an oligosaccharide using a force field modified for carbohydrates
In this thesis a computational complement to experimental observables will be presented. Computational tools such as molecular dynamics and quantum chemical tools will be used to aid in the interpretation of experimentally (NMR) obtained structural data. The techniques are applied to study the dynamical features of biologically important carbohydrates and their interaction with proteins. When evaluating conformations, molecular mechanical methods are commonly used. Paper I, highlights some important considerations and focuses on the force field parameters pertaining to carbohydrate moieties. Testing of the new parameters on a trisaccharide showed promising results. In Paper II, a conformational analysis of a part of the repeating unit of a Shigella flexneri bacterium lipopolysaccharide using the modified force field revealed two major conformational states. The results showed good agreement with experimental data. In Paper III, a trisaccharide using Langevin dynamics was investigated. The ...
http://su.diva-portal.org/smash/record.jsf?pid=diva2:195193
NMR paper NMR-detected hydrogen exchange and molecular dynamics simulations provide structural - BioNMR
NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126.
http://www.bionmr.com/forum/journal-club-9/nmr-detected-hydrogen-exchange-molecular-dynamics-simulations-provide-structural-10056/
Metascalable Quantum Molecular Dynamics Simulations of Hydrogen-on-Demand - IEEE Conference PublicationMetascalable Quantum Molecular Dynamics Simulations of Hydrogen-on-Demand - IEEE Conference Publication
We enabled an unprecedented scale of quantum molecular dynamics simulations through algorithmic innovations. A new lean divide-and-conquer density function
https://ieeexplore.ieee.org/document/7013041/
C. Sun, T. Tang, H. Uludag. Molecular dynamics simulations of complexation of DNA with 2 kDa PEI reveals profound effects of...
C. Sun, T. Tang, H. Uludag. Molecular dynamics simulations of complexation of DNA with 2 kDa PEI reveals profound effects of architecture on complexation. J. Phys. Chem B (2012) 116: 2405-2413 ...
http://uludaglab.com/?wpdmpro=c-sun-t-tang-h-uludag-molecular-dynamics-simulations-of-complexation-of-dna-with-2-kda-pei-reveals-profound-effects-of-architecture-on-complexation-j-phys-chem-b-2012-116-2405-2413
Massively parallel molecular dynamics simulations of lysozyme unfolding - IBM Journals & MagazineMassively parallel molecular dynamics simulations of lysozyme unfolding - IBM Journals & Magazine
We have performed molecular dynamics simulations for a total duration of more than 10 µs (with most molecular trajectories being 1 µs in dura
http://ieeexplore.ieee.org/document/5388652/?reload=true&arnumber=5388652&sortType%3Dasc_p_Sequence%26filter%3DAND
Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis: The case of histone lysine...
TY - JOUR. T1 - Ab initio quantum mechanical/molecular mechanical molecular dynamics simulation of enzyme catalysis. T2 - The case of histone lysine methyltransferase SET7/9. AU - Wang, Shenglong. AU - Hu, Po. AU - Zhang, Yingkai. PY - 2007/4/12. Y1 - 2007/4/12. N2 - To elucidate enzyme catalysis through computer simulation, a prerequisite is to reliably compute free energy barriers for both enzyme and solution reactions. By employing on-the-fly Born-Oppenheimer molecular dynamics simulations with the ab initio quantum mechanical/molecular mechanical approach and the umbrella sampling method, we have determined free energy profiles for the methyl-transfer reaction catalyzed by the histone lysine methyltransferase SET7/9 and its corresponding uncatalyzed reaction in aqueous solution, respectively. Our calculated activation free energy barrier for the enzyme catalyzed reaction is 22.5 kcal/mol, which agrees very well with the experimental value of 20.9 kcal/mol. The difference in potential of mean ...
https://nyu-staging.pure.elsevier.com/en/publications/ab-initio-quantum-mechanicalmolecular-mechanical-molecular-dynami
Biofyzikální ústav AV ČRBiofyzikální ústav AV ČR
We use a wide spectrum of state-of-the-art computational techniques, including explicit solvent molecular dynamics simulations, advanced ab initio quantum-chemical calculations and modern bioinformatics.. The main research aim is to provide unique insights into the role of molecular interactions in structure, dynamics, function and evolution of nucleic acids. In that sense, advanced computations can substantially complement experimental techniques. Our research is highly interdisciplinary and we wish to bring modern physical-chemistry insights into structural and molecular biology, biochemistry and bioinformatics. Our research has impact also in some other areas of chemistry, such as physical, supramolecular and bioinorganic chemistry.. Ab initio quantum chemical (QM) technique is state of the art physical-chemistry methodology that provides accurate and physically complete description of small model systems. The technique reveals direct structure - energy relations that cannot be obtained by ...
http://iupabcz.ibp.cz/cs/oddeleni/struktura-a-dynamika-nukleovych-kyselin/informace-o-oddeleni
Biofyzikální ústav AV ČRBiofyzikální ústav AV ČR
We use a wide spectrum of state-of-the-art computational techniques, including explicit solvent molecular dynamics simulations, advanced ab initio quantum-chemical calculations and modern bioinformatics.. The main research aim is to provide unique insights into the role of molecular interactions in structure, dynamics, function and evolution of nucleic acids. In that sense, advanced computations can substantially complement experimental techniques. Our research is highly interdisciplinary and we wish to bring modern physical-chemistry insights into structural and molecular biology, biochemistry and bioinformatics. Our research has impact also in some other areas of chemistry, such as physical, supramolecular and bioinorganic chemistry.. Ab initio quantum chemical (QM) technique is state of the art physical-chemistry methodology that provides accurate and physically complete description of small model systems. The technique reveals direct structure - energy relations that cannot be obtained by ...
http://iupabcz.ibp.cz/cs/oddeleni/struktura-a-dynamika-nukleovych-kyselin/informace-o-oddeleni/
传热年鉴网络版（1-14卷） - 卷 17, 2014 PREDICTING PHONON PROPERTIES FROM EQUILIBRIUM MOLECULAR DYNAMICS SIMULATIONS - Begell House Digital...传热年鉴网络版（1-14卷） - 卷 17, 2014 PREDICTING PHONON PROPERTIES FROM EQUILIBRIUM MOLECULAR DYNAMICS SIMULATIONS - Begell House Digital...
The objective of this chapter is to describe how equilibrium molecular dynamics simulations (with the help of harmonic lattice dynamics calculations) can be used to predict phonon properties and thermal conductivity using normal mode decomposition. The molecular dynamics and lattice dynamics methods are reviewed and the normal mode decomposition technique is described in detail. The application of normal mode decomposition is demonstrated through case studies on crystalline, alloy, and amorphous Lennard-Jones phases. Notable works that used normal mode decomposition are presented and the future of molecular dynamics simulations in phonon transport modeling is discussed.. ...
http://www.dl.begellhouse.com/cn/references/5756967540dd1b03,7deb9f2f1087a9e3,15a8c1a1156da7dd.html
Phonon modes in single-walled molybdenum disulphide nanotubes: Lattice dynamics calculation and molecular dynamics simulation<...
TY - JOUR. T1 - Phonon modes in single-walled molybdenum disulphide nanotubes. T2 - Lattice dynamics calculation and molecular dynamics simulation. AU - Jiang, Jin Wu. AU - Wang, Bing Shen. AU - Rabczuk, Timon. PY - 2014/3/14. Y1 - 2014/3/14. N2 - We study the phonon modes in single-walled MoS2 nanotubes via lattice dynamics calculation and molecular dynamics simulation. The phonon spectra for tubes of arbitrary chiralities are calculated from a dynamical matrix constructed by the combination of an empirical potential with the conserved helical quantum numbers (κ, n). In particular, we show that the frequency (ω) of the radial breathing mode is inversely proportional to the tube diameter (d) as ω = 665.3/d cm-1. The eigenvectors of the twenty lowest-frequency phonon modes are illustrated. Based on these eigenvectors, we demonstrate that the radial breathing oscillation is initially disturbed by phonon modes of three-fold symmetry, then eventually the tube is squashed by modes of two-fold ...
https://koreauniv.pure.elsevier.com/en/publications/phonon-modes-in-single-walled-molybdenum-disulphide-nanotubes-lat
Structure and Dynamics of Interfacial Water in an L Phase Lipid Bilayer from Molecular Dynamics SimulationsStructure and Dynamics of Interfacial Water in an L Phase Lipid Bilayer from Molecular Dynamics Simulations
Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. Water properties relevant for understanding NMR relaxation are emphasized. The first and second rank orientational order parameters of the water O-H bonds were calculated, where the second rank order parameter is in agreement with experimental determined quadrupolar splittings. Also, two different interfacial water regions (bound water regions) are revealed with respect to different signs of the second rank order parameter. The water reorientation correlation function reveals a mixture of fast and slow decaying parts. The fast (ps) part of the correlation function is due to local anisotropic water reorientation whereas the much slower part is due to more complicated processes including lateral diffusion along the interface and chemical exchange between free and bound water molecules. The 100-ns-long molecular dynamics ...
http://umu.diva-portal.org/smash/record.jsf?pid=diva2:149636
On the Vibration of Single-Walled Carbon Nanocones: Molecular Mechanics Approach versus Molecular Dynamics SimulationsOn the Vibration of Single-Walled Carbon Nanocones: Molecular Mechanics Approach versus Molecular Dynamics Simulations
The vibrational behavior of single-walled carbon nanocones is studied using molecular structural method and molecular dynamics simulations. In molecular structural approach, point mass and beam elements are employed to model the carbon atoms and the connecting covalent bonds, respectively. Single-walled carbon nanocones with different apex angles are considered. Besides, the vibrational behavior of nanocones under various types of boundary conditions is studied. Predicted natural frequencies are compared with the existing results in the literature and also with the ones obtained by molecular dynamics simulations. It is found that decreasing apex angle and the length of carbon nanocone results in an increase in the natural frequency. Comparing the vibrational behavior of single-walled carbon nanocones under different boundary conditions shows that the effect of end condition on the natural frequency is more prominent for nanocones with smaller apex angles.
https://www.hindawi.com/journals/sv/2014/410783/
AFM Force Spectroscopy and Steered Molecular Dynamics Simulation of Protein Contactin 4 - Acta Physica Polonica A - Volume 116,...
We use a single molecule atomic force spectroscopy combined with the steered molecular dynamics simulation to determine a mechanical behavior of neural cell adhesion protein contactin during its unfolding. Force curves typical for modular proteins were observed, showing at most four unfolding peaks. The analysis of force spectra performed within worm-like chain model of polymer elasticity showed the presence of three unfolding lengths. Small plateaus, most likely resulting from forced transitions within domains were observed for the first time. Steered molecular dynamics simulations help to determine atomistic picture of domain unfolding ...
http://psjd.icm.edu.pl/psjd/element/bwmeta1.element.bwnjournal-article-appv116ns43kz
Partitioning of polycyclic aromatic hydrocarbons in heterogeneous clusters | DR-NTU
The morphologies of heterogeneous clusters of polycyclic aromatic hydrocarbons (PAHs) are investigated using molecular modelling. Clusters of up to 100 molecules containing combinations of the different sized PAHs circumcoronene, coronene, ovalene, or pyrene are evaluated. Replica exchange molecular dynamics simulations using an all-atom force field parameterised for PAHs sample many configurations at high and low temperatures to determine stable low energy structures. The resulting cluster structures are evaluated using molecular radial distances and coordination numbers, and are found to be independent of initial configuration and the cluster sizes studied. Stable clusters consist of stacked PAHs in a core-shell structure, where the larger PAHs are found closer to the cluster core and the smaller PAHs are located on the cluster surface. This work provides novel insight into the molecular partitioning of heterogeneous aromatic clusters, with particular relevance to the structure of nascent soot ...
https://dr.ntu.edu.sg/handle/10356/80541?mode=full
Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces<...Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces<...
TY - JOUR. T1 - Molecular dynamics simulation of atomic-scale frictional behavior of corrugated nano-structured surfaces. AU - Kim, Hyun Joon. AU - Kim, Dae Eun. PY - 2012/7/7. Y1 - 2012/7/7. N2 - Surface morphology is one of the critical parameters that affect the frictional behavior of two contacting bodies in relative motion. It is important because the real contact area as well as the contact stiffness is dictated by the micro- and nano-scale geometry of the surface. In this regard, the frictional behavior may be controlled by varying the surface morphology through nano-structuring. In this study, molecular dynamics simulations were conducted to investigate the effects of contact area and structural stiffness of corrugated nano-structures on the fundamental frictional behavior at the atomic-scale. The nano-structured surface was modeled as an array of corrugated carbon atoms with a given periodicity. It was found that the friction coefficient of the nano-structured surface was lower than ...
https://yonsei.pure.elsevier.com/en/publications/molecular-dynamics-simulation-of-atomic-scale-frictional-behavior
Molecular Dynamics Simulations of Amphiphilic Macromolecules at Interfaces | Research Explorer | The University of ManchesterMolecular Dynamics Simulations of Amphiphilic Macromolecules at Interfaces | Research Explorer | The University of Manchester
AbstractThe aim of this thesis is to investigate the structural and thermodynamic properties of biologically and technological relevant macromolecules when placed at soft interfaces. In particular two amphiphilic macromolecules characterized by different topologies have been investigated namely amphiphilic dendrimers and linear block copolymers. This goal is achieved using a multiscale approach which includes all-atom, united atom and coarse grained models by means of molecular dynamic simulations.Amphiphilic dendrimers have shown to be promising building blocks for a range of interfacial materials and can be used in applications such as surface-base sensors or surface nanopatterning. In this part of the thesis by means of all-atom molecular dynamics simulations, we investigated the structure and stability of alkyl-modified polyamido-amide (PAMAM) dendrimers at the air/water interface as a function of the number and the relative position of the modified end groups. We found that the PAMAM ...
https://www.research.manchester.ac.uk/portal/en/theses/molecular-dynamics-simulations-of-amphiphilic-macromolecules-at-interfaces
Molecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtBMolecular Dynamics Simulations on the Mechanism of Transporting Methylamine and Ammonia by Ammonium Transporter AmtB
AmtB is one of the ammonium transporter proteins facilitating the ammonium transport across the cellular membranes. Experimentally, the substrate used in in vitro studies is the radio labeled [14C]methylammonium, rather than ammonium itself. To explore the similarity and difference of the conduction mechanism of methylamine and ammonia molecules through AmtB, molecular dynamics simulations on 22 carefully designed systems were performed, which demonstrated that methylamine could be automatically transported in a very similar way to ammonia. The driving force for the conduction is mainly the hydrogen bond network comprising His168, His318, and Tyr32, working in coordination with NH−π interaction with residue Trp212. Then, Ser263 translocated the substrates from the exit gate into the cytoplasm by hydrogen bond interaction.The aromatic ring of Trp212 acted like a springboard to facilitate the translocation of the substrates from site Am2 to Am4 via NH−π interaction. Without the mediation of ...
https://espace.curtin.edu.au/handle/20.500.11937/17824
Atomistic molecular dynamics simulations of propofol and fentanyl in phosphatidylcholine lipid bilayers - data - Faulkner C,...Atomistic molecular dynamics simulations of propofol and fentanyl in phosphatidylcholine lipid bilayers - data - Faulkner C,...
The data here provides the raw data for the calculations of radial distribution functions, hydrogen bond analysis, lateral lipid diffusion and lipid tail order parameters. This raw data was generated using tools from the CPPTRAJ analysis package which is freely available with the AmberTools program (https://ambermd.org/AmberTools.php). The data presented here shows how two drug molecules (propofol and fentanyl) alter the physical and mechanical properties of DOPC and DPPC lipid bilayers, and for the first time, how a general anesthetic and an opioid analgesic/anesthetic differ in their interactions with phospholipid membranes, by direct comparison. Understanding the differences between opioid and anesthetic interactions with phospholipid bilayers will lead to a more complete understanding of general anesthesia at the molecular level ...
https://research.cardiff.ac.uk/converis/portal/detail/Dataset/92362446?auxfun=&lang=en_GB
Surface structure of methanol/water solutions via sum frequency orientational analysis and molecular dynamics simulation<...
TY - JOUR. T1 - Surface structure of methanol/water solutions via sum frequency orientational analysis and molecular dynamics simulation. AU - Ishihara, Takashi. AU - Ishiyama, Tatsuya. AU - Morita, Akihiro. N1 - Publisher Copyright: © 2015 American Chemical Society.. PY - 2015/5/7. Y1 - 2015/5/7. N2 - Polarization dependence of sum frequency generation (SFG) spectroscopy has been widely discussed to detect molecular orientation at surfaces. The present work examines the orientational analysis by molecular dynamics (MD) simulation of methanol/water mixture surfaces with varying concentrations. We calculated by MD the surface structure of the solutions and their SFG spectra in the methyl C-H stretching region, and directly analyzed the relations. The MD calculations reported that (i) the SFG signal of the methyl symmetric stretching exhibits a turnover behavior with increasing concentration and (ii) the polarization ratio is almost invariant over the concentration, while (iii) the orientation of ...
https://tohoku.pure.elsevier.com/en/publications/surface-structure-of-methanolwater-solutions-via-sum-frequency-or
Molecular dynamics simulation as a tool to study C-terminus residue motion of Norwalk virus capsid - CSU Chico MediaMolecular dynamics simulation as a tool to study C-terminus residue motion of Norwalk virus capsid - CSU Chico Media
Molecular dynamics (MD) simulation of protein helps to study motion and its development with time which may not be studied experimentally. Because of the tremendous advancement in hardware and software computer technologies in recent years, longer and more realistic molecular dynamics (MD) simulations of a protein are possible now in reasonable periods of time. In this presentation, Dr. Thapa explains how he has used molecular dynamics to conduct research on the Norwalk virus, a major cause of epidemic gastroenteritis in humans ...
https://media.csuchico.edu/media/Molecular+dynamics+simulation+as+a+tool+to+study+C-terminus+residue+motion+of+Norwalk+virus+capsid/0_39u17a45
Molecular Dynamics Simulation of the Structure Transformation before and after Ni Melting
Abstract: A series of molecular dynamics simulations for the structure transformation during heating and melting of FCC Ni have been performed with the Tight-binding potential developed by Cleri and Rosato. The simulated melting point of Ni at constant pressure condition is between 1850 K and 1900 K. The static structural informations, such as the radial distribution functions and the distributions of the coordination numbers, have been obtained during the simulation. The calculated diffusion coefficient of the liquid Ni is about 5.02×10−9 m2•s−1 at 1900 K, which is consistent with the experimental result. The possible distortion of local structure of FCC crystal and the relevant changes of the types of the atom pairs (indexed by Honeycutt-Anderesen pair analysis technique) have been analyzed. The distributions of the short-range ordered (SRO) structures of FCC and defective icosahedra at different temperatures are calculated combining the local configuration search and H-A pair analysis ...
http://www.whxb.pku.edu.cn/EN/10.3866/PKU.WHXB20060701
Radiation damage in cubic ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations (Journal Article) | SciTech...Radiation damage in cubic ZrO2 and yttria-stabilized zirconia from molecular dynamics simulations (Journal Article) | SciTech...
Here, we perform molecular dynamics simulation on cubic ZrO 2 and yttria-stabilized zirconia (YSZ) to elucidate defect cluster formation resulting from radiation damage, and evaluate the impact of Y-dopants. Interstitial clusters composed of split-interstitial building blocks, i.e., Zr-Zr or Y-Zr are formed. Moreover, oxygen vacancies control cation defect migration; in their presence, Zr interstitials aggregate to form split-interstitials whereas in their absence Zr interstitials remain immobile, as isolated single-interstitials. Y-doping prevents interstitial cluster formation due to sequestration of oxygen vacancies. ...
https://www.osti.gov/scitech/biblio/1185756-radiation-damage-cubic-zro2-yttria-stabilized-zirconia-from-molecular-dynamics-simulations
CryoEM Structure Refinement by Integrating NMR Chemical Shifts with Molecular Dynamics Simulations. - Nuffield Department of...
Single particle cryoEM has emerged as a powerful method for structure determination of proteins and complexes, complementing X-ray crystallography and NMR spectroscopy. Yet, for many systems, the resolution of cryoEM density map has been limited to 4-6 Å, which only allows for resolving bulky amino acids side chains, thus hindering accurate model building from the density map. On the other hand, experimental chemical shifts (CS) from solution and solid state MAS NMR spectra provide atomic level data for each amino acid within a molecule or a complex; however, structure determination of large complexes and assemblies based on NMR data alone remains challenging. Here, we present a novel integrated strategy to combine the highly complementary experimental data from cryoEM and NMR computationally by molecular dynamics simulations to derive an atomistic model, which is not attainable by either approach alone. We use the HIV-1 capsid protein (CA) C-terminal domain as well as the large capsid assembly to
https://www.ndm.ox.ac.uk/publications/681925
Study of the inhibition of cyclin-dependent kinases with roscovitine and indirubin-3′-oxime from molecular dynamics simulations...
Molecular dynamics simulations were performed to elucidate the interactions of CDK2 and CDK5 complexes with three inhibitors: R-roscovitine, S-roscovitine, and indirubin-3′-oxime. The preference of the two complexes for R-roscovitine over the S enantiomer, as reported by the experiment, was also found by the simulations. More importantly, the simulations showed that the cause of the stronger affinity for the R enantiomer is the presence of an important hydrogen bond between R-roscovitine and the kinases not found with S-roscovitine. The simulations also showed two amino acid mutations in the active site of CDK5/R-roscovitine that favor binding-enhanced electrostatic contributions, making the inhibitor more effective for CDK5 than for CDK2. This suggests that the effectiveness of roscovitine-like inhibitors can be improved by enhancing their electrostatic interaction with the kinases. Finally, molecular mechanics-Possion-Boltzmann/surface area calculations of the CDK5/indirubin-3′-oxime ...
http://scholarbank.nus.edu.sg/handle/10635/61403
The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the...The concerted action of a positive charge and hydrogen bonds dynamically regulates the pKa of the nucleophilic cysteine in the...
NrdH-redoxins shuffle electrons from the NADPH pool in the cell to Class Ib ribonucleotide reductases, which in turn provide the precursors for DNA replication and repair. NrdH-redoxins have a CVQC active site motif and belong to the thioredoxin-fold protein family. As for other thioredoxin-fold proteins, the pK(a) of the nucleophilic cysteine of NrdH-redoxins is of particular interest since it affects the catalytic reaction rate of the enzymes. Recently, the pK(a) value of this cysteine in Corynebacterium glutamicum and Mycobacterium tuberculosis NrdH-redoxins were determined, but structural insights explaining the relatively low pK(a) remained elusive. We subjected C. glutamicum NrdH-redoxin to an extensive molecular dynamics simulation to expose the factors regulating the pK(a) of the nucleophilic cysteine. We found that the nucleophilic cysteine receives three hydrogen bonds from residues within the CVQC active site motif. Additionally, a fourth hydrogen bond with a lysine located N-terminal ...
http://sbrc.vub.ac.be/node/152
Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations :: MPG.PuReInvestigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations :: MPG.PuRe
Author: Verde, Ana Vila et al.; Genre: Journal Article; Published in Print: 2009-08; Title: Investigating the Specificity of Peptide Adsorption on Gold Using Molecular Dynamics Simulations
https://pure.mpg.de/pubman/faces/ViewItemFullPage.jsp?itemId=item_2381806_2&view=EXPORT
Molecular dynamics simulations of breaking metallic nanowires on Environmental XPRTMolecular dynamics simulations of breaking metallic nanowires on Environmental XPRT
Article Molecular dynamics simulations of breaking metallic nanowires. In the present work, we have reviewed the importance of conductance histograms as an experimental tool able to address the statistical behaviour of the electronic transport throug...
https://www.environmental-expert.com/articles/molecular-dynamics-simulations-of-breaking-metallic-nanowires-435651
A new transferable interatomic potential for molecular dynamics simulations of borosilicate glasses - Fingeraftryk -...A new transferable interatomic potential for molecular dynamics simulations of borosilicate glasses - Fingeraftryk -...
Fingeraftryk Dyk ned i forskningsemnerne om A new transferable interatomic potential for molecular dynamics simulations of borosilicate glasses. Sammen danner de et unikt fingeraftryk. ...
https://vbn.aau.dk/da/publications/a-new-transferable-interatomic-potential-for-molecular-dynamics-s/fingerprints/
197b) Simulations of the Bilayer-Mediated Assembly of Cationic Nanoparticles on Phase-Separated Lipid Bilayers | AIChE Academy197b) Simulations of the Bilayer-Mediated Assembly of Cationic Nanoparticles on Phase-Separated Lipid Bilayers | AIChE Academy
Understanding interactions between functionalized gold nanoparticles (NPs) and lipid bilayers is essential for their use in biomedical applications. Experiments and continuum-scale simulations have suggested that small (~5 nm diameter) cationic NPs aggregate when adsorbed to the surface of zwitterionic lipid bilayers despite being stable in aqueous solution, suggesting that bilayer-mediated interactions facilitate assembly. Determining the origin of these effects and the impact of other bilayer features, such as lipid phase separation, on the interfacial assembly of NPs would enable the design of NPs for applications that require NP assembly, such as photothermal therapy.. In this work, we use chemically specific coarse-grained molecular dynamics simulations to show that cationic NP adsorption to lipid bilayers is driven by a balance between favorable NP-lipid interactions and the unfavorable mechanical deformation of the bilayer to create local curvature. The minimization of induced curvature ...
https://www.aiche.org/academy/conferences/aiche-annual-meeting/2020/proceeding/paper/197b-simulations-bilayer-mediated-assembly-cationic-nanoparticles-on-phase-separated-lipid-bilayers
Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics - Fingerprint - University of...Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics - Fingerprint - University of...
Fingerprint Dive into the research topics of Mature HIV-1 capsid structure by cryo-electron microscopy and all-atom molecular dynamics. Together they form a unique fingerprint. ...
https://experts.illinois.edu/en/publications/mature-hiv-1-capsid-structure-by-cryo-electron-microscopy-and-all/fingerprints/
From molecular dynamics to Brownian dynamics | Isaac Newton Institute for Mathematical SciencesFrom molecular dynamics to Brownian dynamics | Isaac Newton Institute for Mathematical Sciences
I will discuss methods for spatio-temporal modelling in molecular and cell biology, including all-atom and coarse-grained molecular dynamics (MD) and stochastic reaction-diffusion models, with the aim of developing and analysing multiscale methods which use MD simulations in parts of the computational domain and (less-detailed) stochastic reaction-diffusion approaches in the remainder of the domain. The main goal of this multiscale methodology is to use a detailed modelling approach in localized regions of particular interest (in which accuracy and microscopic details are important) and a less detailed model in other regions in which accuracy may be traded for simulation efficiency. Applications using all-atom MD include intracellular dynamics of ions and ion channels. Applications using coarse-grained MD include protein binding to receptors on the cellular membrane, where modern stochastic reaction-diffusion simulators of intracellular processes can be used in the bulk and a ccurately coupled ...
http://www.newton.ac.uk/seminar/20160620144515301
Tricia D. Shepherd | St. Edwards University in Austin, Texas
Dr. Shepherd spent the first 12 years of her academic career at Westminster College, Salt Lake City, UT before joining the faculty at St. Edwards, Fall 2014. She leads workshops offered nationwide on both facilitating POGIL in the classroom and incorporating theoretical and computational chemistry into the undergraduate chemistry curriculum. Her research efforts with undergraduates involve the use of coarse-grained molecular dynamics simulations to study aqueous systems at the nanoscale. She is a member of MERCURY (Molecular Education and Research Consortium in Undergraduate computational chemistRY) and advocates for the use of technology in meaningful ways to enhance student learning.. ...
https://www.stedwards.edu/directory/employees/tricia-d-shepherd
Difference between revisions of Canavan Task 9 - Normal Mode Analysis - Bioinformatikpedia
figure, Normal mode analysis aims at explaining the internal motions of a protein. Molecular Dynamics simulations are only capable of simulation very short amount of times (pico seconds). They are very compuationally demanding, since the motion of each atom is calculated with an energy function. The native state of a protein actually represents an ensemble of microstates which contain the overall fold and the same secondary structure elements, but differ in the local atomic coordinates. The microstates are thought to represent fluctuations around the well-defined equilibrium native structure. In this sense, large conformational changes of proteins can be monitored that occur within these defined microstates. These low level conformational changes take much longer (nano seconds) and thus are not accessible by standard molecular dynamics simulation. But they can be addressed by normal mode analysis, where only movements of backbone atoms are considered. The underlying assumption for the ...
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Task_9_-_Normal_Mode_Analysis&diff=prev&oldid=27457
Canavan Task 9 - Normal Mode Analysis - Bioinformatikpedia
figure, Normal mode analysis aims at explaining the internal motions of a protein. Molecular Dynamics simulations are only capable of simulation very short amount of times (pico seconds). They are very compuationally demanding, since the motion of each atom is calculated with an energy function. The native state of a protein actually represents an ensemble of microstates which contain the overall fold and the same secondary structure elements, but differ in the local atomic coordinates. The microstates are thought to represent fluctuations around the well-defined equilibrium native structure. In this sense, large conformational changes of proteins can be monitored that occur within these defined microstates. These low level conformational changes take much longer (nano seconds) and thus are not accessible by standard molecular dynamics simulation. But they can be addressed by normal mode analysis, where only movements of backbone atoms are considered. The underlying assumption for the ...
https://i12r-studfilesrv.informatik.tu-muenchen.de/wiki/index.php?title=Canavan_Task_9_-_Normal_Mode_Analysis&oldid=27521
Organic and Biomolecular ChemistryOrganic and Biomolecular Chemistry
Sasselli, I. R. and Moreira, I. P. and Ulijn, R. V. and Tuttle, T. (2017) Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries. Organic and Biomolecular Chemistry. ISSN 1477-0520 Casals-Cruañas, Èric and Gonzalez-Belman, Oscar F. and Besalú-Sala, Pau and Nelson, David James and Poater, Albert (2017) The preference for dual-gold(I) catalysis in the hydro(alkoxylation vs phenoxylation) of alkynes. Organic and Biomolecular Chemistry. pp. 1-10. ISSN 1477-0520 Cumine, Florimond and Zhou, Shengze and Tuttle, Tell and Murphy, John A. (2017) A study of diketopiperazines as electron-donor initiators in transition metal-free haloarene-arene coupling. Organic and Biomolecular Chemistry, 15. 3324 - 3336. ISSN 1477-0520 McPherson, Christopher G. and Caldwell, Nicola and Jamieson, Craig and Simpson, Iain and Watson, Allan J. B. (2017) Amidation of unactivated ester derivatives mediated by trifluoroethanol. Organic and Biomolecular Chemistry. ISSN 1477-0520 Emery, ...
https://strathprints.strath.ac.uk/view/publications/Organic_and_Biomolecular_Chemistry.html
DSpace@MIT: Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass...[email protected]: Tailoring Thermal Conductivity of Single-stranded Carbon-chain Polymers through Atomic Mass...
Tailoring the thermal conductivity of polymers is central to enlarge their applications in the thermal management of flexible integrated circuits. Progress has been made over the past decade by fabricating materials with various nanostructures, but a clear relationship between various functional groups and thermal properties of polymers remains to be established. Here, we numerically study the thermal conductivity of single-stranded carbon-chain polymers with multiple substituents of hydrogen atoms through atomic mass modification. We find that their thermal conductivity can be tuned by atomic mass modifications as revealed through molecular dynamics simulations. The simulation results suggest that heavy homogeneous substituents do not assist heat transport and trace amounts of heavy substituents can in fact hinder heat transport substantially. Our analysis indicates that carbon chain has the biggest contribution (over 80%) to the thermal conduction in single-stranded carbon-chain polymers. We ...
https://dspace.mit.edu/handle/1721.1/109782
Supplementary data for Co-Exposure with Fullerene May Strengthen Health Effects of Organic Industrial Chemicals - Tampere...
In vitro toxicological studies together with atomistic molecular dynamics simulations show that occupational co-exposure with C60 fullerene may strengthen the health effects of organic industrial chemicals. The chemicals studied are acetophenone, benzaldehyde, benzyl alcohol, m-cresol, and toluene which can be used with fullerene as reagents or solvents in industrial processes. Potential co-exposure scenarios include a fullerene dust and organic chemical vapor, or a fullerene solution aerosolized in workplace air. Unfiltered and filtered mixtures of C60 and organic chemicals represent different co-exposure scenarios in in vitro studies where acute cytotoxicity and immunotoxicity of C60 and organic chemicals are tested together and alone by using human THP-1-derived macrophages. Statistically significant co-effects are observed for an unfiltered mixture of benzaldehyde and C60 that is more cytotoxic than benzaldehyde alone, and for a filtered mixture of m-cresol and C60 that is slightly less ...
https://tutcris.tut.fi/portal/en/datasets/supplementary-data-for-coexposure-with-fullerene-may-strengthen-health-effects-of-organic-industrial-chemicals
Project abstract for group tsapatsi | Minnesota Supercomputing InstituteProject abstract for group tsapatsi | Minnesota Supercomputing Institute
Zeolites are porous silicate materials with pore sizes similar to industrially important molecules (water, carbon dioxide, hydrogen, etc.). Zeolites are used in gas separation (due to their sieving effect), catalysis (due to their shape selectivity), adsorption, and other applications. In the Tsapatsis group, zeolite nanoparticles with lamellar morphologies (zeolite nanosheets) are developed for gas separation, and catalysis. They have also published the use of 2D zeolites to form the thinnest zeolite films ever reported on porous and non porous supports. Because of the thin dimension of the nanosheets, the zeolite nanosheets give higher flux for gas separation applications, and enhance diffusion in catalysis.. The group is currently examining the water-ethanol separation through these membranes. The modeling work requires adsorption coefficients and diffusion coefficients. These coefficients are obtained through molecular dynamics simulations and the researchers are currently in progress to ...
https://www.msi.umn.edu/project-abstract/tsapatsi/Mathematical%20Modeling%20for%20membrane%20separation%20process
Super-tough MXene-functionalized graphene sheets | Nature CommunicationsSuper-tough MXene-functionalized graphene sheets | Nature Communications
Flexible reduced graphene oxide (rGO) sheets are being considered for applications in portable electrical devices and flexible energy storage systems. However, the poor mechanical properties and electrical conductivities of rGO sheets are limiting factors for the development of such devices. Here we use MXene (M) nanosheets to functionalize graphene oxide platelets through Ti-O-C covalent bonding to obtain MrGO sheets. A MrGO sheet was crosslinked by a conjugated molecule (1-aminopyrene-disuccinimidyl suberate, AD). The incorporation of MXene nanosheets and AD molecules reduces the voids within the graphene sheet and improves the alignment of graphene platelets, resulting in much higher compactness and high toughness. In situ Raman spectroscopy and molecular dynamics simulations reveal the synergistic interfacial interaction mechanisms of Ti-O-C covalent bonding, sliding of MXene nanosheets, and π-π bridging. Furthermore, a supercapacitor based on our super-tough MXene-functionalized graphene sheets
https://www.nature.com/articles/s41467-020-15991-6?error=cookies_not_supported&code=014afa85-e32f-430f-8af9-df817f656ee1
Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations - Baumketner - 2011 - Protein...Early stages of the recovery stroke in myosin II studied by molecular dynamics simulations - Baumketner - 2011 - Protein...
In order to make the model more computationally efficient it has to be simplified. First and most natural simplification concerns the treatment of the solvent. In contrast to explicit solvent, which treats every water molecule in atomic detail, implicit solvent represents the effect of water molecules through effective potentials acting on the protein. As a consequence, a large reduction in the total number of degrees of freedom in the simulated system is achieved. In the present work, simulations with implicit solvent model ran about five times faster than the equivalent explicit solvent model, allowing us to extend the total simulation time by that amount. Another benefit of treating solvent implicitly is accelerated conformational dynamics of the protein. In explicit solvents, the dynamics of solute molecules is controlled by the solvents viscosity or internal friction. The magnitude of the friction is used as a parameter in implicit solvent simulations and thus can be varied to obtain ...
http://onlinelibrary.wiley.com/doi/10.1002/pro.737/full?globalMessage=0
Paper Size dependence of the dissociation process of spherical hydrate particles via microsecond molecular dynamics...Paper Size dependence of the dissociation process of spherical hydrate particles via microsecond molecular dynamics...
In collaboration with Clariant Oil Services, Clariant Produkte (Deutschland) and the Centre for Research & Technology Hellas (CERTH), researchers from Nextmol have published the paper Size dependence of the dissociation process of spherical hydrate particles via microsecond molecular dynamics simulations in the journal Physical Chemistry Chemical Physics (PCCP) of the Royal Society of Chemistry.. The paper, published as a Communication, investigates the dissociation process of spherical sII mixed methane-propane hydrate particles in liquid hydrocarbon via microsecond-long molecular dynamics simulations. A strong dependence of the melting temperature on the particle size has been found. Furthermore, analysis in the context of the Gibbs-Thomson effect has provided new insights into the fundamental properties of gas hydrates, such as the estimation of the melting temperature of a flat hydrate surface (bulk hydrate), the calculation of the surface tension between hydrate and hydrocarbon, and the ...
https://www.nextmol.com/news/paper-size-dependence-of-the-dissociation-process-of-spherical-hydrate-particles/
Free Energy Calculations of Serotonin Transporters (SERT) : JDM Research
The serotonin transporter (SERT) exists as the primary target for treating depression. We are conducting free energy calculations to find potential inhibitors of SERT. Absolute binding free energy calculations will accurately calculate the binding energy of protein-ligand complexes. Compounds that result in favorable free energy calculations are synthesized and experimental binding assays are performed to validate the calculations. These calculations will help in improving rational drug design by employing computational methods that will aid in understanding drug recognition in treating CNS disorders such as depression, anxiety, and ADHD.. Bernandie Jean, Graduate Student. ...
http://jdm-research.org/free-energy-calculations-of-serotonin-transporters-sert/
Publications | Molecular Modeling and Bioinformatics GroupPublications | Molecular Modeling and Bioinformatics Group
Finding Conformational Transition Pathways from Discrete Molecular Dynamics Simulations, Sfriso, Pedro, Emperador Agustí, Orellana Laura, Hospital Adam, Gelpí Josep-Lluis, and Orozco Modesto , Journal of Chemical Theory and Computation, 2012/11/13, Volume 8, p.4707 - 4718, (2012) ...
http://mmb.irbbarcelona.org/www/user/75/biblio?page=1&%3Bf%5Bauthor%5D=505&f%5Bauthor%5D=117
Read An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation by Gregory R. Bowman ;...Read An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation by Gregory R. Bowman ;...
Read the book An Introduction To Markov State Models And Their Application To Long Timescale Molecular Simulation by Gregory R. Bowman ; Vijay S. Pande ; Frank Noé, Ed online or Preview the book. Please wait while, the book is loading ...
http://isbnplus.com/read/9789400776067
Understanding Molecular Kinetics with Markov State Models | Biomedical Computation Review
Atomistic simulations have the potential to elucidate the molecular basis of biological processes such as protein misfolding in Alzheimers disease or the conformational changes that drive transcription or translation. However, most simulations can only capture the nanosecond to microsecond timescale, whereas most biological processes of interest occur on millisecond and longer timescales. Also, even with an infinitely fast computer, extracting meaningful insight from simulations is difficult because of the complexity of the underlying free energy landscapes. Fortunately, Markov State Models (MSMs) can help overcome these limitations.. MSMs may be used to model any random process where the next state depends solely on the current state. For example, imagine exploring New York City by rolling a die to randomly select which direction to go in each time you came to an intersection. Such a process could be described by an MSM with a state for each intersection. Each state might have a probability of ...
http://www.bcr.org/content/understanding-molecular-kinetics-markov-state-models
The Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus - InfoscienceThe Role of Post-translational Modifications on the Energy Landscape of Huntingtin N-Terminus - Infoscience
Huntington disease is a neurodegenerative disease characterized by a polymorphic tract of polyglutamine repeats in exon 1 of the huntingtin protein, which is thought to be responsible for protein aggregation and neuronal death. The polyglutamine tract is preceded by a 17-residue sequence that is intrinsically disordered. This region is subject to phosphorylation, acetylation and other post-translational modifications in vivo, which modulate its secondary structure, aggregation and, subcellular localization. We used Molecular Dynamics simulations with a novel Hamiltonian-replica-exchange-based enhanced sampling method, SWISH, and an optimal combination of water and protein force fields to study the effects of phosphorylation and acetylation as well as cross-talk between these modifications on the huntingtin N-terminus. The simulations, validated by circular dichroism, were used to formulate a mechanism by which the modifications influence helical conformations. Our findings have implications for
https://infoscience.epfl.ch/record/271346/usage?ln=fr
How chain length and branching influence the alkene cracking reactivity on H-ZSM-5 | Center for Molecular ModelingHow chain length and branching influence the alkene cracking reactivity on H-ZSM-5 | Center for Molecular Modeling
Catalytic alkene cracking on H-ZSM-5 involves a complex reaction network with many possible reaction routes and often elusive intermediates. Herein, advanced molecular dynamics simulations at 773 K, a typical cracking temperature, are performed to clarify the nature of the intermediates and to elucidate dominant cracking pathways at operating conditions. A series of C4-C8 alkene intermediates are investigated to evaluate the influence of chain length and degree of branching on their stability. Our simulations reveal that linear, secondary carbenium ions are relatively unstable, although their lifetime increases with carbon number. Tertiary carbenium ions, on the other hand, are shown to be very stable, irrespective of the chain length. Highly branched carbenium ions, though, tend to rapidly rearrange into more stable cationic species, either via cracking or isomerization reactions. Dominant cracking pathways were determined by combining these insights on carbenium ion stability with intrinsic ...
https://molmod.ugent.be/publications/how-chain-length-and-branching-influence-alkene-cracking-reactivity-h-zsm-5
Insights into the solvation and selectivity of chiral stationary phases using molecular dynamics simulations and chemical force...Insights into the solvation and selectivity of chiral stationary phases using molecular dynamics simulations and chemical force...
The mechanism by which chiral selectivity takes place is complicated by the surface morphology, the possible involvement of the solvent, and the characteristics of the chiral molecules at the surface. My goal is to model and understand the factors which lead to significant discrimination in the case of three closely related chiral stationary phases: N-(1-phenylethyl)-N-[3-(triethoxysilyl)propyl]-urea (PEPU), [(3,5-dinitrobenzoyl)-amino]-N-[3-(triethoxysilyl)propyl]-2-phenylacetamide (DNB-phenyglycine), and [(3,5-dinitrobenzoyl)amino]-N-[3-(triethoxysilyl)propyl]-4-methylpentanamide (DNB-leucine). Ab initio calculations are used to develop molecular models of these chiral selectors. These models are employed in molecular dynamics (MD) simulations, which provide the theoretical framework for modelling chiral interfaces in different solvent mixtures. The MD simulations of PEPU interfaces show that, in alcohol/water mixtures, the alcohols form domains at the interface with the hydrophobic portions ...
http://qspace.library.queensu.ca/jspui/handle/1974/1348
Efficient parallel algorithms for molecular dynamics simulation involving three-body potential: application to the Axilrod...Efficient parallel algorithms for molecular dynamics simulation involving three-body potential: application to the Axilrod...
We present parallel algorithms for molecular dynamics, which are suitable for a small number of processors. These parallel methods are based on a spatial decomposition of the simulation box, that takes advantage of a linked-cell list. The test of the algorithms is conducted, in the case of the Axilrod-Teller fluid at constant pressure, by evaluating the speed-up induced by the various communications schemes involved. These methods seem promising for studying complex physical properties, i.e. the dynamics of the glassy states and the structure at liquid- solid interface, which requires respectively long time scale simulations on small systems and large simulation boxes ...
http://spie.org/Publications/Proceedings/Paper/10.1117/12.299607
Extended discrete element methodExtended discrete element method
Molecular dynamics developed in the late 1950s by Alder et al. and early 1960s by Rahman may be regarded as a first step toward ... Numerical simulation of fluid injection into a gaseous environment nowadays is adopted by a large number of CFD-codes such as ... Alder, B. J.; Wainwright, T. E. (1959). "Studies in Molecular Dynamics. I. General Method". J. Chem. Phys. 31 (2): 459-466. ... Zhou, H.; Mo, G.; Zhao, J.; Cen, K. (2011). "DEM-CFD simulation of the particle dispersion in a gas-solid two-phase flow for a ...
https://en.wikipedia.org/wiki/Extended_discrete_element_method
Strengthening mechanisms of materialsStrengthening mechanisms of materials
Haile, J.M. (1997). Molecular Dynamics Simulation: Elementary Methods. John Wiley & Sons, Inc. pp. 38-42. ISBN 978-0-471-18439- ... Multimillion Atom Molecular Dynamics Simulations". Annual Review of Materials Research. 32: 377-400. doi:10.1146/annurev.matsci ... Shim, Jae-Hyeok (2009). "Strengthening of Nanosized bcc Cu Precipitate in bcc Fe: A Molecular Dynamics Study". Materials ... Voter, Arthur (1997). "Hyperdynamics: Accelerated Molecular Dynamics of Infrequent Events". Phys. Rev. Lett. 78 (20): 3908. ...
https://en.wikipedia.org/wiki/Strengthening_mechanisms_of_materials
Zinc ricinoleateZinc ricinoleate
A molecular dynamics computer simulation". Journal of Surfactants and Detergents. Springer Berlin/Heidelberg. 3 (3): 335-343. ...
https://en.wikipedia.org/wiki/Zinc_ricinoleate
Titan (supercomputer)Titan (supercomputer)
Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) is a molecular dynamics code that simulates particles across ... VERA is a light-water reactor simulation written at the Consortium for Advanced Simulation of Light Water Reactors (CASL) on ... "LAMMPS Molecular Dynamics Simulator". Sandia National Laboratories. Archived from the original on February 16, 2013. Retrieved ... Bonsai is a gravitational tree code for n-body simulation. It has been used for the 2014 Gordon Bell prize nomination for ...
https://en.wikipedia.org/wiki/Titan_(supercomputer)
ZirconZircon
"Molecular dynamics simulation of zirconia melting". Open Physics. 8 (5): 789. Bibcode:2010CEJPh...8..789D. doi:10.2478/s11534- ...
https://en.wikipedia.org/wiki/Zircon
FemtosecondFemtosecond
... use in molecular dynamics simulation". LAMMPS Molecular Simulator. Andrew M. Weiner (2009). Ultrafast Optics. Wiley. ISBN 978-0 ... Typical time steps for molecular dynamics simulations are on the order of 1 fs. The periods of the waves of visible light have ...
https://en.wikipedia.org/wiki/Femtosecond
Lennard-Jones potentialLennard-Jones potential
Molecular simulations of the Lennard-Jones potential can in general be performed using either molecular dynamics (MD) ... an open access database of force fields for molecular simulations of fluids". Molecular Simulation. 45 (10): 806-814. arXiv: ... D. C. Rapaport (1 April 2004). The Art of Molecular Dynamics Simulation. Cambridge University Press. ISBN 978-0-521-82568-9. ... "Corresponding states law and molecular dynamics simulations of the Lennard-Jones fluid". The Journal of Chemical Physics. 115 ( ...
https://en.wikipedia.org/wiki/Lennard-Jones_potential
Heat transfer physicsHeat transfer physics
Haile, J.M. (1997). Molecular dynamics simulation : elementary methods (Reprinted. ed.). New York: Wiley. ISBN 978-0471184393. ... Bao, H.; Qiu, B.; Zhang, Y.; Ruan, X. (2012). "A first-principles molecular dynamics approach for predicting optical phonon ... Marx, D.; Hutter, J (2009). Ab initio molecular dynamics : basic theory and advanced methods (1. publ., repr. ed.). Cambridge, ... Frenkel, D; Smit, B (2002). Understanding molecular simulation from algorithms to applications (2nd ed.). San Diego: Academic ...
https://en.wikipedia.org/wiki/Heat_transfer_physics
Irreversible electroporationIrreversible electroporation
A molecular dynamics simulation by Tarek illustrates this proposed pore formation in two steps: After the application of an ... Tarek M (June 2005). "Membrane electroporation: a molecular dynamics simulation". Biophysical Journal. 88 (6): 4045-53. Bibcode ... Tieleman DP, Leontiadou H, Mark AE, Marrink SJ (May 2003). "Simulation of pore formation in lipid bilayers by mechanical stress ... Weaver JC (May 1994). "Molecular basis for cell membrane electroporation". Annals of the New York Academy of Sciences. 720 (1 ...
https://en.wikipedia.org/wiki/Irreversible_electroporation
Multiscale Greens functionMultiscale Green's function
ISBN 978-1-78242-228-0. Tewary, V. K. (22 October 2009). "Extending the time scale in molecular dynamics simulations: ... Rapaport, D. (2004). The art of molecular dynamics simulation. Cambridge, UK: Cambridge University Press. Kittel, C. (1996). ... the causal Green's functions in molecular dynamics can significantly accelerate the temporal convergence of molecular dynamics ... "Generalized Green's function molecular dynamics for canonical ensemble simulations". Physical Review E. 97 (5): 053310. doi: ...
https://en.wikipedia.org/wiki/Multiscale_Green's_function
Water modelWater model
In molecular dynamics simulations it gives the correct density and dielectric permittivity of water. Flexible SPC is ... Stillinger FH, Rahman A (1974). "Improved simulation of liquid water by molecular dynamics". The Journal of Chemical Physics. ... Nada H (December 2016). "2O and a molecular dynamics simulation". The Journal of Chemical Physics. 145 (24): 244706. Bibcode: ... Praprotnik M, Janezic D, Mavri J (2004). "Temperature Dependence of Water Vibrational Spectrum: A Molecular Dynamics Simulation ...
https://en.wikipedia.org/wiki/Water_model
Ascalaph DesignerAscalaph Designer
A molecular dynamics computer simulation study". Nucleic Acids Research. 34 (2): 686-696. doi:10.1093/nar/gkj434. PMC 1356527. ... X. Wu; Z. Liu; S. Huang; W. Wang (2005). "Molecular dynamics simulation of room-temperature ionic liquid mixture of [bmim][BF4 ... doi:10.1016/S0010-4655(99)00529-9. A.P.Lyubartsev, A.Laaksonen (1998). "Parallel molecular dynamics simulations of biomolecular ... Ascalaph Designer is a computer program for general purpose molecular modelling for molecular design and simulations. It ...
https://en.wikipedia.org/wiki/Ascalaph_Designer
Anne BoutinAnne Boutin
The fusion of a molecular crystal. A numerical simulation study of molecular dynamics. She completed her post-doctorate at ... A specialist in molecular thermodynamics, she develops molecular simulation tools as well as theoretical approaches for ... chemical physics and molecular dynamics. Since 2009, she has been working in the PASTEUR laboratory (Selective activation ... studying the structure, dynamics, thermodynamics and reactivity of confined molecular fluids. Boutin did her graduate studies ...
https://en.wikipedia.org/wiki/Anne_Boutin
List of biophysicistsList of biophysicists
... introduction of molecular dynamics simulations in biology; introduction of consistent electrostatic calculations in proteins. ... Benoit Roux - continues to conduct research at the University of Chicago in classical molecular dynamics and other theoretical ... Pascual Jordan (German, 1902-1980) Martin Karplus (American, 1930-) - research on molecular dynamical simulations of biological ... Cantor is a molecular geneticist who developed pulse field electrophoresis for very large DNA molecules with David C. Schwartz ...
https://en.wikipedia.org/wiki/List_of_biophysicists
ViscosityViscosity
Rapaport, D.C. (2004). The Art of Molecular Dynamics Simulation (2nd ed.). Cambridge University Press. ISBN 9780521825689. ... available only in computationally expensive simulations such as molecular dynamics. An accurate model for interparticle ... Self-Diffusivity and Viscosity from Equilibrium Molecular Dynamics [Article v1.0]". Living Journal of Computational Molecular ... the viscosity of a dense fluid using these relations currently requires the use of molecular dynamics computer simulations. ...
https://en.wikipedia.org/wiki/Viscosity
Ion trackIon track
Molecular dynamics simulation of collision cascade in gold. Track etch threshold: energy input required for selective etching. ... Molecular BioSystems. 3 (10): 667-685. doi:10.1039/b708725j. PMID 17882330. F. Maurer; A. Dangwal; D. Lysenkov; G. Müller; M.E ...
https://en.wikipedia.org/wiki/Ion_track
ProteinProtein
Beyond classical molecular dynamics, quantum dynamics methods allow the simulation of proteins in atomistic detail with an ... Scheraga HA, Khalili M, Liwo A (2007). "Protein-folding dynamics: overview of molecular simulation techniques". Annual Review ... Mathematical models to simulate these dynamical processes involve molecular mechanics, in particular, molecular dynamics. In ... the HIV accessory protein and hybrid methods combining standard molecular dynamics with quantum mechanical mathematics have ...
https://en.wikipedia.org/wiki/Protein
Gregory PetskoGregory Petsko
Karplus, M.; Petsko, G. A. (1990). "Molecular dynamics simulations in biology". Nature. 347 (6294): 631-639. Bibcode:1990Natur. ... At MIT and Brandeis, he and Dagmar Ringe trained a large number of current leaders in structural molecular biology who now have ... He is past-president of the American Society for Biochemistry and Molecular Biology and of the International Union for ... He received a Rhodes Scholarship, and obtained his doctorate in Molecular Biophysics from Merton College, Oxford supervised by ...
https://en.wikipedia.org/wiki/Gregory_Petsko
XDNAXDNA
Varghese MK, Thomas R, Unnikrishnan NV, Sudarsanakumar C (May 2009). "Molecular dynamics simulations of xDNA". Biopolymers. 91 ... distance between the highest occupied molecular orbital and lowest unoccupied molecular orbital) as a result of modified ... xDNA's electrical conduction properties also make it a prime candidate as a molecular wire, as its π-π interactions help it ... applied to xDNA revealed that the benzene component of the highest occupied molecular orbitals (HOMO) in the x-bases pins the ...
https://en.wikipedia.org/wiki/XDNA
Structural biologyStructural biology
Computational techniques such as Molecular Dynamics simulations can be used in conjunction with empirical structure ... Karplus M, McCammon JA (September 2002). "Molecular dynamics simulations of biomolecules". Nature Structural Biology. 9 (9): ... For example, molecular dynamics (MD) is commonly used to analyze the dynamic movements of biological molecules. In 1975, the ... Molecular Cell Biology. 19 (12): 755-773. doi:10.1038/s41580-018-0060-8. PMID 30237470. S2CID 52307956. Fitzpatrick, Anthony W ...
https://en.wikipedia.org/wiki/Structural_biology
James B. AndersonJames B. Anderson
Trajectory calculations for the HI + HI reaction, a rare event, led to his work on predicting rare events in molecular dynamics ... Monte Carlo simulation of radiative processes, and direct Monte Carlo simulation of reaction systems. Anderson's first ... Jaffe, R. L.; Henry, J. M.; Anderson, J. B. (1976). "Molecular Dynamics of the Hydrogen Iodide and Hydrogen-Iodine Exchange ... The main areas of impact are: reaction kinetics and molecular dynamics, the 'rare-event' approach to chemical reactions, ...
https://en.wikipedia.org/wiki/James_B._Anderson
TriclocarbanTriclocarban
Orsi Mario; Noro Massimo; Essex Jonathan (2010). "Dual-resolution molecular dynamics simulation of antimicrobials in ...
https://en.wikipedia.org/wiki/Triclocarban
Bonding in solidsBonding in solids
Belashchenko, D.K; Ostrovski, O.I (2001). "Molecular dynamics simulation of oxides with ionic-covalent bonds". Thermochimica ... which forms metallic solids Weak inter molecular bonding, which forms molecular solids (sometimes anomalously called "covalent ... Molecular solids are typically insulators with large band gaps. The four classes of solids permit six pairwise intermediate ... Although weakly bound molecular components are incompatible with strong metallic bonding, low densities of shared, delocalized ...
https://en.wikipedia.org/wiki/Bonding_in_solids
Succinate dehydrogenaseSuccinate dehydrogenase
Homology modeling, cofactor docking, and molecular dynamics simulation studies". The Journal of Biological Chemistry. 279 (10 ... This electron transfer is demonstrated in image 8. In molecular biology, the protein domain named Sdh5 is also named SdhE which ... Its role is to prevent the interaction of the intermediate with molecular oxygen to produce reactive oxygen species (ROS). The ... Avenot HF, Michailides TJ (2010). "Progress in understanding molecular mechanisms and evolution of resistance to succinate ...
https://en.wikipedia.org/wiki/Succinate_dehydrogenase
Nikolay DokholyanNikolay Dokholyan
"Molecular dynamics simulation of polymer chains with excluded volume". "Discrete molecular dynamics studies of the folding of a ... His lab has explored the approaches to molecular dynamics simulations and modeling, and drug discovery, while focusing on both ... Using the approach of Rapaport, he further developed discrete molecular dynamics studies of the folding of a protein-like model ... Discrete molecular dynamics studies of the folding of a protein-like model. Folding and design, 3(6), 577-587. Vendruscolo, M ...
https://en.wikipedia.org/wiki/Nikolay_Dokholyan
Adaptive samplingAdaptive sampling
... in computational molecular biology to efficiently simulate protein folding when coupled with molecular dynamics simulations. ... [email protected] Hidden Markov model Computational biology Molecular biology Robert B Best (2012). "Atomistic molecular simulations ... A Special-Purpose Machine for Molecular Dynamics Simulation". Communications of the ACM. 51 (7): 91-97. doi:10.1145/ ... Using adaptive sampling, molecular simulations that previously would have taken decades can be performed in a matter of weeks. ...
https://en.wikipedia.org/wiki/Adaptive_sampling
Anton (computer)Anton (computer)
It is a special-purpose system for molecular dynamics (MD) simulations of proteins and other biological macromolecules. An ... Millisecond-Scale Molecular Dynamics Simulations on Anton (PDF). Proceedings of the ACM/IEEE Conference on Supercomputing (SC09 ... A Special-Purpose Machine for Molecular Dynamics Simulation. Communications of the ACM. Vol. 51. ACM. pp. 91-97. doi:10.1145/ ... a Specialized Machine for Molecular Dynamics Simulation (PDF). Proceedings of the 14th Annual International Symposium on High- ...
https://en.wikipedia.org/wiki/Anton_(computer)
D. E. Shaw ResearchD. E. Shaw Research
May 2007). "Anton, a special-purpose machine for molecular dynamics simulation". ACM SIGARCH Computer Architecture News. ACM. ... "Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters" (PDF). ACM/IEEE SC 2006 Conference (SC'06). ACM. ... "Millisecond-scale molecular dynamics simulations on Anton". Proceedings of the Conference on High Performance Computing ... Shaw Research develops technologies for molecular dynamics simulations (including Anton, a massively parallel special-purpose ...
https://en.wikipedia.org/wiki/D._E._Shaw_Research
Sympathetic coolingSympathetic cooling
Schiller, S.; Lämmerzahl, C. (2003). "Molecular dynamics simulation of sympathetic crystallization of molecular ions". Phys. ... This technique is used to cool ions and atoms that cannot be cooled directly by laser cooling, which includes most molecular ... v t e (Atomic, molecular, and optical physics, Cooling technology, Thermodynamics, All stub articles, Nuclear and atomic ...
https://en.wikipedia.org/wiki/Sympathetic_cooling
Drug discoveryDrug discovery
Molecular modelling and molecular dynamics simulations can be used as a guide to improve the potency and properties of new drug ... "The future of molecular dynamics simulations in drug discovery". Journal of Computer-Aided Molecular Design. 26 (1): 15-26. doi ... Durrant JD, McCammon JA (October 2011). "Molecular dynamics simulations and drug discovery". BMC Biology. 9: 71. doi:10.1186/ ... In 2010, the research and development cost of each new molecular entity was about US$1.8 billion. In the 21st century, basic ...
https://en.wikipedia.org/wiki/Drug_discovery
நிறை மையம் - தமிழ் விக்கிப்பீடியாநிறை மையம் - தமிழ் விக்கிப்பீடியா
Millikan, Robert Andrews (1902), Mechanics, molecular physics and heat: a twelve weeks' college course, Chicago: Scott, ... Beatty, Millard F. (2006), Principles of Engineering Mechanics, Volume 2: Dynamics-The Analysis of Motion, Mathematical ... The Solar System's barycenter, simulations showing the effect each planet contributes to the Solar System's barycenter. ... Beatty, Millard F. (2006), Principles of Engineering Mechanics, Volume 2: Dynamics-The Analysis of Motion, Mathematical ...
https://ta.wikipedia.org/wiki/நிறை_மையம்
Callisto (satelit)Callisto (satelit)
The Direct Simulation Monte Carlo Method". Computers in Physics (în engleză). 11 (6): 588. doi:10.1063/1.168619.. ... oxigen molecular și hidrogen molecular. În cadrul modelului de cinetică moleculară utilizat pentru simulare, densitatea ... Interior composition, structure and dynamics of the Galilean satellites". În Bagenal, F.; Dowling, T. E.; McKinnon, W. B. ... Numerical Simulations of the Orbits of the Galilean Satellites". Icarus. 159 (2): 500-504. Bibcode:2002Icar..159..500M. doi: ...
https://ro.wikipedia.org/wiki/Callisto_
Amyloid betaAmyloid beta
... monomer in water using unbiased molecular dynamics simulations and spectral algorithms". Journal of Molecular Biology. 405 (2 ... As such, it cannot be crystallized and most structural knowledge on amyloid beta comes from NMR and molecular dynamics. Early ... A molecular dynamics study". Biochimica et Biophysica Acta (BBA) - Biomembranes. 1858 (6): 1380-9. doi:10.1016/j.bbamem.2016.03 ... Replica exchange molecular dynamics studies suggested that amyloid beta can indeed populate multiple discrete structural states ...
https://en.wikipedia.org/wiki/Beta_amyloid
NebularhypotesenNebularhypotesen
Clark, Paul C.; Bonnell, Ian A. (2005). «The onset of collapse in turbulently supported molecular clouds». Mon.Not.R.Astron.Soc ... Raymond, Sean N.; Quinn, Thomas; Lunine, Jonathan I. (2006). «High-resolution simulations of the final assembly of earth-like ... planets 1: terrestrial accretion and dynamics». Icarus (engelsk). 183 (2). Bibcode:2006Icar..183..265R. arXiv:astro-ph/0510284 ... Raymond, Sean N.; Quinn, Thomas; Lunine, Jonathan I. (2007). «High-resolution simulations of the final assembly of Earth-like ...
https://no.wikipedia.org/wiki/Nebularhypotesen
Statistical mechanicsStatistical mechanics
Molecular dynamics computer simulations can be used to calculate microcanonical ensemble averages, in ergodic systems. With the ... Keldysh formalism (a.k.a. NEGF-non-equilibrium Green functions): A quantum approach to including stochastic dynamics is found ... Ludwig Boltzmann subsequently showed that, by taking this molecular chaos for granted as a complete randomization, the motions ... The Boltzmann transport equation has been found to be very useful in simulations of electron transport in lightly doped ...
https://en.m.wikipedia.org/wiki/Statistical_mechanics
Deep learningDeep learning
"Merck Molecular Activity Challenge". kaggle.com. Archived from the original on 2020-07-16. Retrieved 2020-07-16.. ... These developmental models share the property that various proposed learning dynamics in the brain (e.g., a wave of nerve ... "Training Variational Networks With Multidomain Simulations: Speed-of-Sound Image Reconstruction". IEEE Transactions on ... In 2012, a team led by George E. Dahl won the "Merck Molecular Activity Challenge" using multi-task deep neural networks to ...
https://en.m.wikipedia.org/wiki/Deep_learning
Центар масе - ВикипедијаЦентар масе - Википедија
Millikan, Robert Andrews (1902), Mechanics, molecular physics and heat: a twelve weeks' college course, Chicago: Scott, ... Beatty, Millard F. (2006). Principles of Engineering Mechanics, Volume 2: Dynamics-The Analysis of Motion. Mathematical ... The Solar System's barycenter, simulations showing the effect each planet contributes to the Solar System's barycenter. ... Beatty, Millard F. (2006). Principles of Engineering Mechanics, Volume 2: Dynamics-The Analysis of Motion. Mathematical ...
https://sr.m.wikipedia.org/wiki/Težište
MD - Simple English Wikipedia, the free encyclopediaMD - Simple English Wikipedia, the free encyclopedia
Molecular dynamics, a method of computer simulation of molecular interaction. *Membrane distillation, a process of membrane ...
https://simple.m.wikipedia.org/wiki/MD
Yellingbo Nature Conservation ReserveYellingbo Nature Conservation Reserve
Estimating the provenance of Yellingbo Leadbeater's possums by genetic analysis and bottleneck simulation. Molecular Ecology, ... McCarthy, M.A., Extinction dynamics of the helmeted honeyeater: effects of demography, stochasticity, inbreeding and spatial ... Molecular Ecology, 2016. 25(6): p. 1242-1258. *^ Lindenmayer, D.B. and H.P. Possingham, Ranking Conservation and Timber ...
https://en.wikipedia.org/wiki/Yellingbo_Nature_Conservation_Reserve
MutationMutation
Bertram JS (December 2000). "The molecular biology of cancer". Molecular Aspects of Medicine. 21 (6): 167-223. doi:10.1016/ ... Knowing the DFE of advantageous mutations may lead to increased ability to predict the evolutionary dynamics. Theoretical work ... Because of this convenience, compensatory mutations have been studied in computational simulations using RNA folding algorithms ... Bernstein H, Hopf FA, Michod RE (1987). "The molecular basis of the evolution of sex". Molecular Genetics of Development. ...
https://en.wikipedia.org/wiki/Genetic_mutation
Intermediate-mass black holeIntermediate-mass black hole
Merritt, David (2013). Dynamics and Evolution of Galactic Nuclei. Princeton, NJ: Princeton University Press. ISBN 9781400846122 ... In 2018, the Keio University team found several molecular gas streams orbiting around an invisible object near the galactic ... They performed simulations and concluded that a model with a black hole of around one hundred thousand solar masses would be ... "Signature of an Intermediate-Mass Black Hole in the Central Molecular Zone of Our Galaxy". Astrophysical Journal. 816 (1): L7. ...
https://en.m.wikipedia.org/wiki/Intermediate-mass_black_hole
Aluminium oxide - Simple English Wikipedia, the free encyclopediaAluminium oxide - Simple English Wikipedia, the free encyclopedia
"Dynamics of Oxidation of Aluminium Nanoclusters using Variable Charge Molecular-Dynamics Simulations on Parallel Computers" ( ...
https://simple.wikipedia.org/wiki/Aluminium_oxide
泰坦 (超級電腦) - 维基百科，自由的百科全泰坦 (超級電腦) - 维基百科，自由的百科全
LAMMPS Molecular Dynamics Simulator. Sandia National Laboratories. [2012-10-29].. *^ Messer, Bronson. Using Titan to Model ... VERA」專案是一個輕水反應爐的仿真，在美洲虎超級電腦上的CASL（Consortium for Advanced Simulation of Light Water Reactors，聯合輕水反應爐進階仿真）編寫並運作。VERA允許工程師監視反應爐使用 ... LAMMPS」專案，全稱「Large-scale Atomic/Molecular Massively
https://zh.m.wikipedia.org/wiki/泰坦_
نيانډرټال - ويکيپېډيانيانډرټال - ويکيپېډيا
Kislev, M.; Barkai, R. (2018). [اصطلاحي تېروتنه: د ناپېژندلې ليکنښې لوښه '۱'. "Neanderthal and woolly mammoth molecular ... 2017). [اصطلاحي تېروتنه: د ناپېژندلې ليکنښې لوښه '۱'. "Nasal airflow simulations suggest convergent adaptation in Neanderthals ... Rapid climate change and population dynamics in Late Pleistocene Europe"]. Quaternary International 247: 38-49. doi:10.1016/j. ...
https://ps.wikipedia.org/wiki/نيانډرټال
Timeline of scientific computingTimeline of scientific computing
Molecular dynamics invented by Bernie Alder and Wainwright [43][44]. *A S Householder invents his eponymous matrices and ... First hydro simulations occurred at Los Alamos.[34][35]. 1950s[edit]. *First successful weather predictions on a computer ... Car-Parrinello molecular dynamics developed by Roberto Car and Michele Parrinello. 1990s[edit]. *1990 - In computational ... 1964 - Molecular dynamics invented independently by Aneesur Rahman.[57]. *1965 - fast Fourier transform developed by James W. ...
https://en.wikipedia.org/wiki/Timeline_of_scientific_computing
LaserLaser
Free software for Simulation of random laser dynamics. *Video Demonstrations in Lasers and Optics Produced by the Massachusetts ... Unlike gas, liquid, or solid-state lasers, which rely on bound atomic or molecular states, FELs use a relativistic electron ... The molecular fluorine laser, emitting at 157 nm in the vacuum ultraviolet is sometimes referred to as an excimer laser, ...
https://en.wikipedia.org/wiki/Laser
கன நீர் - தமிழ் விக்கிப்பீடியாகன நீர் - தமிழ் விக்கிப்பீடியா
Svishchev, I. M.; Kusalik, P. G. (January 1994). "Dynamics in liquid water, water-d2, and water-t2: a comparative simulation ... Protonated molecular hydrogen. *சோடியம் சயனைடு. *சோடியம் ஐதராக்சைடு. *Silicon carbonitride. *c-Silicon dicarbide ...
https://ta.wikipedia.org/wiki/கன_நீர்
Carbon nanotubeCarbon nanotube
Molecular dynamics simulation at realistic limit" (PDF). Computer Physics Communications. 146 (1): 30-37. Bibcode:2002CoPhC.146 ... a molecular dynamics study". Nanotechnology. 21 (3): 035704. Bibcode:2010Nanot..21c5704W. doi:10.1088/0957-4484/21/3/035704. ... Dekker C (May 1999). "Carbon Nanotubes as Molecular Quantum Wires". Physics Today. 52 (5): 22-28. Bibcode:1999PhT....52e..22D. ... Phonon transport simulations indicate that substitutional defects such as nitrogen or boron will primarily lead to scattering ...
https://en.wikipedia.org/wiki/MWNT
Mie scatteringMie scattering
... (sometimes referred to as a non-molecular scattering or aerosol particle scattering) takes place in the lower ... Gaitan, D. Felipe; Lawrence A. Crum; Charles C. Church; Ronald A. Roy (1992). "Sonoluminescence and bubble dynamics for a ... Provides far-field and near-field simulation results for multilayered spheres. Online Mie scattering calculator provides ... simulation of scattering properties (including multipole decomposition) and near-field maps for bulk, core-shell, and ...
https://en.wikipedia.org/wiki/Mie_scattering
MetabolismMetabolism
... electron microscopy and molecular dynamics simulations. These techniques have allowed the discovery and detailed analysis of ... Cooper GM (2000). "The Molecular Composition of Cells". The Cell: A Molecular Approach (2nd ed.). Archived from the original on ... Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P (2002). "How Cells Obtain Energy from Food". Molecular Biology of ... From metabolites to molecular genetics". Diabetes Care. 13 (6): 582-99. doi:10.2337/diacare.13.6.582. PMID 2162755. S2CID ...
https://en.wikipedia.org/wiki/Metabolism
MOLCASMOLCAS
Tully Surface Hopping Molecular Dynamics Method for localization and characterization of conical intersections and seams MOLCAS ... The NEMO procedure for creating intermolecular force fields for MC/MD simulations; these force fields include electrostatics, ... molecular dynamics code There are several Graphical User Interface codes for MOLCAS: and MolGUI. Veryazov, Valera; Widmark, Per ... Combined QM and molecular mechanics calculations for systems such as proteins and molecular clusters. ...
https://en.wikipedia.org/wiki/MOLCAS
Sodium-potassium pumpSodium-potassium pump
found 87% amino acid identity among insect sequences, which shows a high level of molecular convergence among four orders of ... Forrest MD (April 2015). "Simulation of alcohol action upon a detailed Purkinje neuron model and a simpler surrogate model that ... Zylbertal A, Kahan A, Ben-Shaul Y, Yarom Y, Wagner S (December 2015). "Prolonged Intracellular Na+ Dynamics Govern Electrical ... January 2006). "Binding of Src to Na+/K+-ATPase forms a functional signaling complex". Molecular Biology of the Cell. 17 (1): ...
https://en.wikipedia.org/wiki/Sodium–potassium_pump
Klaus SchultenKlaus Schulten
Heller, Helmut; Schaefer, Michael; Schulten, Klaus (August 1993). "Molecular dynamics simulation of a bilayer of 200 lipids in ... Freddolino, PL; Arkhipov, AS; Larson, SB; McPherson, A; Schulten, K (March 2006). "Molecular dynamics simulations of the ... "Molecular Dynamics Simulations Suggest that Electrostatic Funnel Directs Binding of Tamiflu to Influenza N1 Neuraminidases". ... The molecular dynamics package NAMD and the visualization software VMD are estimated to be used by at least 300,000 researchers ...
https://en.wikipedia.org/wiki/Klaus_Schulten
Center of excellenceCenter of excellence
This investment uses modeling and simulation tools at the Center of Excellence which predict the performance of its test-bed ... ARC Centre of Excellence in Advanced Molecular Imaging ARC Centre of Excellence for Children and Families over the Life Course ... ARC Centre of Excellence in Convergent Bio-Nano Science and Technology ARC Centre of Excellence for the Dynamics of Language ...
https://en.wikipedia.org/wiki/Center_of_excellence
Cone algorithmCone algorithm
Melting of Icosahedral Gold Nanoclusters from Molecular Dynamics Simulations. Journal of Chemical Physics vol. 122, pp 214722- ... Articles with short description, Short description matches Wikidata, Molecular modelling software, Geometric algorithms). ...
https://en.wikipedia.org/wiki/Cone_algorithm
List of Puerto Rican scientists and inventorsList of Puerto Rican scientists and inventors
She is also responsible for planning experimental studies to validate analytical techniques and study solar sails dynamics. ... "Hawaii Space Exploration Analog and Simulation," that will help to determine why astronauts don't eat enough, having noted that ... other maladies of the eye Gualberto Ruaño is a pioneer in the field of personalized medicine and the inventor of molecular ...
https://en.wikipedia.org/wiki/List_of_Puerto_Rican_scientists_and_inventors
Surface hoppingSurface hopping
Molecular dynamics simulations numerically solve the classical equations of motion. These simulations, though, assume that the ... Computational chemistry Molecular dynamics Path integral molecular dynamics Quantum chemistry Herman, Michael F. (1984). " ... The forces in the molecular dynamics simulations are derived only from one adiabatic surface, and are given by: F R = − ∇ R ⟨ ϕ ... To tackle this issue, one approach is the mean field or Ehrenfest method, where the molecular dynamics is run on the average ...
https://en.wikipedia.org/wiki/Surface_hopping
RNA-targeting small molecule drugsRNA-targeting small molecule drugs
They docked a library of small molecules onto RNA dynamic structures generated by NMR and Molecular Dynamics (MD) simulations. ...
https://en.wikipedia.org/wiki/RNA-targeting_small_molecule_drugs
List of companies involved in quantum computing or communicationList of companies involved in quantum computing or communication
"HQS Quantum Simulations Brings In 12 Million Euros In Series A Funding". Insidequantumtechnology.com. "Collaborative Innovation ... "Research at HP Labs : Information Dynamics Lab : Research Areas : Quantum Computing". www.hpl.hp.com. Retrieved 2017-11-01. ... Molecular and Optical Physics. 49 (Special issue on Rydberg atomic physics): 202001. arXiv:1605.05207. Bibcode:2016JPhB... ...
https://en.wikipedia.org/wiki/List_of_companies_involved_in_quantum_computing_or_communication
Antennae GalaxiesAntennae Galaxies
Observations and simulations of colliding galaxies (e.g., by Alar Toomre) suggest that the Antennae Galaxies will eventually ... J. E. Barnes; L. Hernquist (1992). "Dynamics of interacting galaxies". Annual Review of Astronomy and Astrophysics. 30 (1): 705 ... massive molecular clouds. The densest regions of the collapsing and compressing clouds are believed to be the birthplace of the ...
https://en.wikipedia.org/wiki/Antennae_Galaxies
Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations | Nature Biomedical...Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations | Nature Biomedical...
A computational method leveraging deep learning and molecular dynamics simulations enables the rapid discovery of antimicrobial ... The combination of deep learning and molecular dynamics may accelerate the discovery of potent and selective broad-spectrum ... using deep-learning classifiers as well as physicochemical features derived from high-throughput molecular dynamics simulations ... Accelerated antimicrobial discovery via deep generative models and molecular dynamics simulations. *Payel Das. ORCID: orcid.org ...
https://www.nature.com/articles/s41551-021-00689-x?utm_campaign=Your%20guide%20to%20AI&utm_medium=email&utm_source=Revue%20newsletter&error=cookies_not_supported&code=59357d2f-5461-4c3b-9f80-5706ca176a2d
The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics SimulationThe Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation
... using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were s … ... We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical ... The Dynamics of the Neuropeptide Y Receptor Type 1 Investigated by Solid-State NMR and Molecular Dynamics Simulation Molecules ... using a combination of solid-state NMR and molecular dynamics (MD) simulation. First, the equilibrium dynamics of Y1R were ...
https://pubmed.ncbi.nlm.nih.gov/33255213/
Partition of protein solvation into group contributions from molecular dynamics simulations | BSC-CNSPartition of protein solvation into group contributions from molecular dynamics simulations | BSC-CNS
Partition of protein solvation into group contributions from molecular dynamics simulations. Journal 2005 ...
https://www.bsc.es/es/research-and-development/publications/partition-protein-solvation-group-contributions-molecular
IJMS | Free Full-Text | Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein...IJMS | Free Full-Text | Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein...
In the present study, homology models of MK5 were used for molecular dynamics (MD) simulations of: (1) MK5 alone; (2) MK5 in ... molecular dynamics simulations; molecular mechanisms; electrostatic potential surfaces ... Comparative Molecular Dynamics Simulations of Mitogen-Activated Protein Kinase-Activated Protein Kinase 5 by Inger Lindin ... In the present study, homology models of MK5 were used for molecular dynamics (MD) simulations of: (1) MK5 alone; (2) MK5 in ...
https://www.mdpi.com/1422-0067/15/3/4878
Leveraging the IPU for Molecular Dynamics SimulationLeveraging the IPU for Molecular Dynamics Simulation
Here, IPU hardware is leveraged for water molecule simulation and the DeePMD-kit is used for force analysis. ... Here, IPU hardware is leveraged for water molecule simulation and the DeePMD-kit is used for force analysis. ... Molecular dynamics simulation is essential for calculating molecular forces. The traditional method uses the empirical force ... Molecular dynamics uses computers to simulate the movement of molecular and atomic systems. It is a basic method for simulating ...
https://www.graphcore.ai/posts/leveraging-the-ipu-for-molecular-dynamics-simulation
Molecular dynamics simulations on devitrification: the PbF2 caseMolecular dynamics simulations on devitrification: the PbF2 case
... dc.contributor.author. Silva, MAP. ... In this work molecular dynamics simulations were performed to reproduce the kinetic and thermodynamic transformations occurring ...
https://repositorio.unesp.br/handle/11449/37995?show=full
namd-l: RE: Monitoring progress of an ongoing molecular dynamics simulation
RE: Monitoring progress of an ongoing molecular dynamics simulation. From: Bennion, Brian (Bennion1_at_llnl.gov). Date: Fri Mar ... In reply to: Ivan Gregoretti: "Monitoring progress of an ongoing molecular dynamics simulation" *Messages sorted by: [ date ] ... In reply to: Ivan Gregoretti: "Monitoring progress of an ongoing molecular dynamics simulation" *Messages sorted by: [ date ] ... Subject: namd-l: Monitoring progress of an ongoing molecular dynamics simulation Hello everybody, Could you share the way you ...
https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2014-2015/0346.html
Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates - NASA/ADSSynchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates - NASA/ADS
The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\bf 4}, 041011 (2014)] is ... Synchronized molecular-dynamics simulation for the thermal lubrication of a polymeric liquid between parallel plates *Yasuda, ... The Synchronized Molecular-Dynamics simulation which was recently proposed by authors [Phys. Rev. X {\bf 4}, 041011 (2014)] is ...
https://ui.adsabs.harvard.edu/abs/2015arXiv150307289Y/abstract
Towards exact molecular dynamics simulations with invariant machine-learned modelsTowards exact molecular dynamics simulations with invariant machine-learned models
Our approach provides the key missing ingredient for achieving spectroscopic accuracy in molecular simulations. ... which hinders truly predictive modeling of dynamics and function of (bio)molecular systems. Classical potentials often fail to ... level of accuracy and allows converged MD simulations with fully quantized electrons and nuclei. We present MD simulations, for ... However, one of the widely recognized and increasingly pressing issues in MD simulations is the lack of accuracy of underlying ...
https://depositonce.tu-berlin.de/items/111a8bc8-1ccd-45d9-a202-aaf5e85a19c5
PDF] Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer...PDF] Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer: an application to polymer...
In this method, the molecular dynamics simulations are assigned to small fluid elements to calculate the local stresses and ... The present simulation demonstrates that strong shear thinning and transitional behavior of the conformation of the polymer ... The synchronized molecular dynamics simulation via macroscopic heat and momentum transfer is proposed for the non-isothermal ... Using molecular dynamics simulations, we study dynamics of a model polymer melt composed of short chains with bead number N=10 ...
https://www.semanticscholar.org/paper/Synchronized-molecular-dynamics-simulation-via-heat-Yasuda-Yamamoto/32178e07f3fa53c941b085f3c721ca40bc76bad4
Characterization of interface structures in nanocrystalline germanium by means of high-resolution electron microscopy and...Characterization of interface structures in nanocrystalline germanium by means of high-resolution electron microscopy and...
The influence of lattice relaxations is taken into consideration by molecular dynamics simulations of the structure models. ... It will be shown by HREM contrast simulations that these interface types can be described by Σ = 3 n boundaries. ... The influence of lattice relaxations is taken into consideration by molecular dynamics simulations of the structure models. ... structures in nanocrystalline germanium by means of high-resolution electron microscopy and molecular dynamics simulations ...
https://www.degruyter.com/document/doi/10.1524/zkri.1996.211.3.147/html
Molecular dynamics simulations of hard sphere solidification at consta by T Gruhn and PA Monson"Molecular dynamics simulations of hard sphere solidification at consta" by T Gruhn and PA Monson
Gruhn, T and Monson, PA, "Molecular dynamics simulations of hard sphere solidification at constant pressure" (2001). PHYSICAL ...
https://scholarworks.umass.edu/che_faculty_pubs/527/
1401.1244v1] Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer for polymer lubrication
Title:Synchronized molecular dynamics simulation via macroscopic heat and momentum transfer for polymer lubrication. Authors: ... In this method, the molecular dynamics simulations which are assigned to small fluid elements to calculate the local stresses ... Abstract: The synchronized molecular dynamics simulation is proposed to calculate the distribution of local stresses and ... The present simulation demonstrates that strong shear thinning and transitional behavior of the conformation of the polymer ...
https://jp.arxiv.org/abs/1401.1244v1
International Tables for Crystallography) Molecular-dynamics simulation of protein crystals: convergence of molecular...International Tables for Crystallography) Molecular-dynamics simulation of protein crystals: convergence of molecular...
Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin ... Molecular-dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin. Contents. *20.1. Molecular ... dynamics simulation of protein crystals: convergence of molecular properties of ubiquitin (pp. 633-641) , html , pdf , chapter ... Occurrence of intramolecular hydrogen bonds (%) during the final 1.6 ns of the simulation (pp. 636-637) , html , pdf , ...
https://it.iucr.org/Fb/ch20o1v0001/contents/
Formation and initial evolution of nanoparticles at ultrashort laser ablation of gold: molecular dynamics simulation | (2008) |...Formation and initial evolution of nanoparticles at ultrashort laser ablation of gold: molecular dynamics simulation | (2008) |...
Formation and initial evolution of nanoparticles at ultrashort laser ablation of gold: molecular dynamics simulation Author(s ... analyses of the nanoparticle formation mechanisms and their initial evolution are performed on the basis of molecular dynamics ... MD) simulation. The study is carried out for Au target irradiated by laser pulses of 100 fs duration at laser wavelengths of ...
https://spie.org/Publications/Proceedings/Paper/10.1117/12.822446
Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.
Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for ... as found in dihedral-boost aMD simulation of alanine dipeptide. In dual-boost aMD simulations of the studied systems, ... Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for ... as found in dihedral-boost aMD simulation of alanine dipeptide. In dual-boost aMD simulations of the studied systems, ...
https://escholarship.org/uc/item/12s9n8h0
BJOC - 6-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulationsBJOC - 6'-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations
6-Fluoro[4.3.0]bicyclo nucleic acid: synthesis, biophysical properties and molecular dynamics simulations. Sibylle Frei, ... Molecular and macromolecular electrochemistry: synthesis, mechanism, and redox properties Shinsuke Inagi and Mahito Atobe. ...
https://www.beilstein-journals.org/bjoc/articles/14/288/downloads
UB Weimar OPUS 4.6.3 | Thermal conductivity of graphene nanoribbons under shear deformation: A molecular dynamics simulationUB Weimar OPUS 4.6.3 | Thermal conductivity of graphene nanoribbons under shear deformation: A molecular dynamics simulation
In this work, we employ reverse nonequilibrium molecular dynamics (RNEMD) to the systematical study of the thermal conductivity ... Thermal conductivity of graphene nanoribbons under shear deformation: A molecular dynamics simulation. ... In this work, we employ reverse nonequilibrium molecular dynamics (RNEMD) to the systematical study of the thermal conductivity ... In this work, we employ reverse nonequilibrium molecular dynamics (RNEMD) to the systematical study of the thermal conductivity ...
https://e-pub.uni-weimar.de/opus4/frontdoor/index/index/searchtype/authorsearch/author/%22Wang%2C+Cui-Xia%22/rows/100/subjectfq/Graphen/docId/3171/start/0
Molecular dynamics simulation investigation on the plastic flow behaviour of silicon during nanometric cutting - Projects ...Molecular dynamics simulation investigation on the plastic flow behaviour of silicon during nanometric cutting - Projects ...
Molecular dynamics simulation investigation on the plastic flow behaviour of silicon during nanometric cutting. *Saeed Zare ...
https://pureportal.strath.ac.uk/en/datasets/molecular-dynamics-simulation-investigation-on-the-plastic-flow-b/projects/?ordering=startDate&descending=false
Molecular dynamics simulations of MXenes: Ab initio, reactive, and non-reactive empirical force fields<...
Lotfi, R., Yilmaz, D. E., Vlcek, L., & van Duin, A. (2019). Molecular dynamics simulations of MXenes: Ab initio, reactive, and ... Molecular dynamics simulations of MXenes: Ab initio, reactive, and non-reactive empirical force fields. In 2D Metal Carbides ... Molecular dynamics simulations of MXenes : Ab initio, reactive, and non-reactive empirical force fields. 2D Metal Carbides and ... Lotfi, R, Yilmaz, DE, Vlcek, L & van Duin, A 2019, Molecular dynamics simulations of MXenes: Ab initio, reactive, and non- ...
https://pennstate.pure.elsevier.com/en/publications/molecular-dynamics-simulations-of-mxenes-ab-initio-reactive-and-n
A Wavefunction-Based Criterion for the Detection of Intermolecular Interactions in Molecular Dynamics Simulations - Research...A Wavefunction-Based Criterion for the Detection of Intermolecular Interactions in Molecular Dynamics Simulations - Research...
A Wavefunction-Based Criterion for the Detection of Intermolecular Interactions in Molecular Dynamics Simulations. * Mendeley ...
https://www.research-collection.ethz.ch/handle/20.500.11850/102306?locale-attribute=de
BIFI talk: Breaking the timescale limit in molecular dynamics simulations with a fast sampling implicit solvent model (Agustí...BIFI talk: Breaking the timescale limit in molecular dynamics simulations with a fast sampling implicit solvent model (Agustí...
Home / Event / BIFI talk: Breaking the timescale limit in molecular dynamics simulations with a fast sampling implicit solvent ... BIFI talk: Breaking the timescale limit in molecular dynamics simulations with a fast sampling implicit solvent model (Agustí ... BIFI talk: Breaking the timescale limit in molecular dynamics simulations with a fast sampling implicit solvent model (Agustí ... Título: Breaking the timescale limit in molecular dynamics simulations with a fast sampling implicit solvent model ...
https://bifi.es/schedule/bifi-talk-breaking-the-timescale-limit-in-molecular-dynamics-simulations-with-a-fast-sampling-implicit-solvent-model-agusti-emperador/
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and...Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and...
Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and ... We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including ... Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and ... All MD simulations were carried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field. ...
http://sro.sussex.ac.uk/id/eprint/24925/
DOPC versus DOPE as a helper lipid for gene-therapies: molecular dynamics simulations with DLin-MC3-DMADOPC versus DOPE as a helper lipid for gene-therapies: molecular dynamics simulations with DLin-MC3-DMA
In this work an atomistic model for the neutral form of DLin-MC3-DMA was derived and all-atom molecular dynamics (MD) ... simulations were carried out in order to investigate the effect of the phospholipid headgroup on the possible properties of the ... DOPC versus DOPE as a helper lipid for gene-therapies: molecular dynamics simulations with DLin-MC3-DMA Artikel i vetenskaplig ... In this work an atomistic model for the neutral form of DLin-MC3-DMA was derived and all-atom molecular dynamics (MD) ...
https://research.chalmers.se/publication/93666c9b-f72b-459a-b0d3-26bf1fa6aa4d
Molecular dynamics simulations of Man-α-(1-6)Man-α and Man-α-(1-3) Man-αMolecular dynamics simulations of Man-α-(1-6)Man-α and Man-α-(1-3) Man-α
Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cis-1...
Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cis-1- ... Atomistic molecular dynamics simulation of the temperature and pressure dependences of local and terminal relaxations in cis-1- ...
https://www.iceht.forth.gr/en/publications/atomistic-molecular-dynamics-simulation-of-the-temperature-and-pressure-dependences-of-local-and-terminal-relaxations-in-cis-1-4-polybutadiene/
In Situ SAXS Measurement and Molecular Dynamics Simulation of Magnetic Alignment of Hexagonal LLC Nanostructures[v1] | PreprintsIn Situ SAXS Measurement and Molecular Dynamics Simulation of Magnetic Alignment of Hexagonal LLC Nanostructures[v1] | Preprints
Molecular dynamics simulations reveal the relationship between the imposed force of the magenetic nanoparticles under magnetic ... In situ small angle X-ray scattering (SAXS) and molecular dynamics were employed for the first time to understand the hexagonal ... The combinational study with experimental measurement and computational simulation will enable the development and control of ... In Situ SAXS Measurement and Molecular Dynamics Simulation of Magnetic Alignment of Hexagonal LLC Nanostructures. Weiwei Cong ...
https://www.preprints.org/manuscript/201810.0110/v1
The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations. - ORA - Oxford...The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations. - ORA - Oxford...
Here, we apply coarse-grained (CG) molecular dynamics (MD) simulations to probe the interaction of porcine pancreati... ... The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.. ... "The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations." Biophysical ... "The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations." Biophysical ...
https://ora.ox.ac.uk/objects/uuid:b91463f0-1f6b-4152-bd46-ed7dae98bb45
A molecular dynamics simulation of fracture in nanocrystalline copperA molecular dynamics simulation of fracture in nanocrystalline copper
... Journal Article Download full-text (Open Access). ... A large-scale molecular dynamics simulation was used to investigate the propagation of cracks in three dimensional samples of ... A large-scale molecular dynamics simulation was used to investigate the propagation of cracks in three dimensional samples of ... Pei, L., Lu, C., Tieu, K., Zhu, H., Zhao, X., Cheng, K. & Zhang, L. (2013). A molecular dynamics simulation of fracture in ...
https://scholars.uow.edu.au/display/publication81546
Stability of gold clusters: molecular-dynamics simulationsStability of gold clusters: molecular-dynamics simulations
Molecular-dynamics simulations of gold clusters. Bastug, T; Hirata, M; Varga, S; Fricke, B; Erkoç, Şakir; Mukoyama, T (2001-01- ... Molecular-dynamics simulations have also been performed for spherical gold clusters generated from FCC crystal structure with ... Stable structures of the microclusters for (n=3-13) have been determined by a molecular-dynamics simulation. It has been found ... Stable structures of the microclusters for n = 3-13 have been determined by molecular-dynamics simulation. It has been found ...
https://open.metu.edu.tr/handle/11511/57869
Initio molecular dynamics simulationStructuralCoarse-grainedImplicit solventAtomisticTrajectoryChemistryCalculationsBiomolecularNuclear MagneticStructuresDensity functiProc2016CouplingsPeptideThermal conductivityBehaviorClassical molecular dynamicsVisualizationOligomersTimescaleModelingMechanismsStudySpectroscopicInsightsCharacterizationShearChemicalPoreModellingEmpiricalComputationAtomicInvestigate the effectLipidProtein structureIncreased solventAtomsComputationalNucleiReplicaGraphenePhospholipidElectron transferMechanismClustersCorrelationsExperimentalSiliconMoleculeCrystalsMoleculesExperimentsLatticeSystemsPharmacology
Initio molecular dynamics simulation1
  • The ab initio molecular dynamics simulation calculations for the related reactions of Al2O3、Al4CO4、Al2CO and Al4C3with AlCl3at temperature of1760K, pressure of60Pa showed that under the experimental conditions(1760K,60Pa), when Al4CO4in the presence of carbon, Al4C3in the presence of oxygen tend to react easier with AlCl3to produce AlCl than there is no oxygen(or carbon). (dissertationtopic.net)
Structural8
  • We report data on the structural dynamics of the neuropeptide Y (NPY) G-protein-coupled receptor (GPCR) type 1 (Y1R), a typical representative of class A peptide ligand GPCRs, using a combination of solid-state NMR and molecular dynamics (MD) simulation. (nih.gov)
  • structural dynamics. (nih.gov)
  • Structural stability and energetics of gold clusters, Au, (n = 3-555), have been investigated by molecular-dynamics simulations. (metu.edu.tr)
  • Structural stability and energetics of nickel clusters, Nih (N = 3 - 459), have been inves tigated by molecular-dynamics simulations, A size-dependent empirical model potential energy function has been used in the simulations. (metu.edu.tr)
  • The structural stability of carbon nanotori have been investigated by performing molecular--dynamics simulations. (metu.edu.tr)
  • Structural stability of empty and endohedrally doped carbon nanocapsules have been investigated by performing molecular-dynamics computer simulations. (metu.edu.tr)
  • An autoencoder is used to map snapshots from MD simulations onto a user-defined conformational landscape defined by principal components analysis or specific structural features, and we show that we can predict, with useful accuracy, conformations that are not present in the training data. (bvsalud.org)
  • The high-throughput capability will allow use of characterization approaches from simulation studies to link solution correlations with influences on lithium ion-transport behavior in electrolytes and enable the ability to seek multiscale structural attributes that allow facile and selective incorporation of the charge carrier while prohibiting the dissolution of cathodic transition-metal components. (anl.gov)
Coarse-grained3
  • The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations. (ox.ac.uk)
  • Here, we apply coarse-grained (CG) molecular dynamics (MD) simulations to probe the interaction of porcine pancreati. (ox.ac.uk)
  • Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent. (ibpc.fr)
Implicit solvent1
  • A structurally diverse ensemble of conformations of the monomer was sampled in microsecond timescale implicit solvent replica exchange molecular dynamics simulations. (canada.ca)
Atomistic3
  • Molecular dynamics (MD) simulations constitute the cornerstone of contemporary atomistic modeling in chemistry, biology, and materials science. (tu-berlin.de)
  • In this work an atomistic model for the neutral form of DLin-MC3-DMA was derived and all-atom molecular dynamics (MD) simulations were carried out in order to investigate the effect of the phospholipid headgroup on the possible properties of the shell-membranes of LNPs. (chalmers.se)
  • Atomistic molecular dynamics simulations have been performed on two types of PfHGXPRT dimers (D1 and D3) and its tetramer in their apo and ligand-bound states. (utmb.edu)
Trajectory2
  • Trajectory analysis and molecular dynamics simulations of the Gly407Ser variant. (cdc.gov)
  • VMD can be used to animate and analyze the trajectory of a molecular dynamics (MD) simulation. (seikei.ac.jp)
Chemistry4
  • Theoretical chemistry studies ( quantum chemistry, classical and ab initio molecular dynamics simulations ) at LCCEF focus on lanthanides and actinides compounds. (cea.fr)
  • Using classical molecular dynamics simulations, Petr Král, assistant professor of chemistry at UIC, and his laboratory coworkers were able to study realistic conditions in this microscopic environment to learn how the tiny propellers pump liquids. (phys.org)
  • Král's group found that at the molecular level -- unlike at the macro level -- the chemistry of the propeller's blades and their sensitivity to water play a big role in determining whether the propeller pumps efficiently or just spins with little effect. (phys.org)
  • This virtual screening tool helps R&D scientists to predict solubility parameter of liquids by smartly extracting inter-molecular forces from Molecular Dynamics simulations for any given chemistry. (siemens.com)
Calculations5
  • In this thesis, we develop a combined machine learning (ML) and quantum mechanics approach that enables the direct reconstruction of flexible molecular force fields from high-level ab initio calculations. (tu-berlin.de)
  • We present path integral molecular dynamics (PIMD) calculations of an electron transfer from a heliophobic Cs2 dimer in its (3Σu) state, located on the surface of a He droplet, to a heliophilic, fully immersed C60 molecule. (elsevier.com)
  • To go beyond the static approach, classical and quantum PIMD simulations are performed at 2 K, slightly below the critical temperature for helium superfluidity (2.172 K). Calculations are executed in the NVT ensemble as well as the NVE ensemble to provide insights into real-time dynamics. (elsevier.com)
  • Molecular dynamics methodologies such as Hamiltonian Annealing and sampling enhanced free energy calculations are ideal both for the research problems described here and the computer resources available for the allocation. (anl.gov)
  • Projects such as a) density functional theory calculations b) molecular dynamics simulations c) data science d) AI/ML e) modeling etc. (uchicago.edu)
Biomolecular3
  • Accelerated molecular dynamics (aMD) simulations greatly improve the efficiency of conventional molecular dynamics (cMD) for sampling biomolecular conformations, but they require proper reweighting for free energy calculation. (escholarship.org)
  • Journal of Biomolecular Structure and Dynamics , 34 (7), 1590-1605. (utmb.edu)
  • Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments ( Musharrafieh Rami, Lagarias Panagiotis, Ma Chunlong, Hau Raymond, Romano Alex, Lambrinidis George, Kolocouris Antonios. (grnet.gr)
Nuclear Magnetic1
  • Since S -palmitoylation and cholesterol homeostasis are crucial for viral infections, we investigated IFITM interactions with cholesterol by molecular dynamic stimulations, nuclear magnetic resonance analysis in vitro and photoaffinity crosslinking in mammalian cells. (bvsalud.org)
Structures5
  • Characterization of interface structures in nanocrystalline germanium by means of high-resolution electron microscopy and molecular dynamics simulations" Zeitschrift für Kristallographie - Crystalline Materials , vol. 211, no. 3, 1996, pp. 147-152. (degruyter.com)
  • Stable structures of the microclusters for n = 3-13 have been determined by molecular-dynamics simulation. (metu.edu.tr)
  • Stable structures of the microclusters with sizes N = 3 - 55 and clusters generated from fee crystal structure with sizes N = 79 - 459 have been determined by molecular-dynamics simulations. (metu.edu.tr)
  • This method offers a new approach to the prediction of new low energy/physically realistic structures of conformationally dynamic proteins and allows an alternative approach to enhanced sampling of MD simulations. (bvsalud.org)
  • Simcenter Culgi 15 offers computational chemists and lab scientists a fast and easy molecular vibrational analysis for even the most complex molecular structures. (siemens.com)
Density functi1
  • In the case of first-principles molecular dynamics based on density functional theory, the calculation precision is high, but the calculation amount is large. (graphcore.ai)
Proc1
  • Multicanonical Simulations Based On Contact Maps for Square-Well Heteropolymers Using Event Driven Molecular Dynamics: Proc. (elsevier.com)
20162
  • In inner 2016 Louis played to replace varieties that some total download The Art of Molecular Dynamics was on the sense, data grouped and transformed with Marine fields and windows, and which have Australian researchers. (peinze.de)
  • 2016. Realistic molecular model of kerogen's nanostructure . (mit.edu)
Couplings1
  • First, the equilibrium dynamics of Y1R were studied using 15 N-NMR and quantitative determination of 1 H- 13 C order parameters through the measurement of dipolar couplings in separated-local-field NMR experiments. (nih.gov)
Peptide2
  • The unphosphorylated peptide maintains a helical conformation from 3 to 15 throughout a 26-ns simulation, in agreement with spectroscopic data. (umn.edu)
  • Comparison with simulations of a fourth peptide truncated at Pro21 showed the importance of the region from 17 to 21 in preventing local unfolding of the helix. (umn.edu)
Thermal conductivity2
  • In this work, we employ reverse nonequilibrium molecular dynamics (RNEMD) to the systematical study of the thermal conductivity of GNRs (with model size of Tensile strain and compress strain can greatly affect the thermal conductivity of graphene nanoribbons (GNRs). (uni-weimar.de)
  • In this work, we employ reverse nonequilibrium molecular dynamics (RNEMD) to the systematical study of the thermal conductivity of GNRs (with model size of 4 nm × 15 nm) under the shear strain. (uni-weimar.de)
Behavior5
  • We present MD simulations, for flexible molecules with up to a few dozen atoms and provide insights into the dynamical behavior of these molecules. (tu-berlin.de)
  • The present simulation demonstrates that strong shear thinning and transitional behavior of the conformation of the polymer chains occurs with a rapid temperature rise when the Nahme-Griffith number exceeds unity. (arxiv.org)
  • In this work, Molecular Dynamics (MD) simulations have been conducted to evaluate the influence of the topology on ionene⋅⋅⋅ionene and ionene⋅⋅water interactions, as well as their effect on the selfhealing behavior. (ull.es)
  • Molecular Dynamics Simulation of Shape-memory Behavior. (bvsalud.org)
  • Understanding the mixing behavior as a function of shear, including aggregation effects, reaction dynamics and crystallization effects is crucial in the development of formulations, polymer blends and emulsions. (siemens.com)
Classical molecular dynamics1
  • Vapor condensation on silicon nanotubes has been simulated by classical molecular dynamics to understand how the nucleation and condensation process for pores is affected. (nebraska.edu)
Visualization2
  • Bernardi ran his experiment solely on Blue Waters' GPU nodes, using CUDA -accelerated molecular dynamics and visualization software. (nvidia.com)
  • VMD (Visual Molecular Dynamics) is designed for the visualization and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies, etc. (seikei.ac.jp)
Oligomers2
  • We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. (sussex.ac.uk)
  • Experimental characterization of the molecular structure of small amyloid (A)β oligomers that are currently considered as toxic agents in Alzheimer's disease is a formidably difficult task due to their transient nature and tendency to aggregate. (canada.ca)
Timescale1
  • Macroscopic characteristics such as the kinetic temperature, pressure and momentum profiles are monitored during the simulation in order to examine the heat propagation behaviour under a timescale comparable with the relaxation time. (neicon.ru)
Modeling3
  • However, one of the widely recognized and increasingly pressing issues in MD simulations is the lack of accuracy of underlying classical interatomic potentials, which hinders truly predictive modeling of dynamics and function of (bio)molecular systems. (tu-berlin.de)
  • Modeling of MCM-41 type porous silica was performed using the molecular dynamics (MD) simulation. (elsevier.com)
  • Ookawa, M, Kawamura, K & Yamaguchi, T 2004, ' Pore wall structure modeling of MCM-41 type silica using molecular dynamics simulation ', Studies in Surface Science and Catalysis , vol. 154 B, pp. 1478-1484. (elsevier.com)
Mechanisms1
  • The analyses of the nanoparticle formation mechanisms and their initial evolution are performed on the basis of molecular dynamics (MD) simulation. (spie.org)
Study7
  • The combinational study with experimental measurement and computational simulation will enable the development and control of nanostructures in novel materials for various applications. (preprints.org)
  • With increase in computational power we have turned to Density Function Theory (DFT), semi-empirical Molecular Dynamics (MD) and other types of simulations to study the effect which can be verified with experimental techniques up to a certain extent. (chalmers.se)
  • High pressure deformation mechanism of Li-ABW: sinchrotron XRPD study and ab initio molecular dynamics simulations. (unimore.it)
  • The technique of molecular simulation allows for the study of ionic liquid nanodroplets in atomic detail which is a limitation in mass spectrometric experiments. (nd.edu)
  • In this study, molecular simulations and protein-protein docking are employed to explore a possible connection between the structure of Aβ monomers and the properties of the intermonomer interface in the Aβ42 dimer. (canada.ca)
  • Our preliminary study shows how supercomputers and molecular dynamics techniques enable cost-effective analysis of important societal/environmental issues that impact the daily lives of ordinary people. (access-ci.org)
  • The goal of this study was to identify the epidemiological and molecular characteristics of TBEV associated with fatal meningoencephalitis in Mongolia. (who.int)
Spectroscopic1
  • Our approach provides the key missing ingredient for achieving spectroscopic accuracy in molecular simulations. (tu-berlin.de)
Insights2
  • Detailed insights into rheological processes, easy characterization of molecular vibrational infrared modes, high fidelity predictions of miscibility and permeability and accurate transport property predictions feeding CFD simulations. (siemens.com)
  • 2015. Creep of Bulk C-S-H: Insights from Molecular Dynamics Simulations . (mit.edu)
Characterization1
  • Applications like polymer curing, reactive blends, formulations and adhesives heavily depend on a detailed upfront characterization of the molecular properties to ensure their functionality in the end product. (siemens.com)
Shear1
  • The viscous-heating-induced solidification of a Lennard-Jones fluid near wall in high-speed shear flows is discovered by the molecular-dynamics simulation. (semanticscholar.org)
Chemical7
  • The developed symmetric GDML (sGDML) approach faithfully reproduces global force fields at quantum-chemical CCSD(T) level of accuracy and allows converged MD simulations with fully quantized electrons and nuclei. (tu-berlin.de)
  • A wide range of computed properties such as stereochemistry, symmetry elements, molecular graphs and molecular mechanics energies facilitate problem solving across all chemical disciplines. (wolfram.com)
  • Overall, this research will enable enhanced, fundamental understanding of how the charge carriers transport in hierarchical structuring of electrolytes and how simulation knowledge can be transferred to chemical synthesis and industrial environments. (anl.gov)
  • This separation allows one to consider nuclear chemical dynamics independently from that of the electronic subsystem. (umich.edu)
  • In this talk, I will discuss how non-trivial topological phases associated with conical intersections of electronic surfaces affect chemical dynamics of molecular systems and what intuitive picture can be extracted from exact numerical simulations for simple models. (umich.edu)
  • With the new release of Simcenter Culgi 15, computational chemists across industries can leverage a host of new features and enhancements to model the complexity of chemical systems while going faster in their simulations. (siemens.com)
  • A major task of computational chemists in Food & Beverage, Chemical or Polymer segment is to characterize highly complex materials and correlate their molecular characteristics to the final material or product performance. (siemens.com)
Pore1
  • Molecular dynamics simulations show that the sensitivity to molecular shape derives from a highly nonuniform electric field along the pore. (nanion.de)
Modelling1
  • Modelling and Simulation in Materials Science and Engineering , 24 (1). (strath.ac.uk)
Empirical3
  • The optimizing simulations were done using MD simulations with semi-empirical Embedded atom method (EAM) potential in BCC iron with different input parameters including energy of the primary knock on atom (PKA), position of the PKA relative to damped boundary conditions, number of atoms, direction of the PKA and damping effects. (chalmers.se)
  • An empirical model potential energy function has been used in the simulations. (metu.edu.tr)
  • The effect of radiation damage on copper clusters has been investigated by performing molecular-dynamics simulation using empirical potential energy function for interaction between copper atoms. (metu.edu.tr)
Computation1
  • The proposed computation constitutes the simulation part of the current EERE VTO project, non-traditional electrolyte design from ionic liquid. (anl.gov)
Atomic3
  • Molecular dynamics uses computers to simulate the movement of molecular and atomic systems. (graphcore.ai)
  • Taking coordinate Coord as an example, the typical MD (Molecular Dynamics) input configuration contains information such as atom type in addition to atomic coordinates (see Table 1 for details). (graphcore.ai)
  • An essential ingredient of the present work is the use of coupled cluster theory for the description of the dynamics of the atomic nuclei. (au.dk)
Investigate the effect1
  • We have used molecular dynamics simulations to investigate the effect of phosphorylation and mutation on the cytoplasmic domain of phospholamban (PLB), a 52-residue protein that regulates the calcium pump in cardiac muscle. (umn.edu)
Lipid1
  • Through a combination of microscopic simulations and fluorescence microscopy we find the lipid transport rate catalyzed by the DNA nanostructure exceeds 10 7 molecules per second, which is three orders of magnitude higher than the rate of lipid transport catalyzed by biological enzymes. (nature.com)
Protein structure1
  • Molecular dynamics (MD) simulations are a popular method of studying protein structure and function, but are unable to reliably sample all relevant conformational space in reasonable computational timescales. (bvsalud.org)
Increased solvent1
  • The simulations show that initiation of unfolding is due to increased solvent accessibility of the backbone atoms near the smaller Cys. (umn.edu)
Atoms7
  • In a specific system, it can simulate a system at the scale of tens of billions of atoms, but the precision is limited and it is difficult to handle the simulation of complex systems. (graphcore.ai)
  • The simulation scale is usually limited to hundreds of atoms, within 100 picoseconds. (graphcore.ai)
  • Phase I of the ABC project involves a total of similar to0.6 mus of simulation for systems containing similar to24,000 atoms. (sussex.ac.uk)
  • It is essential to optimize because simulating large number of atoms significantly increases the time required for the simulation which also makes it more expensive to carry out the MD simulations. (chalmers.se)
  • In the long perspective our aim is to develop methods applicable to molecular systems containing 10-1000s of atoms. (au.dk)
  • However, the nature of the underlying transient molecular dynamics often makes it difficult to comprehend the flow patterns that are driven by the stochastic motion of individual molecules or atoms. (siemens.com)
  • Simcenter Culgi 15 now provides the ability to calculate time- and space-interval averaged scalar (e.g., density, X-component of velocity) and vector (e.g., velocity, force) fields of selected atoms or beads from a particle-based system simulation. (siemens.com)
Computational2
  • A major focus point of our current research is the development of fundamentally new computational methods for the quantum description of molecular dynamics. (au.dk)
  • With this new particle motion average, computational chemists can now comprehend rheology results faster, identify patterns and easily visualize molecular motion patterns in a formulation. (siemens.com)
Nuclei1
  • The Born-Oppenheimer approximation for the electron-nuclear wave-function introduces natural separation between time scales of electrons and nuclei in molecular and condensed matter systems. (umich.edu)
Replica1
  • All systems in the download The Art of Molecular Dynamics have Germany advanced replica, visual pads, which has the Process and PC at world paperback. (peinze.de)
Graphene1
  • Using molecular dynamics simulations, we probe a suspended graphene layer by a diamond-like-carbon tip at various temperatures. (arxiv.org)
Phospholipid4
  • IMSEAR at SEARO: Molecular dynamics simulation of hydrated phospholipid bilayers. (who.int)
  • Kothekar V. Molecular dynamics simulation of hydrated phospholipid bilayers. (who.int)
  • The review has its main focus on molecular dynamics (MD) simulation of phospholipid bilayers. (who.int)
  • We discuss here mainly results of MD simulations in the recent years on hydrated phospholipid bilayers and their interaction with ligands. (who.int)
Electron transfer1
  • Ab inito real-time nonadiabatic (NA) molecular dynamics (MD) simulations are performed to investigate the photoinduced electron transfer (ET) from alizarin to the hydrated Ti(Super 4+) ion. (readabstracts.com)
Mechanism3
  • In this paper, molecular dynamics (MD) simulation has been deployed with a realistic analytical bond order potential (ABOP) formalism based potential energy function to understand tool wear mechanism during single point diamond turning of SiC. (hw.ac.uk)
  • It thus becomes non trivial to develop an accurate understanding of tool wear mechanism during SPDT of SiC in order to identify measures to suppress wear to minimize operational cost.In this paper, molecular dynamics (MD) simulation has been deployed with a realistic analytical bond order potential (ABOP) formalism based potential energy function to understand tool wear mechanism during single point diamond turning of SiC. (hw.ac.uk)
  • Molecular dynamics simulations were performed for highlighting the mechanism of cross resistance displayed by the Gly407Ser mutation. (cdc.gov)
Clusters1
  • Molecular-dynamics simulations have also been performed for spherical gold clusters generated from FCC crystal structure with sizes n = 13-555. (metu.edu.tr)
Correlations1
  • Using the Ultra-relativistic Quantum Molecular Dynamics (UrQMD) model, we investigate the azimuthal correlations in p-Pb collisions at √ s NN = 5.02 TeV. (epj-conferences.org)
Experimental2
  • These experimental findings were detailed and supported by all-atom molecular dynamics simulations. (cdc.gov)
  • Recognition motifs for Importin 4 [(L)PPRS(G/P)P] and Importin 5 [KP(K/Y)LV] binding, identified by bio-informatic simulation and experimental in vitro validation ( Athanasios A. Panagiotopoulos , Konstantina Kalyvianaki , Paraskevi K. Tsodoulou , Maria N. Darivianaki , Dimitris Dellis , George Notas , Vangelis Daskalakis , Panayiotis A. Theodoropoulos , Christos Α. (grnet.gr)
Silicon1
  • Molecular dynamics (MD) simulation was carried out to acquire an in-depth understanding of the flow behaviour of single crystal silicon during nanometric cutting on three principal crystallographic planes and at different cutting temperatures. (strath.ac.uk)
Molecule2
  • When performing water molecule simulation on the IPU, we use a model in SavedModel format. (graphcore.ai)
  • In particular, VMD can act as a graphical front end for an external MD program by displaying and animating a molecule undergoing simulation on a remote computer. (seikei.ac.jp)
Crystals1
  • Molecular Crystals and Liquid Crystals Science and Technology, Section A: Molecular Crystals and Liquid Crystals. (elsevier.com)
Molecules3
  • The method leverages guidance from classifiers trained on an informative latent space of molecules modelled using a deep generative autoencoder, and screens the generated molecules using deep-learning classifiers as well as physicochemical features derived from high-throughput molecular dynamics simulations. (nature.com)
  • A significant event in the catalytic cycle is the dynamics of a gate that provides access for the ligand molecules to the reaction center. (utmb.edu)
  • With an initial focus on describing the electronic structure of molecules, I have over time sought a more complete picture emphasizing also environmental effects and (quantum) molecular dynamics. (au.dk)
Experiments2
  • Pna21) was explored by synchrotron X-ray powder diffraction experiments, using silicone oil as non-penetrating pressure transmitting medium, and Car Parrinello Molecular Dynamics simulations. (unimore.it)
  • Using GPU-accelerated supercomputer simulations and lab experiments, researchers discovered why staph bacteria - the leading cause of healthcare-related infections - can be so tough to beat. (nvidia.com)
Lattice1
  • The influence of lattice relaxations is taken into consideration by molecular dynamics simulations of the structure models. (degruyter.com)
Systems3
  • In dual-boost aMD simulations of the studied systems, exponential average generally leads to high energetic fluctuations, largely due to the fact that the Boltzmann reweighting factors are dominated by a very few high boost potential frames. (escholarship.org)
  • Simulations were carried out in explicit water systems at 300 K for three peptides spanning the first 25 residues of PLB: wildtype (PLB 1-25 ), PLB- 1-25 phosphorylated at Ser16 and PLB 1-25 with the R9C mutation, which is known to cause human heart disease. (umn.edu)
  • They use for download The Art of Molecular and language in the beginning and war of past module products and systems. (peinze.de)
Pharmacology1
Structural basis for microtubule recognition by the human kinetochore Ska complex | Nature Communications
Structural basis for microtubule recognition by the human kinetochore Ska complex | Nature Communications (nature.com)
Biomolecules | Free Full-Text | Multi-Target In Silico Prediction of Inhibitors for Mitogen-Activated Protein Kinase...
Biomolecules | Free Full-Text | Multi-Target In Silico Prediction of Inhibitors for Mitogen-Activated Protein Kinase... (mdpi.com)
Frontiers | Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network...
Frontiers | Comparative Exploratory Analysis of Intrinsically Disordered Protein Dynamics Using Machine Learning and Network... (frontiersin.org)
Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins | Scientific Reports
Molecular mechanisms of heterogeneous oligomerization of huntingtin proteins | Scientific Reports (nature.com)
T-Cell Receptor Variable β Domains Rigidify During Affinity Maturation | Scientific Reports
T-Cell Receptor Variable β Domains Rigidify During Affinity Maturation | Scientific Reports (nature.com)
Polymer Science and Technology - Nova Science Publishers
Polymer Science and Technology - Nova Science Publishers (novapublishers.com)
Utilising NV based quantum sensing for velocimetry at the nanoscale | Scientific Reports
Utilising NV based quantum sensing for velocimetry at the nanoscale | Scientific Reports (nature.com)
Beam Me Up: 'Teleportation' Is Year's Biggest Breakthrough | Fox News
Beam Me Up: 'Teleportation' Is Year's Biggest Breakthrough | Fox News (foxnews.com)
Targeted protein degradation as a powerful research tool in basic biology and drug target discovery | Nature Structural &...
Targeted protein degradation as a powerful research tool in basic biology and drug target discovery | Nature Structural &... (nature.com)
Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia |...
Psychomotor impairments and therapeutic implications revealed by a mutation associated with infantile Parkinsonism-Dystonia |... (elifesciences.org)
PDF] A Simplified Approach to Simulating Raman Spectra from Ab Initio Molecular Dynamics. | Semantic Scholar
PDF] A Simplified Approach to Simulating Raman Spectra from Ab Initio Molecular Dynamics. | Semantic Scholar (semanticscholar.org)
Browsing Engineering (Faculty of) by Supervisor Tan, Zhongchao
Browsing Engineering (Faculty of) by Supervisor "Tan, Zhongchao" (uwspace.uwaterloo.ca)
Reverse Transcriptase News, Research
Reverse Transcriptase News, Research (news-medical.net)
Structure and dynamics of the M3 muscarinic acetylcholine receptor | Nature
Structure and dynamics of the M3 muscarinic acetylcholine receptor | Nature (nature.com)
Carbon nanotube - Wikipedia
Carbon nanotube - Wikipedia (en.wikipedia.org)
Dr Paul Mulheran | University of Strathclyde
Dr Paul Mulheran | University of Strathclyde (strath.ac.uk)
Workshop on the Mathematics of Drug Design/Discovery | Fields Institute for Research in Mathematical Sciences
Workshop on the Mathematics of Drug Design/Discovery | Fields Institute for Research in Mathematical Sciences (fields.utoronto.ca)
Examining Ligand and Protein Interactions - Biid.org
Examining Ligand and Protein Interactions - Biid.org (biid.org)
EuroHPC Summit Week 2019 (13-May 17, 2019): Molecular dynamics simulation of complex systems · PRACE Agenda Systems (Indico)
EuroHPC Summit Week 2019 (13-May 17, 2019): Molecular dynamics simulation of complex systems · PRACE Agenda Systems (Indico) (events.prace-ri.eu)
Interfaces | iMechanica
Interfaces | iMechanica (imechanica.org)
PDF) Effective mechanical properties of multilayer nano-heterostructures
PDF) Effective mechanical properties of multilayer nano-heterostructures (researchgate.net)
Thermal conductance of metal-diamond interfaces at high pressure | Nature Communications
Thermal conductance of metal-diamond interfaces at high pressure | Nature Communications (nature.com)
Leveraging the IPU for Molecular Dynamics Simulation
Leveraging the IPU for Molecular Dynamics Simulation (graphcore.ai)
Nested order-disorder framework containing a crystalline matrix with self-filled amorphous-like innards | Nature Communications
Nested order-disorder framework containing a crystalline matrix with self-filled amorphous-like innards | Nature Communications (nature.com)
Computational Biophysics | NHLBI, NIH
Computational Biophysics | NHLBI, NIH (nhlbi.nih.gov)
Molecules | Special Issue : Experimental and Computational Photochemistry of Bioorganic Molecules
Molecules | Special Issue : Experimental and Computational Photochemistry of Bioorganic Molecules (mdpi.com)
Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers: Biophysical Journal
Molecular Mechanism of Lipid Nanodisk Formation by Styrene-Maleic Acid Copolymers: Biophysical Journal (cell.com)
Difference between revisions of Nikola Tchipev, M.Sc. - Sccswiki
Difference between revisions of "Nikola Tchipev, M.Sc." - Sccswiki (www5.in.tum.de)
Physics Department, TUM | Module PH0020 of SS 2022
Physics Department, TUM | Module PH0020 of SS 2022 (ph.tum.de)