A computer simulation developed to study the motion of molecules over a period of time.
Computer-based representation of physical systems and phenomena such as chemical processes.
Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures.
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)
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.
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)
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).
The characteristic three-dimensional shape of a molecule.
Theoretical representations that simulate the behavior or activity of chemical processes or phenomena; includes the use of mathematical equations, computers, and other electronic equipment.
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.
The accumulation of an electric charge on a object
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.
Layers of lipid molecules which are two molecules thick. Bilayer systems are frequently studied as models of biological membranes.
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)
The study of PHYSICAL PHENOMENA and PHYSICAL PROCESSES as applied to living things.
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.
The parts of a macromolecule that directly participate in its specific combination with another molecule.
The study of crystal structure using X-RAY DIFFRACTION techniques. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
The thermodynamic interaction between a substance and WATER.
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.
Processes involved in the formation of TERTIARY PROTEIN STRUCTURE.
The physical characteristics and processes of biological systems.
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)
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.
A synthetic phospholipid used in liposomes and lipid bilayers for the study of biological membranes.
Synthetic phospholipid used in liposomes and lipid bilayers to study biological membranes. It is also a major constituent of PULMONARY SURFACTANTS.
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.
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.
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)
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.
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).
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.
The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape.
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)
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.
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.
The region of an enzyme that interacts with its substrate to cause the enzymatic reaction.
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.
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.
The ability of a protein to retain its structural conformation or its activity when subjected to physical or chemical manipulations.
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.
Conformational transitions of the shape of a protein to various unfolded states.
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.
The assembly of the QUATERNARY PROTEIN STRUCTURE of multimeric proteins (MULTIPROTEIN COMPLEXES) from their composite PROTEIN SUBUNITS.
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)
A procedure consisting of a sequence of algebraic formulas and/or logical steps to calculate or determine a given task.
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.
The rate dynamics in chemical or physical systems.
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.
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.
Sequential operating programs and data which instruct the functioning of a digital computer.
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.
The characteristic 3-dimensional shape and arrangement of multimeric proteins (aggregates of more than one polypeptide chain).
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)
Pairing of purine and pyrimidine bases by HYDROGEN BONDING in double-stranded DNA or RNA.
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.
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.
A change of a substance from one form or state to another.
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.
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.
Disruption of the non-covalent bonds and/or disulfide bonds responsible for maintaining the three-dimensional shape and activity of the native protein.
Characteristics or attributes of the outer boundaries of objects, including molecules.
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.
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).
Elements of limited time intervals, contributing to particular results or situations.
A conjugated protein which is the oxygen-transporting pigment of muscle. It is made up of one globin polypeptide chain and one heme group.
The process by which two molecules of the same chemical composition form a condensation product or polymer.
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)
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.
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)
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.
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.
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.
The quality or state of being able to be bent or creased repeatedly. (From Webster, 3d ed)
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.
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.
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.
Small holes of nanometer dimensions in a membrane, that can be used as single molecule detectors. The pores can be biological or synthetic.
The facilitation of a chemical reaction by material (catalyst) that is not consumed by the reaction.
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.
Proteins produced from GENES that have acquired MUTATIONS.
Mathematical procedure that transforms a number of possibly correlated variables into a smaller number of uncorrelated variables called principal components.
Eight-carbon saturated hydrocarbon group of the methane series. Include isomers and derivatives.
Proteins found in any species of bacterium.
Resistance and recovery from distortion of shape.
A delayed rectifier subtype of shaker potassium channels that is selectively inhibited by a variety of SCORPION VENOMS.
The facilitation of biochemical reactions with the aid of naturally occurring catalysts such as ENZYMES.
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)
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.
A characteristic feature of enzyme activity in relation to the kind of substrate on which the enzyme or catalytic molecule reacts.
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.
The lipid- and protein-containing, selectively permeable membrane that surrounds the cytoplasm in prokaryotic and eukaryotic cells.
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.
Six-carbon saturated hydrocarbon group of the methane series. Include isomers and derivatives. Various polyneuropathies are caused by hexane poisoning.
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.
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.
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.
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)
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.
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)
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.
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.
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.
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)
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)
Genetically engineered MUTAGENESIS at a specific site in the DNA molecule that introduces a base substitution, or an insertion or deletion.
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.
The formation of crystalline substances from solutions or melts. (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)
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.
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.
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.
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.
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.
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.
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.
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.
The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).
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)
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.
The motion of fluids, especially noncompressible liquids, under the influence of internal and external forces.
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 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.
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)
Proteins obtained from ESCHERICHIA COLI.
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.
The characteristic 3-dimensional shape of a carbohydrate.
The degree of similarity between sequences of amino acids. This information is useful for the analyzing genetic relatedness of proteins and species.
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.
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.
Partial proteins formed by partial hydrolysis of complete proteins or generated through PROTEIN ENGINEERING techniques.
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)
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.
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.
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.
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.
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.
Macromolecular complexes formed from the association of defined protein subunits.
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)
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)
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.
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.
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.
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.
The color-furnishing portion of hemoglobin. It is found free in tissues and as the prosthetic group in many hemeproteins.
Processes that incorporate some element of randomness, used particularly to refer to a time series of random variables.
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.
The study of CHEMICAL PHENOMENA and processes in terms of the underlying PHYSICAL PHENOMENA and processes.
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)
The study of chemical changes resulting from electrical action and electrical activity resulting from chemical changes.
Peptides composed of between two and twelve amino acids.
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.
Property of membranes and other structures to permit passage of light, heat, gases, liquids, metabolites, and mineral ions.
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)
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.
The development and use of techniques to study physical phenomena and construct structures in the nanoscale size range or smaller.
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.
An essential amino acid that is required for the production of HISTAMINE.
A member of the alkali group of metals. It has the atomic symbol Na, atomic number 11, and atomic weight 23.
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.
Positively charged atoms, radicals or groups of atoms which travel to the cathode or negative pole during electrolysis.
The properties, processes, and behavior of biological systems under the action of mechanical forces.
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.
The forces and principles of action of matter and energy.
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)
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.
The sequence of PURINES and PYRIMIDINES in nucleic acids and polynucleotides. It is also called nucleotide sequence.
Conformational transitions of a protein from unfolded states to a more folded state.
Databases containing information about PROTEINS such as AMINO ACID SEQUENCE; PROTEIN CONFORMATION; and other properties.
A class of enzymes that catalyze the hydrolysis of one of the three ester bonds in a phosphotriester-containing compound.
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.
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.
An essential amino acid. It is often added to animal feed.
Materials in intermediate state between solid and liquid.
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)
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.
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.
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.
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.
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)
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.
Measurement of the intensity and quality of fluorescence.
An actinomycete used for production of commercial ANTIBIOTICS and as a host for gene cloning.
A class of porins that allow the passage of WATER and other small molecules across CELL MEMBRANES.
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)
The behaviors of materials under force.
The temperature at which a substance changes from one state or conformation of matter to another.
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)
The pattern of any process, or the interrelationship of phenomena, which affects growth or change within a population.
A purine base and a fundamental unit of ADENINE NUCLEOTIDES.
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.
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 (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)
An essential amino acid that is physiologically active in the L-form.
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.
A continuing periodic change in displacement with respect to a fixed reference. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed)
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)
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)
A species of halophilic archaea distinguished by its production of acid from sugar. This species was previously called Halobacterium marismortui.
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. The stable isotope of hydrogen. It has one neutron and one proton in the nucleus.
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.
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)

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
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
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
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. ...
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 ...
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. ...
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.
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 ...
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 ...
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 ...
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.
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.
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 ...
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 ...
Mechanical and Aerospace Engineering, ICMAE2011: Nanocomputational Observation of Interaction of Two Cytotoxins and Nanobio Membrane: Molecular Dynamics Simulation Study
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
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. ...
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 ...
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 ...
Collagen mimetic peptides (CMPs) and collagen-like proteins (CLPs) that mimic either structural or functional characteristics of natural collagens hav..
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 ...
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 ...
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
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 ...
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 ...
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 ...
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, ...
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.. ...
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 ...
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 ...
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 ...
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 ...
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
Molecular dynamics simulations of a phospholipid-detergent mixture. An improved empirical potential energy function for molecular simulations of phospholipids
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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 ...
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
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
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
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.
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.. ...
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 ...
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 ...
NMR-detected hydrogen exchange and molecular dynamics simulations provide structural insight into fibril formation of prion protein fragment 106-126.
We enabled an unprecedented scale of quantum molecular dynamics simulations through algorithmic innovations. A new lean divide-and-conquer density function
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 ...
We have performed molecular dynamics simulations for a total duration of more than 10 µs (with most molecular trajectories being 1 µs in dura
URAHATA, Sergio Minoru; RIBEIRO, Mauro Carlos Costa. Molecular dynamics simulation of molten LiNO3 with flexible and polarizable anions. Physical Chemistry Chemical Physics, London, v. 5, n. 12, p. 2619-2624, 2003. DOI: 10.1039/b303713d ...
The team brought together data gathered using X-ray crystallography, NMR spectroscopy, cryoelectron microscopy, and lipidomics into whats called a coarse-grained molecular dynamics simulation. This technique allows the model virus to be put through different virtual environments, each having varying temperatures and lipid compositions. The current simulations are still quite limited, but the technique should lead to more complicated tests involving potential therapies and different chemical agents ...
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 ...
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 ...
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 ...
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.. ...
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 ...
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 ...
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.
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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 ...
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. ...
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
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 ...
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 ...
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
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...
Fingeraftryk Dyk ned i forskningsemnerne om A new transferable interatomic potential for molecular dynamics simulations of borosilicate glasses. Sammen danner de et unikt fingeraftryk. ...
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 ...
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. ...
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 ...
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.. ...
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, ...
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 ...
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 ...
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 ...
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
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 ...
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 ...
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. ...
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) ...
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 ...
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 ...
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
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 ...
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 ...
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 ...
O. Alcaraz, J. Trullàs. The longitudinal optic-like mode in molten alkali halides: A molecular dynamics approximation to inelastic x-ray scattering experiments. Journal of Chemical Physics 132, 054503 (2010). I. Skarmoutsos, E. Guàrdia. Effect of the local hydrogen bonding network on the reorientational and translational dynamics in supercritical water. Journal of Chemical Physics 132, 074502/1-10 (2010). I. Skarmoutsos, E. Guàrdia, J. Samios. Hydrogen bond, electron donor acceptor dimer and residence dynamics in supercritical CO2 - ethanol mixtures and the effect of hydrogen bonding on single reorientational and translational dynamics. A molecular dynamics simulation study. Journal of Chemical Physics 133, 014504/1-13 (2010). J. Martí, J. Sala, E. Guàrdia. Molecular dynamics simulations of water confined in graphene nanochannels: From ambient to supercritical environments. Journal of Molecular Liquids 153, 72-78 (2010). M. C. Gordillo, J. Marti. Effect of surface roughness on the static ...
Computer simulations of condensed phases and biochemical systems have lead to profound new insight into molecular-scale phenomena occurring in these complex systems. Many processes that occur in liquids, soft materials, and biochemical systems however occur over length and time scales that are well beyond the current capabilities of atomic-level simulations. In the field of polymers, there are many simulation techniques and models that span a range from the atomistic scale to the continuum. In recent years, much research has been focused on linking models of different length scales, especially from detailed, fully atomistic to mesoscopic scales and back. A common way of addressing this issue is to develop coarse-grained (CG) models from full-atomistic simulations by merging groups of chemically connected atoms into superatoms. This PhD thesis describes new developments in the field of CG simulations of polymers. In addition to CG simulations, atomistic molecular dynamics calculations are ...
Computer simulations of condensed phases and biochemical systems have lead to profound new insight into molecular-scale phenomena occurring in these complex systems. Many processes that occur in liquids, soft materials, and biochemical systems however occur over length and time scales that are well beyond the current capabilities of atomic-level simulations. In the field of polymers, there are many simulation techniques and models that span a range from the atomistic scale to the continuum. In recent years, much research has been focused on linking models of different length scales, especially from detailed, fully atomistic to mesoscopic scales and back. A common way of addressing this issue is to develop coarse-grained (CG) models from full-atomistic simulations by merging groups of chemically connected atoms into superatoms. This PhD thesis describes new developments in the field of CG simulations of polymers. In addition to CG simulations, atomistic molecular dynamics calculations are ...
TY - JOUR. T1 - Simulations of zwitterionic and anionic phospholipid monolayers. AU - Kaznessis, Yiannis N.. AU - Kim, Sangtae. AU - Larson, Ronald G.. N1 - Funding Information: YNK wishes to thank Pfizer Global Research and Development, Ann Arbor Laboratories for funding of his postdoctoral fellowship. We thank Scott Feller for useful suggestions on the simulations, and we thank Ka Yee Lee and Ajaykumar Gopal for invaluable insight into the experimental behavior of lipid monolayers. We also gratefully acknowledge support by the National Computational Science Alliance under grant MCB000007N at the NCSA Origin2000. PY - 2002. Y1 - 2002. N2 - Results of atomistic molecular dynamics simulations of dipalmitoylphosphatidylcholine and dipalmitoylphosphatidylglycerol monolayers at the air/water interface are presented. Dipalmitoylphosphatidylcholine is zwitterionic and dipalmitoylphosphatidylglycerol is anionic at physiological pH. NaCI and CaCI2 water subphases are simulated. The simulations are ...
GROningen MAchine for Chemical Simulations (GROMACS) is a molecular dynamics package mainly designed for simulations of ... The molecular dynamics specific routines were rewritten in the programming language C from the Fortran 77-based program GROMOS ... and Scalable Molecular Simulation". J Chem Theory Comput. 4 (2): 435-447. doi:10.1021/ct700301q. PMID 26620784.. ... and Scalable Molecular Simulation". Journal of Chemical Theory and Computation. 4 (3): 435-447. doi:10.1021/ct700301q. PMID ...
Molecular dynamics solvers[31]. *Direct simulation Monte Carlo solvers[32]. *Electromagnetics solvers[33] ... Solid dynamics solvers[34]. In addition to the standard solvers, OpenFOAM syntax lends itself to the easy creation of custom ... "CFD simulation software using OpenFOAM® made as simple as possible". MantiumFlow. Retrieved 2018-08-27.. ... April 2014). "OpenFOAM for Computational Fluid Dynamics". Notices of the American Mathematical Society. 61 (4): 354-363. doi: ...
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 ...
Scheraga HA, Khalili M, Liwo A (2007). "Protein-folding dynamics: overview of molecular simulation techniques". Annual Review ... 2012). "Prediction of protein functions". Methods in Molecular Biology. Methods in Molecular Biology. 815: 15-24. ISBN 978-1- ... which performs molecular modeling on GPUs). In silico simulations discovered the folding of small α-helical protein domains ... Methods in Molecular Biology. Methods in Molecular Biology™. 424: 225-39. ISBN 978-1-58829-722-8. PMID 18369866. doi:10.1007/ ...
Scheraga HA, Khalili M, Liwo A (2007). "Protein-folding dynamics: overview of molecular simulation techniques". Annual Review ... Methods in Molecular Biology. Methods in Molecular Biology™. 424. pp. 225-39. doi:10.1007/978-1-60327-064-9_19. ISBN 978-1- ... which performs molecular modeling on GPUs). In silico simulations discovered the folding of small α-helical protein domains ... molecular dynamics. Monte Carlo techniques facilitate the computations, which exploit advances in parallel and distributed ...
A molecular dynamics computer simulation". Journal of Surfactants and Detergents. Springer Berlin/Heidelberg. 3 (3): 335-343. ...
... the molecular dynamics. TREMOLO-X was originally developed at the Institute for Numerical Simulation (INS) at the University of ... Numerical Simulation in Molecular Dynamics. Berlin, Heidelberg: Springer. ISBN 978-3-540-68094-9. CS1 maint: discouraged ... TREMOLO-X is a software package used for the numerical simulation of interactions between atoms and molecules, ... CS1 maint: discouraged parameter (link) TREMOLO-X website Fraunhofer SCAI website Institute for Numerical Simulation, ...
Homology modeling, cofactor docking, and molecular dynamics simulation studies". The Journal of Biological Chemistry. 279 (10 ... "Critical Reviews in Biochemistry and Molecular Biology. 50 (2): 168-80. doi:10.3109/10409238.2014.990556. PMC 4653115. PMID ... In molecular biology, the protein domain named Sdh5 is also named SdhE which stands for succinate dehydrogenase protein E. In ... Its role is to prevent the interaction of the intermediate with molecular oxygen to produce reactive oxygen species (ROS). The ...
"ReaxFF molecular dynamics simulations on lithiated sulfur cathode materials". Phys. Chem. Chem. Phys. 17 (5): 3383-3393. ... "ReaxFF molecular dynamics simulations on lithiated sulfur cathode materials". Phys. Chem. Chem. Phys. 17 (5): 3383-3393. ... "ReaxFF Reactive Force Field Simulations on the Influence of Teflon on Electrolyte Decomposition during Li/SWCNT Anode ...
"Molecular dynamics simulation of zirconia melting". Open Physics. 8 (5): 789. Bibcode:2010CEJPh...8..789D. doi:10.2478/s11534- ...
... 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 ...
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 ...
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 ...
A molecular dynamics computer simulation study". Nucleic Acids Research. 34 (2): 686-696. doi:10.1093/nar/gkj434. PMC 1356527. ... Molecular Dynamics of Mixtures (MDynaMix) is a computer software package for general purpose molecular dynamics to simulate ... 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 ...
Rapaport, D. (2004). The art of molecular dynamics simulation. Cambridge, UK: Cambridge University Press. Kittel, C. (1996). ... It is also referred to as Tewary method in the literature The LSGF method complements molecular dynamics (MD) method for ... For any calculation of practical interest N ~ 10,000 but preferably a million for more realistic simulations. Inversion of such ... Maradudin, A.; Montroll, E.; Weiss, G.; Ipatova, I. (1971). Theory of lattice dynamics in the harmonic approximation. Solid ...
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 ...
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 ...
Molecular modelling[28] and molecular dynamics simulations can be used as a guide to improve the potency and properties of new ... "The future of molecular dynamics simulations in drug discovery". Journal of Computer-Aided Molecular Design. 26 (1): 15-26. doi ... "Molecular dynamics simulations and drug discovery". BMC Biology. 9: 71. doi:10.1186/1741-7007-9-71. PMC 3203851. PMID 22035460. ... "International Journal of Molecular Sciences. 13 (10): 12857-79. doi:10.3390/ijms131012857. PMC 3497300. PMID 23202926.. ...
... 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 ...
mit V. Daggett: Protein Unfolding Pathways Explored Through Molecular Dynamics Simulations. In: Journal of Molecular Biology. ... Protein Folding by Restrained Energy Minimization and Molecular Dynamics. In: Journal of Molecular Biology. Band 170, 1983, S. ... mit R. Sharon: Accurate Simulation of Protein Dynamics in Solution. In: Proceedings of the National Academy of Sciences. Band ... Protein Conformation, Dynamics and Folding by Computer Simulation. In: Annual Review of Biophysics and Bioengineering. Band 11 ...
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 ...
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 ... Methods in Molecular Biology. Methods in Molecular Biology™. 424. pp. 225-39. doi:10.1007/978-1-60327-064-9_19. ISBN 978-1- ...
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 ...
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 ...
Computational techniques like Molecular Dynamics simulations can be used in conjunction with empirical structure determination ... Karplus M, McCammon JA (September 2002). "Molecular dynamics simulations of biomolecules". Nature Structural Biology. 9 (9): ... Structural biology is a branch of molecular biology, biochemistry, and biophysics concerned with the molecular structure of ... Media related to Structural biology at Wikimedia Commons Nature: Structural & Molecular Biology magazine website Journal of ...
Rate constant can be calculated for elementary reactions by molecular dynamics simulations. One possible approach is to ... the latter is easily accessible from short molecular dynamics simulations [3] ... "Extending molecular dynamics time scales with milestoning: Example of complex kinetics in a solvated peptide". The Journal of ... It can be done with the help of computer simulation software. Rate constant calculations[edit]. ...
Zundel to Zundel (Z-Z), on the basis of molecular dynamics simulation. ...
Orsi Mario; Noro Massimo; Essex Jonathan (2010). "Dual-resolution molecular dynamics simulation of antimicrobials in ...
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 ...
GENESIS, a general neural simulation system.. Conferences[edit]. *Computational and Systems Neuroscience (COSYNE) - a ... Anderson, Charles H.; Eliasmith, Chris (2004). Neural Engineering: Computation, Representation, and Dynamics in Neurobiological ... We know from molecular biology that distinct parts of the nervous system release distinct chemical cues, from growth factors to ... Models of this type are typically built in large simulation platforms like GENESIS or NEURON. There have been some attempts to ...
... in a molecular dynamics (MD) simulation study". Biophys. Chem. 120 (1): 1-9. doi:10.1016/j.bpc.2005.10.002. PMID 16253415.. ... though molecular dynamic simulations may indicate the existence of an octahedral hexaaqua ion. There are also probably six ... Molecular Metal-Metal Bonds: Compounds, Synthesis, Properties. John Wiley and Sons. pp. 23-24. ISBN 978-3-527-33541-1. .. ... hydrogen can take on the same structural role as the alkali metals in some molecular crystals, and has a close relationship ...
Physical simulation (e.g. cloth modeling, animation of fluid dynamics, etc.). Rendering[edit]. ... Historically, most work in this field has focused on parametric and data-driven models, but recently physical simulation has ... Molecular graphics. *Product visualization. *Scientific visualization. *Software visualization. *Technical drawing. *User ...
... molecular dynamics, Monte Carlo algorithm, dislocation dynamics, Phase field models, Finite element method, and many more. ... The prominent change in materials science during the recent decades is active usage of computer simulations to find new ... and another variety called ultra-high-molecular-weight polyethylene (UHMWPE) is an engineering plastic which is used ... with significant advances in simulation resulting in exponentially increasing understanding of how defects can be used to ...
Merritt, D. (2013). Dynamics and Evolution of Galactic Nuclei. Princeton University Press. ISBN 978-1-4008-4612-2. .. ... It is more transparent to far-infrared, which can be used to observe the interior regions of giant molecular clouds and ... "Simulations Show How Growing Black Holes Regulate Galaxy Formation". Carnegie Mellon University. February 9, 2005. Archived ... Stars are created within galaxies from a reserve of cold gas that forms into giant molecular clouds. Some galaxies have been ...
... monomer in water using unbiased molecular dynamics simulations and spectral algorithms". J. Mol. Biol. 405 (2): 570-83. PMC ... Methods in Molecular Biology 849: 493-506. ISBN 978-1-61779-550-3. PMID 22528111. doi:10.1007/978-1-61779-551-0_33.. ... Methods in Molecular Biology 849: 507-527. ISBN 978-1-61779-550-3. PMID 22528112. doi:10.1007/978-1-61779-551-0_34.. ... Parker MH, Reitz AB (2000). "Assembly of β-Amyloid Aggregates at the Molecular Level". Chemtracts-Organic Chemistry 13 (1): 51- ...
Quantum dynamics. *Quantum electronics. *Quantum error correction. *Quantum imaging. *Quantum information. *Quantum key ... Molecular communication. *Radio waves *wireless. *Transmission line *data transmission circuit. *telecommunication circuit ...
Properties of Si Nanowires as Revealed by in Situ Transmission Electron Microscopy and Molecular Dynamics Simulations» Nano ... experiment and objective molecular dynamics calculations» Phys. Rev. Lett. 109[2] (2012) 025504-1 DOI:10.1103/Phys.Rev.Lett. ... P. M.F.J. Costa, U. K. Gautam, Y. Bando and D. Golberg : «Direct imaging of Joule heating dynamics and temperature profiling ... Structural analysis and atomic simulation of Ag/BN nanoparticle hybrids obtained by Ag ion implantation» Mater. Des. 98 (2016) ...
Computer simulations and molecular dynamics approaches revealed the atomistic motions associated with the molecular recognition ... "Molecular systems biology. 4 (1): 182. PMC 2387233 . PMID 18414483. doi:10.1038/msb.2008.21. Retrieved 5 May 2014.. ... "Molecular Biology & Evolution. 24 (2): 457-464. PMC 1808353 . PMID 17099057. doi:10.1093/molbev/msl172.. ... Molecular basis[edit]. Epigenetic changes modify the activation of certain genes, but not the genetic code sequence of DNA. The ...
Justice and the Dynamics of Research and Publication in Africa: Interrogating the Performance of "Publish or Perish". Uganda ... Insights from a Simulation Study". Journal of the American Society for Information Science and Technology. 64 (4): 701-726. doi ... A Case Study on Internationalisation in the Disciplines of Biochemistry and Molecular Biology". doi:10.31237/osf.io/8cypr.. ... There are power dynamics at play that do not benefit authors, and instead often compromise certain academic freedoms.[307] This ...
Saouma, Victor; Sivaselvan, Mettupalayam (2014). Hybrid Simulation: Theory, Implementation and Applications. CRC Press. p. 217 ... In 2004, the Faculty of Engineering completed work on the Bristol Laboratory for Advanced Dynamics Engineering (BLADE). This £ ... School of Cellular and Molecular Medicine. *School of Physiology, Pharmacology and Neuroscience ... 18.5m project[49] is intended to further the study of dynamics and is the most advanced such facility in Europe.[50] It was ...
Scheraga HA, Khalili M, Liwo A (2007). "Protein-folding dynamics: overview of molecular simulation techniques". Annual Review ... Methods in Molecular Biology (Clifton, N.j.). Methods in Molecular Biology. 815. pp. 15-24. doi:10.1007/978-1-61779-424-7_2. ... Methods in Molecular Biology. Methods in Molecular Biology™. 424. pp. 225-39. doi:10.1007/978-1-60327-064-9_19. ISBN 978-1- ... which performs molecular modeling on GPUs). In silico simulations discovered the folding of small α-helical protein domains ...
"Molecular Biology and Evolution. 23 (6): 1144-1155. doi:10.1093/molbev/msj124. PMID 16533822.. CS1 maint: Multiple names: ... Brugger, Julia; Feulner, Georg; Petri, Stefan (2016). "Baby, it's cold outside: Climate model simulations of the effects of the ... Mathias M. Pires; Brian D. Rankin; Daniele Silvestro; Tiago B. Quental (2018). "Diversification dynamics of mammalian clades ... Based on molecular sequencing and fossil dating, Neoaves appeared to radiate after the K-Pg boundary.[23][155] They even ...
... with the dynamics (evolution) given by the shift operator.. System dynamics[edit]. System dynamics is an approach to ... The key problems of such systems are difficulties with their formal modeling and simulation. From such perspective, in ... molecular biology and inquiries into the nature of living cells themselves.. Control theory[edit]. Control theory is an ... Symbolic dynamics[edit]. Symbolic dynamics is the practice of modelling a topological or smooth dynamical system by a discrete ...
... the viscosity of a dense fluid using these relations currently requires the use of molecular dynamics computer simulations. On ... the molecular mass, and α. {\displaystyle \alpha }. a numerical constant on the order of 1. {\displaystyle 1}. . The quantity λ ... For more complicated molecular models, however, λ. {\displaystyle \lambda }. depends on temperature in a non-trivial way, and ... is frequently not necessary in fluid dynamics problems. For example, an incompressible fluid satisfies ∇. ⋅. v. =. 0. {\ ...
The group dynamics of dingoes should have successfully kept devils away from carrion, and since dingoes are able to break bones ... "Computer simulation of feeding behaviour in the thylacine and dingo as a novel test for convergence and niche overlap" ... "The molecular ecology of Australian wild dogs: hybridization, gene flow and genetic structure at multiple geographic scales" ... However, it is unlikely that the dynamics of the various ecosystems will be excessively disturbed by this process.[72] ...
Perdih A, Kotnik M, Hodoscek M, Solmajer T (July 2007). "Targeted molecular dynamics simulation studies of binding and ... Smith CA (September 2006). "Structure, function and dynamics in the mur family of bacterial cell wall ligases". J. Mol. Biol. ... Ziegler K, Diener A, Herpin C, Richter R, Deutzmann R, Lockau W (May 1998). "Molecular characterization of cyanophycin ...
FDTD (1D) video simulation of a soliton with forces[edit]. The following video shows a simulation of two parking solitons. Both ... "Neuronic system inside neurons: molecular biology and biophysics of neuronal microtubules". Biomedical Reviews. 15: 67-75. doi ...
Eric R. Bittner, Associate Professor of Chemistry, University of Houston: Quantum dynamics in molecular electronic devices. ... Darío A. Estrin, Associate Professor, University of Buenos Aires, and Principal Researcher, CONICET: Computer simulation of ... Marco A. Romano-Silva, Associate Professor of Psychiatry, Federal University of Minas Gerais: Clinical and molecular aspects of ... Mark Winey, Professor of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder: Gene discovery in ...
C.D. Murray & S.F. Dermott (1999). Solar System Dynamics (engelsk). Cambridge University Press. ISBN 0-521-57295-9.. ... J. Braine, U. Lisenfeld, P. A. Duc, E. Brinks, V. Charmandaris, S. Leon (2004). «Colliding molecular clouds in head-on galaxy ... Sean N. Raymond, Thomas Quinn, Jonathan I. Lunine (2007). «High-resolution simulations of the final assembly of Earth-like ... Dynamics of Populations of Planetary Systems. 197. doi:10.1017/S1743921304008865.. CS1-vedlikehold: Eksplisitt bruk av m.fl. ( ...
OpenPIC3D - 3D Hybrid Particle-In-Cell simulation of plasma dynamics. *Plasma Formulary Interactive ... This also can be accompanied by the dissociation of molecular bonds,[10] though this process is distinctly different from ... The dynamics of plasmas interacting with external and self-generated magnetic fields are studied in the academic discipline of ... Morozov, A.I. (2012). Introduction to Plasma Dynamics. CRC Press. p. 17. ISBN 978-1-4398-8132-3. .. ...
Fluid dynamics *Darcy-Weisbach equation. *Eddy. *Navier-Stokes equations. *Large eddy simulation ... A flow situation in which the kinetic energy is significantly absorbed due to the action of fluid molecular viscosity gives ... as a sub-field of fluid dynamics. While the mean values are taken as predictable variables determined by dynamics laws, the ... In fluid dynamics, turbulence or turbulent flow is fluid motion characterized by chaotic changes in pressure and flow velocity ...
... molecular engineering, polymer chemistry and physics, surface chemistry, molecular biology, cell biology, and medicine. ... Evans, Evan A.; Calderwood, David A. (25 May 2007). "Forces and Bond Dynamics in Cell Adhesion". Science. 316 (5828): 1148-1153 ... and then to compare with forces given by DFT simulations. The team found that the tip interacted most strongly with silicon ... In molecular biology, AFM can be used to study the structure and mechanical properties of protein complexes and assemblies. For ...
RIKEN press release, Completion of a one-petaFLOPS computer system for simulation of molecular dynamics ... Molecular Dynamics Simulation (Tianhe-1A)[108]. 2020s Scientific research for outbreak prevention/Electrochemical Reaction ... MDGRAPE-3 for protein structure computation molecular dynamics[50] and Deep Crack,[51] for breaking the DES cipher. ... and physical simulations (such as simulations of the early moments of the universe, airplane and spacecraft aerodynamics, the ...
A model can be a simulation, mathematical or chemical formula, or set of proposed steps. Science is like mathematics in that ... The discovery became the starting point for many further studies involving the genetic material, such as the field of molecular ... In subsequent modifications, it has also subsumed aspects of many other fields such as biochemistry and molecular biology. ... namely high energy physics and molecular biology) to conclude that the epistemic practices and reasonings within both ...
Scheraga HA, Khalili M, Liwo A (2007) Protein-folding dynamics: overview of molecular simulation techniques Annual Review of ... Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (5th ed ... Lodish H, Berk A, Matsudaira P, Kaiser CA, Krieger M, Scott MP, Zipurksy SL, Darnell J (2004). Molecular Cell Biology (5th ed ... Plewczyński D, Ginalski K (2009). The interactome: predicting the protein-protein interactions in cells Cellular & Molecular ...
Bernstein H, Hopf FA, Michod RE (1987). The molecular basis of the evolution of sex. Adv. Genet. Advances in Genetics. 24. pp. ... Computer-population simulations indicate that all populations continuing to avoid incestuous mating will become extinct within ... Sparkman, AM; Adams, JR; Steury, TD; Waits, LP; Murray, DL (July 2012). "Pack social dynamics and inbreeding avoidance in the ...
The following two laws govern the dynamics of charged particles in electric and magnetic fields in vacuum: F. =. Q. (. E. +. v ... Such simulation is often supported by a fragmentation library[39] that contains published patterns of known decomposition ... Mass spectrometry can measure molar mass, molecular structure, and sample purity. Each of these questions requires a different ... Computer simulation of ionization and fragmentation processes occurring in mass spectrometer is the primary tool for assigning ...
Steered molecular dynamics (SMD)Edit. Steered molecular dynamics (SMD) simulations, or force probe simulations, apply forces to ... Molecular Dynamics Simulation: Elementary Methods. ISBN 0-471-18439-X. *R. J. Sadus, Molecular Simulation of Fluids: Theory, ... Design of a molecular dynamics simulation should account for the available computational power. Simulation size (n = number of ... Molecular dynamics simulation of a synthetic molecular motor composed of three molecules in a nanopore (outer diameter 6.7 nm) ...
Numerical Simulation in Molecular Dynamics. Book Subtitle. Numerics, Algorithms, Parallelization, Applications. Authors. * ... Numerical Simulation in Molecular Dynamics. Numerics, Algorithms, Parallelization, Applications. Authors: Griebel, Michael, ... They can be studied on the computer with the help of molecular dynamics simulations. This book presents in detail both the ... "Authors aim for this book was to present the necessary numerical techniques of molecular dynamics in a compact form, to enable ...
... of solvent and temperature on protein structure and dynamics Why molecular dynamics simulations are important Simulations can ... During the following 10 years, a wide range of motional phenomena were investigated by molecular dynamics simulations of ... It has been 25 years since the first molecular dynamics simulation of a macromolecule of biological interest was published 1 . ... Although this simulation was performed in vacuum with a crude molecular mechanics potential and lasted for only 9.2 ps, the ...
DescriptionIsothermal-Isobaric Molecular Dynamics Simulation of Water.webm. English: A molecular dynamics simulation of water ( ... File:Isothermal-Isobaric Molecular Dynamics Simulation of Water.webm. From Wikimedia Commons, the free media repository ... Retrieved from "https://commons.wikimedia.org/w/index.php?title=File:Isothermal-Isobaric_Molecular_Dynamics_Simulation_of_Water ... A Nosé-Hoover thermostat and barostat are applied so that the simulation samples the isothermal-isobaric (NpT) ensemble. ...
Pushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning. ... Molecular Dynamics (AIMD) is an approach that differs slightly from Standard Molecular Dynamics (SMD) in how interatomic forces ... Groundbreaking molecular dynamics simulation recognized with ACM Gordon Bell Prize New tool simulates interactions of 100 ... Groundbreaking molecular dynamics simulation recognized with ACM Gordon Bell Prize. Association for Computing Machinery ...
Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual ... A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational ... A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. ... molecular dynamics; fluid-wall interaction; surface roughness; nano-scale gas flow virtual-wall model; molecular dynamics; ...
... dynamics, and function of biopolymers at the atomic level. In recent years, it has become possible to... ... Molecular dynamics simulation is a powerful method for investigating the structural stability, ... Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of ... Naritomi Y, Fuchigami S (2013) Slow dynamics of a protein backbone in molecular dynamics simulation revealed by time-structure ...
... of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. ... The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on ... Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the ... Koshiyama, K. & Wada, S. Molecular dynamics simulations of pore formation dynamics during the rupture process of a phospholipid ...
MDAnalysis: a toolkit for the analysis of molecular dynamics simulations.. Michaud-Agrawal N1, Denning EJ, Woolf TB, Beckstein ... MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation ... Python programming language; analysis; membrane systems; molecular dynamics simulations; object-oriented design; proteins; ... A molecular dynamics trajectory is accessed through the trajectory attribute, which is an instance of a Reader class. ...
Energy history, depo-sition temperature and the cracked groups of simulation process in different force fields was gotten, of ... PM3 method was used in this paper to optimize cellulose molecular structure which is the main component of biomass and a series ...
Molecular dynamics simulations of intrinsically disordered proteins: On the accuracy of the TIP4P-D water model and the ... Validating solution ensembles from molecular dynamics simulation by wide-angle X-ray scattering data. Biophys. J. 107, 435-447 ... Molecular dynamics simulations of intrinsically disordered proteins: Force field evaluation and comparison with experiment. J. ... Generation of the configurational ensemble of an intrinsically disordered protein from unbiased molecular dynamics simulation. ...
Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations. Ignasi Buch, Toni Giorgino, ... Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations ... Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations ... Complete reconstruction of an enzyme-inhibitor binding process by molecular dynamics simulations ...
In this study, random acceleration molecular dynamics simulations combined with steered molecular dynamics and potential of ... can oxidize not only low molecular weight xenobiotic compounds such as ethanol, but also many endogenous fatty acids. The ... Molecular dynamics Is the Subject Area "Molecular dynamics" applicable to this article? Yes. No. ... Correction: Investigation of Indazole Unbinding Pathways in CYP2E1 by Molecular Dynamics Simulations ...
... with most molecular trajectories being 1 µs in dura ... We have performed molecular dynamics simulations for a total ...
S. C. Chowdhury and T. Okabe, "Computer simulation of carbon nanotube pull-out from polymer by the molecular dynamics method," ... D. Hossain, M. A. Tschopp, D. K. Ward, J. L. Bouvard, P. Wang, and M. F. Horstemeyer, "Molecular dynamics simulations of ... Interfacial Characteristics of Carbon Nanotube-Polyethylene Composites Using Molecular Dynamics Simulations. Z. Q. Zhang,1,2 D ... S. Plimpton, "Fast parallel algorithms for short-range molecular dynamics," Journal of Computational Physics, vol. 117, no. 1, ...
... surface by molecular dynamics method using semi-empirical many-body Brenner potential (#2). The... ... We studied the deposition dynamics of C2H2 molecules on diamond reconstructed (001)-(2[equation]1) ... We studied the deposition dynamics of C2H2 molecules on diamond reconstructed (001)-(2\(\)1) surface by molecular dynamics ... 79.20.Rf Atomic, molecular, and ion beam impact and interactions with surfaces - 61.20.Ja Computer simulation of liquid ...
... Marco Berghoff, Michael Selzer, and Britta ... Early solidification is investigated using two different simulation techniques: the molecular dynamics (MD) and the phase-field ... The bulk and interfacial properties required in the PF method are obtained from MD simulations. Also the initial configuration ...
We enabled an unprecedented scale of quantum molecular dynamics simulations through algorithmic innovations. A new lean divide- ...
Here we report the results of first-principles molecular dynamics simulations of solid hydrogen at pressures up to 270 GPa. We ... 11). Although limitations on the simulation time and size may result in an over-estimate of the absolute pressure, our ... in part because the structure that molecular hydrogen adopts at high pressure is not known. ... THE behaviour of molecular hydrogen at high pressures has implications for the interiors of the giant planets, which consist ...
Article Molecular dynamics simulations of breaking metallic nanowires. In the present work, we have reviewed the importance of ... Molecular dynamics simulations of breaking metallic nanowires. Molecular dynamics simulations of breaking metallic nanowires. 0 ... No comments were found for Molecular dynamics simulations of breaking metallic nanowires. Be the first to comment! ... Keywords: metallic nanocontacts, metallic nanowires, conductance histograms, molecular dynamics, simulation, embedded atom ...
... Alaei, Zohreh KTH, School of Technology and Health ... Using Molecular Dynamic (MD) simulation and a coarse grain model, a series of bilayers with various bilayer structure (single ... Traumatic brain injury, diffuse axonal injury, molecular simulation, axonal bilayer, strain, shear force, nano-scale ... MD simulation of axonal membrane in TBI-Zohreh Alaei(5002 kB). 128 downloads. ...
Static and dynamic contact angles of water droplet on a solid surface using molecular dynamics simulation.. Hong SD1, Ha MY, ... angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation ...
247w) Molecular Dynamics Simulation of Lipid Bilalyer Consisting of DPPC and Mppc: Effect of Configuration. ... Therefore, this study runs fully atomistic molecular dynamics (MD) simulations of the lipid bilayer systems with two different ... Group: Computational Molecular Science and Engineering Forum. *Session: Poster Session: Computational Molecular Science and ...
The dependence of molecular system size and scaling with number of processors was also investigated. Considering performance ... simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water ... models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in ... Molecular Dynamics Simulations of Clathrate Hydrates on Specialised Hardware Platforms. Nicola Varini 1,†. ...
Computer simulation using the molecular dynamics (MD) technique have been carried out on amorphous silicon nitride (a-Si_3N_4) ... Structural Characterization of Amorphous Silicon Nitride by Molecular Dynamics Simulation(Materials, Metallugy & Weldability) * ... From the MD simulation, the following points have been deduced: (1) The average Si-N bond length obtained from our MD results ... The a-Si_3N_4 structure can be reproduced by our MD simulation. ...
... providing insight into the nature of structural dynamics occurring within the crystalline lattice. This simulation allows us to ... to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, ... Atomic-resolution structural dynamics in crystalline proteins from NMR and molecular simulation Luca Mollica 1 Maria Baias 2 ... Atomic-resolution structural dynamics in crystalline proteins from NMR and molecular simulation. Journal of Physical Chemistry ...
... when the microscopic model is a molecular dynamics (MD) description of a mono-atomic dense fluid. We assume a macroscopic model ... based on appropriately initialized microscopic simulations. In this paper, we investigate the initialization of the microscopic ... Lifting in equation-free methods for molecular dynamics simulations of dense fluids. Yves Frederix 1, , Giovanni Samaey 1, , ... Lifting in equation-free methods for molecular dynamics simulations of dense fluids. Discrete & Continuous Dynamical Systems - ...
Molecular Dynamics Simulations and Thermal Transport at the Nano-Scale , IntechOpen, Published on: 2012-04-05. Authors: ... Molecular Dynamics Simulations and Thermal Transport at the Nano-Scale. By Konstantinos Termentzidis and Samy Merabia DOI: ... Mathematics » Molecular Dynamics - Theoretical Developments and Applications in Nanotechnology and Energy, book edited by ... Agricultural and Biological Sciences Biochemistry, Genetics and Molecular Biology Environmental Sciences Immunology and ...
Molecular dynamic simulations. Molecular dynamic simulations of CnsP2 protease complexed with ligand were performed using the ... Chikungunya, nsP2 protease, Homology modeling, AutoDock4.2, Molecular dynamics simulation. In recent years, re‑emerging ... Further, molecular dynamic simulation of protein ligand complex was carried out to analyze the stability of the complex. ... Singh KD, Kirubakaran P, Nagarajan S, Sakkiah S, Muthusamy K, Velmurgan D, et al. Homology modeling, molecular dynamics, e‑ ...
Journal Article: Molecular simulations and lattice dynamics determination of Stillinger-Weber GaN thermal conductivity ... Title: Molecular simulations and lattice dynamics determination of Stillinger-Weber GaN thermal conductivity ... MOLECULAR DYNAMICS METHOD; PHONONS; POTENTIALS; SIMULATION; THERMAL CONDUCTIVITY. ... direction at a temperature of 300 K is calculated using equilibrium molecular dynamics (EMD), non-equilibrium MD (NEMD), and ...
  • italics added] Two years after the BPTI simulation, it was recognized 5,6 that thermal (B) factors calculated during X-ray crystallographic refinement could be used to infer the internal motions of proteins. (psu.edu)
  • During the following 10 years, a wide range of motional phenomena were investigated by molecular dynamics simulations of proteins and nucleic acids. (psu.edu)
  • Practical applications of molecular dynamics include studying large molecules such as proteins for drug development. (eurekalert.org)
  • Ding F, Tsao D, Nie H, Dokholyan NV (2008) Ab initio folding of proteins with all-atom discrete molecular dynamics. (springer.com)
  • Eisenman, G. and Alvarez, O. (1992) Ionic selectivity of proteins: Lessons from molecular dynamics simulations on valinomycin. (scirp.org)
  • Molecular dynamics (MD) simulations enable in silico investigations of the dynamic behavior of proteins and protein complexes. (springer.com)
  • Durrieu MP, Lavery R, Baaden M (2008) Interactions between neuronal fusion proteins explored by molecular dynamics. (springer.com)
  • Bock LV, Hutchings B, Grubmuller H, Woodbury DJ (2010) Chemomechanical regulation of SNARE proteins studied with molecular dynamics simulations. (springer.com)
  • qsar from qsar.org Subject: [QSAR] Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Hi all, Here's an interesting topic I'd like your thoughts on - please pass along to your colleagues. (bio.net)
  • Millisecond-Long Molecular Dynamics Simulations of Proteins on a Special-Purpose Machine Molecular dynamics simulation provides a potentially powerful tool for understanding the behavior of proteins at an atomic level of detail, but its relevance to drug design has been limited in part by the computational demands of such simulations. (bio.net)
  • Since dysregulation of Bcl-2 proteins is implicated in a number of cancers, examining the basic structural dynamics at a molecular level yielded information that can aid in the design novel Bcl-2 family-targeting chemotherapeutics. (aacrjournals.org)
  • Eukaryotic protein kinases (PKs) are a large family of proteins critical for cellular response to external signals, acting as molecular switches. (biochemj.org)
  • Intrinsically disordered proteins are recognized to play key biological roles, however current structural biology and simulation techniques are often poorly suited to characterizing them. (nih.gov)
  • Remarkably, they reveal that both proteins remain essentially completely disordered when bound -- results which are backed up by independent all-atom simulations of the same complex. (nih.gov)
  • Molecular dynamics simulation of the engineered proteins with adenine as substrate revealed favourable hydrogen bond distances between N7 of the purine ring and the Asp-243 carboxylate at 2.93 and 2.88 Å, for Asn-243-Asp and the Asn-243-Asp;Lys-244-Gln constructs respectively. (portlandpress.com)
  • Multiscale simulation approaches that combine coarse-grained and atomistic MD simulations may now be applied with confidence to investigate the molecular mechanisms of the association of peripheral proteins with model bilayers. (portlandpress.com)
  • We discuss the application of multiscale MD simulation and related approaches to investigate the association of peripheral proteins which contain PH, C2 or FERM-binding modules with lipid bilayers of differing phospholipid composition, including bilayers containing multiple PIP molecules. (portlandpress.com)
  • Complementary to the conventional structural analysis, computational simulations have the advantage to reflect the dynamic nature of proteins or enzymes. (tennessee.edu)
  • Abstract: Molecular dynamics simulations were carried out to investigate the plastic deformation mechanism of fcc crystalline materials using the conventional Lennard-Jones potential. (scientific.net)
  • Abstract 5138: Structural insights into the dynamic functionality of Bax through molecular dynamics simulations. (aacrjournals.org)
  • Therefore, this study runs fully atomistic molecular dynamics (MD) simulations of the lipid bilayer systems with two different configurations: dispersed and segregated model. (aiche.org)
  • Using atomistic molecular dynamics (MD) simulations, we provide in-depth analysis to reveal structural signatures of wild and mutant complexes with their bound agonist and antagonist ligands. (nih.gov)
  • barrel pore have been studied via atomistic molecular dynamics simulations. (soton.ac.uk)
  • A virtual-wall model is proposed in this study to describe fluid-wall molecular interactions, for reducing the computational time. (mdpi.com)
  • 79.20.Rf Atomic, molecular, and ion beam impact and interactions with surfaces - 61.20.Ja Computer simulation of liquid structure - 81.15.Gh Chemical vapor deposition (including plasma-enhanced CVD, MOCVD, etc. (springer.com)
  • CG-MD simulations demonstrate that interactions between precursors can cause the low formation yield of hexapeptides in the mixtures of dipeptides and show that this ability to disrupt is influenced by the concentration of the different species in the DPL. (rsc.org)
  • Molecular Dynamics simulations were performed to check the overall structural stability (RMSD), Cα fluctuations (RMSF) and protein-ligand interactions. (nih.gov)
  • Molecular dynamics were carried out to simulate binding interactions between S' subsites of thrombin and hirudin-based thrombin inhibitors. (unboundmedicine.com)
  • AU - Yue,S Y, AU - Konishi,Y, PY - 1994/7/1/pubmed PY - 1994/7/1/medline PY - 1994/7/1/entrez SP - 1 EP - 17 JF - Drug design and discovery JO - Drug Des Discov VL - 12 IS - 1 N2 - Molecular dynamics were carried out to simulate binding interactions between S' subsites of thrombin and hirudin-based thrombin inhibitors. (unboundmedicine.com)
  • Currently, he is focusing on theoretical studies on the structure, dynamics and energetics of nucleic acid-protein/ligand interactions. (omicsonline.org)
  • Molecular structure in the interlayers of lithium-Wyoming montmorillonite with one, two, or three adsorbed water layers was investigated for the first time by concurrent Monte Carlo and molecular dynamics simulation, based on the MCY model of water-water interactions. (columbia.edu)
  • Together, the simulations highlight the role of molecular interactions between the nucleic acid molecules and the protein pore. (bl.uk)
  • Here, we describe MD simulations of the SNARE complex and its interactions with the neuronal protein complexin. (springer.com)
  • Owing to the disordered nature and nanoscopic dimension of the interlayer pores of clay minerals, computer simulations have become an increasingly useful tool for studying clay-swelling inhibitor interactions. (scielo.br)
  • In this work we briefly review the history of the development of technical drilling fluids, the environmental impact of drilling fluids and the use of computer simulations to study the interactions between clay minerals and swelling inhibitors. (scielo.br)
  • To the extent that more recent measurements of etch rates are more reliable than older ones, preliminary MD simulations using bond-order corrections to the atomic interactions between neighboring Si atoms on the surface improves agreement with experiment through an increase in etch rate and improved agreement with XPS measurements of surface stoichiometry. (nsti.org)
  • Comparisons with experimental data indicate that such simulations can predict specific peripheral protein-lipid interactions. (portlandpress.com)
  • Given that the calculated fast reorientational correlation times and the "microscopic" lateral diffusion of the lipids show excellent agreement with the experimental results, it is concluded that the apparently high viscosity of the membrane is more closely related to molecular interactions on the surface rather than in the interior. (sciencemag.org)
  • Altogether, our simulations reveal significant aspects at the atomistic scale of interactions of α-TTP with the plasma membrane and with PIP, providing clarifications on the mechanism of intracellular vitamin E trafficking and helping establishing the role of key residue for the functionality of α-TTP. (uio.no)
  • Using Molecular Dynamic (MD) simulation and a coarse grain model, a series of bilayers with various bilayer structure (single bilayer, parallel bilayer and cylindrical bilayer) and similar composition to biological axonal membrane were simulated. (diva-portal.org)
  • MD simulation results could be a prerequisite for studying a more complex scenario-for estimating ion transport in the cell membrane or physiological electric potential which is formed in the membrane or inside the cell relative to its surrounding medium. (scirp.org)
  • More recently, the activation pathway of different GPCR complexes have been investigated using molecular dynamics (MD), where the solvent and membrane environment is taken into account [ 8 - 11 ]. (pubmedcentralcanada.ca)
  • Molecular dynamics simulation was used to determine how the trans-membrane region of Bax conferred stability to the protein, identifying regions of high flexibility and differential exposure. (aacrjournals.org)
  • On the 100-picosecond time scale of the present simulations, there is effectively no difference in the reorientational dynamics of the carbons in the membrane interior and in pure hexadecane. (sciencemag.org)
  • To study the properties of these structures and understand the mechanism by which pore expansion leads to membrane rupture, a series of molecular dynamics simulations of a dipalmitoylphosphatidylcholine (DPPC) bilayer have been conducted. (semanticscholar.org)
  • Mesoscopic simulation of cell membrane damage, morphology change and rupture by nonionic surfactants. (semanticscholar.org)
  • In this study, coarse grained molecular dynamics (CG-MD) simulations are used to understand the DPL results for F 2 , L 2 and mixed libraries. (rsc.org)
  • Coarse-grained molecular simulations with a simple empirical potential are able to explain a range of FRET and NMR data for the complex. (nih.gov)
  • We used multiple sets of simulations both at the atomistic and coarse-grained level of resolution to investigate interaction and binding of α-tochoperol transfer protein (α-TTP) to phosphatidylinositol phosphate lipids (PIPs). (uio.no)
  • Molecular dynamics simulation is a powerful method for investigating the structural stability, dynamics, and function of biopolymers at the atomic level. (springer.com)
  • However, it is necessary to derive the important factors contributing to structural change or function from the complicated movements of biopolymers obtained from long simulations. (springer.com)
  • The RMA method approximately extracts slow relaxation modes and rates from trajectories and decomposes the structural fluctuations into slow relaxation modes, which characterize the slow relaxation dynamics of the system. (springer.com)
  • MDAnalysis is an object-oriented library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures. (nih.gov)
  • Attempts to determine this ensemble computationally have been hitherto hampered by the necessity of reweighting molecular dynamics (MD) results or biasing simulation in order to match ensemble-averaged experimental observables, operations that reduce the precision of the generated model because different structural ensembles may yield the same experimental observable. (pnas.org)
  • We compare experimentally determined dynamic parameters, spin relaxation, chemical shifts, and dipolar couplings, to values calculated from a 200 ns MD simulation of protein GB1 in its crystalline form, providing insight into the nature of structural dynamics occurring within the crystalline lattice. (archives-ouvertes.fr)
  • The second stage of the recovery stroke structural transition, rotation of the converter domain, was not observed in our simulations. (wiley.com)
  • Ghahremanpour MM, Mehrnejad F, Moghaddam ME (2010) Structural studies of SNARE complex and its interaction with complexin by molecular dynamics simulation. (springer.com)
  • Probing Structural Variation and Dynamics in the HIV-1 Env Fusion Glycoprotein. (umassmed.edu)
  • Such structural and biochemical studies are useful for identifying functional domains within Bax that can be developed into therapeutic peptides, but are limiting when ascribing function to domains at a molecular level. (aacrjournals.org)
  • dynamics simulations (MDS) of the structural rearrangements on the pathway leading to procaspase 3 (I) activation are presented. (epfl.ch)
  • Based on homology modeling and molecular dynamics simulation, the dysfunctional point mutations introduced structural deformations into the quadrilateral b-helix structure of PRPs. (ebscohost.com)
  • Here, I illustrate how molecular simulation can be used as an aid in determining a molecular model reflecting the structural and dynamic properties observed in experiment. (nih.gov)
  • We are investigating the molecular and structural basis of complex mechanisms and processes in chemistry and biology. (mpg.de)
  • One of the computational simulation methods, the quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations, has been widely applied to the research in structural analysis, ligand-receptor binding and enzymatic catalysis. (tennessee.edu)
  • In theory, 'low-dimensional' smFRET measurements are interpreted in terms of the atomic structural models obtained with MD simulations. (elifesciences.org)
  • Molecular dynamics (MD) is a computer simulation method that analyzes how atoms and molecules move and interact during a fixed period of time. (eurekalert.org)
  • A large number of molecules are usually required to model atomic walls in molecular dynamics simulations. (mdpi.com)
  • We studied the deposition dynamics of C 2 H 2 molecules on diamond reconstructed (001)-(2 \(\) 1) surface by molecular dynamics method using semi-empirical many-body Brenner potential (#2). (springer.com)
  • Therefore, in the work, molecular dynamics (MD) simulation was employed to study transport of methane and n-butane molecules in the bulk and interface region of polyethylene (PE), poly (4-methyl-2-pentyne) (PMP) and polydimethylsiloxane (PDMS). (rsc.org)
  • Smorenburg, H.E., Crevecoeur, R.M., de Schepper, I.M. and de Graaf, L.A. (1995) Structure and dynamics of C60 molecules in liquid CS2 from neutron scattering. (scirp.org)
  • However, if a process is non-activated, such as the adsorption of some diatomic molecules on a metal surface, or the reaction coordinate is complex and multiple saddle points exist, molecular dynamics (MD) simulations performed on a dynamically relevant region of the potential energy surface (PES) should be used to estimate reactivity. (aiche.org)
  • A computer simulation developed to study the motion of molecules over a period of time. (umassmed.edu)
  • We report on results from some recent large-scale molecular dynamics simulation studies on low molecular weight water-soluble macromolecular inhibitor molecules. (scielo.br)
  • The 100-ns-long molecular dynamics simulation at constant pressure (1 atm) and at a temperature of 50°C of 64 lipid molecules and 64 x 23 water molecules lack a slow water reorientation correlation component in the ns time scale. (diva-portal.org)
  • ACM, the Association for Computing Machinery, named a nine-member team, drawn from Chinese and American institutions, recipients of the 2020 ACM Gordon Bell Prize for their project, "Pushing the limit of molecular dynamics with ab initio accuracy to 100 million atoms with machine learning. (eurekalert.org)
  • Ab initio (meaning in Latin "from the beginning" or "from first principles") Molecular Dynamics (AIMD) is an approach that differs slightly from Standard Molecular Dynamics (SMD) in how interatomic forces are calculated during the simulation. (eurekalert.org)
  • While other machine learning-based protocols have been introduced for MD simulations in recent years, the authors contend that their protocol achieves the first efficient MD simulation of 100 million atoms with ab initio accuracy. (eurekalert.org)
  • Neural networks have recently been employed as a tool to obtain highly accurate ab-initio based PES for performing six dimensional MD simulations aimed at estimating the reactivity of hydrogen on Pd(100) surfaces [1,2]. (aiche.org)
  • The mean square displacement (MSD) of the diffusing atoms is used to obtain the diffusion coefficients which could be simulated by Ab initio Molecular Dynamics (AIMD). (diva-portal.org)
  • To allow for chemical reactions, the electrons have to be included explicitly, requiring ab initio molecular dynamics techniques [3]. (gauss-centre.eu)
  • The drawback of ab initio techniques is the huge computational cost, even if highly efficient state-of-the-art simulation packages as CPMD [4] in the present case are used. (gauss-centre.eu)
  • 2) Metadynamics sampling: 3D free energy surface with the "synthesized" chemical species which were obtained from analysis of the ab initio molecular dynamics trajectory underlying the metadynamics. (gauss-centre.eu)
  • In addition to efforts towards determining crystal structures of PKs, research on human PKs has incorporated molecular dynamics (MD) simulations to study the conformational dynamics underlying the switching of PK function. (biochemj.org)
  • In our study, the molecular insights of inhibition in polymerization were investigated by monitoring the conformational dynamics in solution phase using hydrogen/deuterium exchange-based mass spectrometry. (biochemj.org)
  • Single-molecule experiments and molecular dynamics (MD) simulations are indispensable tools for investigating protein conformational dynamics. (elifesciences.org)
  • Here, we devise a machine-learning method to combine the complementary information from the two approaches and construct a consistent model of conformational dynamics. (elifesciences.org)
  • Classical equilibrium molecular dynamics (MD) simulations have been performed to investigate the computational performance of the Simple Point Charge (SPC) and TIP4P water models applied to simulation of methane hydrates, and also of liquid water, on a variety of specialised hardware platforms, in addition to estimation of various equilibrium properties of clathrate hydrates. (mdpi.com)
  • Journal of Computational Dynamics , 2014, 1 (1) : 111-134. (aimsciences.org)
  • Journal of Computational Dynamics , 2014, 1 (2) : 377-389. (aimsciences.org)
  • This assignment is to be completed following lectures 3 and 4 using the "Lennard-Jones Molecular Dynamics" program in the Berkeley Computational Nanoscience Toolkit . (nanohub.org)
  • Jeffrey C Grossman (2008), "Computational Nanoscience, Homework Assignment 2: Molecular Dynamics Simulation of a Lennard-Jones Liquid," https://nanohub.org/resources/4052. (nanohub.org)
  • 100 times the length of the longest such simulations previously published - revealing pharmaceutically relevant aspects of protein dynamics that were previously inaccessible to both computational and experimental study. (bio.net)
  • With increasing computational power, it is now possible to generate very long and complex simulations, which are cumbersome to explore using traditional 3D animations of protein movements. (muni.cz)
  • Computational modeling and molecular dynamics simulations of Bax provides a high-power analysis of the subtle changes that modulate the regulatory and effector activities of the protein. (aacrjournals.org)
  • In addition, we have also applied computational methods with different density functionals and basis sets in conjunction with molecular dynamics simulations to gain further insights regarding the structures of ETD-formed peptide cation radicals. (washington.edu)
  • To address several key questions of alternating access model and to elucidate the underlying molecular mechanism at atomic level, we conducted computational studies mainly using molecular dynamics (MD) simulations on two secondary active transporters, i.e., bacterial Na+-coupled glucose transporter (vSGLT), and the benzyl-hydantoin transporter (Mhp1). (illinois.edu)
  • Based on the crystal structures of these two transporters, the computational studies elucidated several key functional molecular events in the transport cycle, and provided deeper insights of the underlying molecular mechanism of alternating access model. (illinois.edu)
  • Molecular dynamics simulations are iterative calculations performed using Newton's equations of motion to predict the movement of atoms or particles over time. (springer.com)
  • The simulation was carried out in a Ni block (295020 atoms) with a Σ = 5 (210) grain boundary and an embedded atom potential for Ni was used for the MD calculation. (scientific.net)
  • Moreover, due to the removal of high-frequency motions, such as the vibrational movements of hydrogen atoms, larger steps can be made in MD simulations, allowing longer simulations. (pubmedcentralcanada.ca)
  • In particular, the simulations of a stretched nanowire showed that the strains between neighboring atoms were large at crystal grain boundaries , but negligible within the grains or at the free surfaces. (phys.org)
  • Borosilicate glasses are traditionally challenging to model using atomic scale simulations due to the composition and thermal history dependence of the coordination state of B atoms. (aau.dk)
  • In the present work, these potentials are used to calculate the diffusivity of single self-interstitial atoms (SIA) in an α-Fe matrix with randomly distributed chromium atoms, by means of classical molecular dynamics (MD). The main difference between the two potentials used consists in a different prediction of the most stable interstitial configuration in Fe and Fe-Cr. (spie.org)
  • First of all, simulations of surfaces require a model system containing a rather large number of atoms. (gauss-centre.eu)
  • Simulations of dynamical properties require molecular dynamics techniques, where the movement of individual atoms is calculated. (gauss-centre.eu)
  • Study on the molecular dynamics of petroleum-derived asphaltene aggregate," Acta Petrolei Sinica (Petroleum Processing Section) , vol. 23, no. 4, pp. 25-31, 2007. (hindawi.com)
  • The present study investigates the variation of static contact angle of a water droplet in equilibrium with a solid surface in the absence of a body force and the dynamic contact angles of water droplet moving on a solid surface for different characteristic energies using the molecular dynamics simulation. (nih.gov)
  • It is necessary to have a molecular level profound knowledge of gas transport in bulk and interface regimes of different polymers, but few researchers have done molecular level study of bulk and interface behavior of gases in several types of non-homologen polymers thoroughly or developed expressions to correlate gas transport properties with cavity size distribution and chain oscillation flexibility. (rsc.org)
  • Finally, nonequilibrium MD simulation was done to study the interface property and gas transport in the interface region, where the ratio of free volume are apparently higher than that in the bulk, offering penetrants more chances to get into the interface region from gas phase. (rsc.org)
  • Summary of molecular dynamics simulations of human hemoglobin A carried out for the present study. (plos.org)
  • Caflisch A, Paci E (2005) Molecular dynamics simulations to study protein folding and unfolding. (springer.com)
  • The aim of this work is to estimate the value of the electric field (potentials) for the system of valinomycin + К+ and Na+ ions based on a molecular dynamics (MD) study. (scirp.org)
  • Forester, T.R., Smith, W. and Clarke, J.H.R. (1995) Capture of potassium ions by valinomycin: A molecular dynamics simulation study. (scirp.org)
  • Molecular dynamics (MD) simulation has been carried out for study of size effects on physical properties of Al nanoclusters with different sizes (N = 256, 500, 864, 1372, 2048 and 4000) in the temperature range 300 K ≤ T ≤ 1200 K for both free and periodic boundary conditions. (scirp.org)
  • We study the microscopic details of this transition using molecular dynamics simulations of atomistic models in implicit and explicit solvent. (wiley.com)
  • In this research, a series of large-scale molecular dynamics simulations have been conducted to study ion transport inside the endothelial glycocalyx layer under varying flow velocities. (frontiersin.org)
  • Molecular dynamics (MD) simulation was performed to study the stress induced grain boundary migration caused by the interaction of dislocations with a grain boundary. (scientific.net)
  • We then determine in detail the spatial distributions of different observables, that are related to the thermocapillary effect, and study their influences in parameter variations of the simulation system. (tu-darmstadt.de)
  • A numerical study of dynamics of a temporally evolving swirling jet. (ebscohost.com)
  • Molecular dynamics (MD) and binary collision approximation (BCA) computer simulations are employed to study surface damage by single ion impacts. (harvard.edu)
  • Molecular dynamics simulations have been used here to study the interaction of cardiotoxins A3 and A4 from Naja atra cobra venom with hydrated 1-palmitoyl-2-oleoyl-1- sn -3-phosphatidylcholine (POPC) lipid bilayer in two separate systems. (scientific.net)
  • We use the molecular dynamics computer simulation technique to study the behavior of electron plasmas in the presence of highly charged ions and strong magnetic fields. (cnki.net)
  • A new nonequilibrium molecular dynamics computer simulation method has been developed for the study of rapid interface kinetics. (cnki.net)
  • Our study was inspired by the convergence of sample size in experiments and simulations," explains Wu. (phys.org)
  • Citation Guardia, E., Skarmoutsos, I., Masia, M. Hydrogen bonding and related properties in liquid water: a Car-Parrinello molecular dynamics simulation study. (upc.edu)
  • These simulations are conducted for a variety of purposes such as to analyze the stability and dynamics of the structures around crystal structures and to determine folding from an extended structure into a native structure. (springer.com)
  • We report that enhancing the sampling of the simulations can generate an ensemble of IDP structures in quantitative agreement with scattering and NMR, without the need for biasing the simulation or reweighting the results. (pnas.org)
  • Brodie NI, Konstantin I, Petrochenko EV, Dokholyan NV, Brochers CH (2017) Solving protein structures using short-distance cross-linking constraints as a guide for discrete molecular dynamics simulations. (springer.com)
  • We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. (omicsonline.org)
  • In virtually all such simulations, a key challenge is to select one or more input structures that represent the real polymer matrix at the nanoscale. (nanohub.org)
  • Molecular dynamics simulations and homology modeling demonstrated that QnrC overall adopts a stable b-helix fold and shares more similarities with MfpA than with other PRP structures. (ebscohost.com)
  • A practical method to create optimized amorphous silicon and silica structures for molecular dynamics simulations is developed and tested. (harvard.edu)
  • In order to provide a detailed understanding of the origin of selectivity determinants of ATP competitive inhibitors, molecular dynamics simulations in combination with MM-PBSA binding energy calculations were performed using crystal structures of GSK-3β and CDK-2 in complex with 12 ATP competitive inhibitors. (figshare.com)
  • In the first part of this work, which includes Chapters 2-5, the electronic structures of ETD-formed z-fragment ions were studied in detail using tandem mass spectrometry and molecular dynamics simulations. (washington.edu)
  • 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. (chemaxon.com)
  • GROMACS is a full-featured suite of programs to perform molecular dynamics simulations, i.e., to simulate the behavior of systems with hundreds to millions of particles using Newtonian equations of motion. (ubuntu.com)
  • On long time behavior of Moore-Gibson-Thompson equation with molecular relaxation. (aimsciences.org)
  • Alper, H.E. and Politzer, P. (1999) Molecular Dynamics Simulation of the Temperature-Dependent Behavior of Solid Copper. (scirp.org)
  • We performed a molecular dynamics computer simulation to determine if the PTC mechanism is responsible for the observed behavior of Δζ. (cnki.net)
  • Here we use molecular dynamics simulation to investigate trends in cation and water diffusion in montmorillonite interlayers, looking specifically at the effects of layer charge, interlayer cation and cation charge (sodium or calcium), water content, and temperature. (osti.gov)
  • In this paper, we investigate the initialization of the microscopic simulator using the macroscopic variables only (called lifting in the equation-free framework) when the microscopic model is a molecular dynamics (MD) description of a mono-atomic dense fluid. (aimsciences.org)
  • Computer simulations are an invaluable means to investigate microscopic systems and thereby provide a unique, atomistic perspective of important states and processes. (bl.uk)
  • The MD simulations under external forces imitating the repulsion between lipid bilayers enabled us to investigate unraveling and assembly of the SNARE complex. (springer.com)
  • The AIMD simulations are performed for binary diffusion systems to investigate the diffusion between the liquid Co matrix and one type of alloying element. (diva-portal.org)
  • Direct numerical simulation (DNS) of a swirling jet near the outlet of a nozzle with axisymmetric and non-axisymmetric disturbances is performed to investigate the dynamic characteristics of the flow. (ebscohost.com)
  • With traditional all-atom molecular modeling techniques it is difficult to investigate the dynamics of long time scales or large systems, such as protein aggregation or activation. (pubmedcentralcanada.ca)
  • Molecular dynamics simulations, both classical and Car-Parrinello, have been carried out to investigate ubiquinone (UQ), a proton mediator in both oxidative and photo-phosphorylation. (diva-portal.org)
  • THE behaviour of molecular hydrogen at high pressures has implications for the interiors of the giant planets, which consist mainly of hydrogen. (nature.com)
  • In particular, the question of whether solid hydrogen becomes metallic under these conditions has been much debated 1-9 , in part because the structure that molecular hydrogen adopts at high pressure is not known. (nature.com)
  • Here we report the results of first-principles molecular dynamics simulations of solid hydrogen at pressures up to 270 GPa. (nature.com)
  • Although limitations on the simulation time and size may result in an over-estimate of the absolute pressure, our calculations show that solid hydrogen does not become metallic, even at pressures approaching 260 GPa. (nature.com)
  • Simulation also supported a favourable hydrogen bond distance between the purine C6-amino group and Asp-243 at 2.83 and 2.88 Å for each construct respectively. (portlandpress.com)
  • The Asn-243-Thr substitution did not yield activity with adenosine and simulation gave unfavourable hydrogen bond distances between Thr-243 and both the C6-amino group and N7 of the purine ring. (portlandpress.com)
  • The local hydrogen-bonding structure and dynamics of liquid water have been investigated using the Car-Parrinello molecular dynamics simulation technique. (upc.edu)
  • 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. (upc.edu)
  • They include the analysis of fluorescence depolarization of tryptophan residues 7 , the role of dynamics in measured NMR parameters 8 and inelastic neutron scattering 9 , the effect of solvent and temperature on protein structure and dynamics Why molecular dynamics simulations are important Simulations can provide the ultimate detail concerning individual particle motions as a function of time. (psu.edu)
  • An analysis of the molecular dynamics (МD) of the interaction between a carbon nanotube (CNT) and a carbon disulfide active solvent (CS2) has been carried out. (scirp.org)
  • Kholmurodov, K. , Aru, G. and Yasuoka, K. (2010) Molecular dynamics simulations of the interaction of carbon nanotube and a carbon disulfide solvent. (scirp.org)
  • Aksenov, V.L., Avdeev, M.V. and Kholmurodov, Kh.T. (2007) Organization of solvent at interface with fullerene in solution C60/carbon disulfide by molecular bynamics simulations. (scirp.org)
  • Thus, in this work we studied the dynamics and stability profiles of wild-type human prion protein by Molecular Dynamics (MD) simulation at different solvent temperatures. (scirp.org)
  • Frontiers in Molecular Biosciences. (uio.no)
  • Since these experiments are generally conducted in solvents, it is necessary to simulate protein and water molecular systems, which are complicated systems. (springer.com)
  • This thesis explores how two molecular dynamics methodologies can simulate the translocation of nucleotides through the nanopore α-hemolysin. (bl.uk)
  • In recent years, the composites community has increasingly used molecular dynamics to simulate and explore material properties such as glass-transition temperature and yield strain. (nanohub.org)
  • This is particularly important because theoretical estimates of systematic errors inherent in simulations have not been possible -that is, the errors introduced by the use of empirical potentials are difficult to quantify. (psu.edu)
  • Another significant aspect of simulations is that, although the potentials used in simulations are approximate, they are completely under the control of the user, so that by removing or altering specific contributions their role in determining a given property can be examined. (psu.edu)
  • Computer simulation using the molecular dynamics (MD) technique have been carried out on amorphous silicon nitride (a-Si_3N_4) with simple Busing-type potentials. (nii.ac.jp)
  • Two many-body interatomic potentials for the atomistic simulation of radiation effects in the Fe-Cr system have been recently proposed. (spie.org)
  • 4] Huang W.N., Sue, S.C., Wang, D.S., Wu, P.L., Wu,W.G. (2003) Peripheral binding mode and penetration depth of cobra cardiotoxin on phospholipid membranes as studied by a combined FTIR and computer simulation approach. (scientific.net)
  • Doshi U, Hamelberg D (2015) Towards fast, rigorous and efficient conformational sampling of biomolecules: advances in accelerated molecular dynamics. (springer.com)
  • Karplus M, McCammon JA (2002) Molecular dynamics simulations of biomolecules. (springer.com)
  • Results of the virtual and atomic wall simulations agree well with each other, thereby indicating the usefulness of the virtual-wall model. (mdpi.com)
  • The simulation results also indicate the GaN SW potential, which was originally developed for studying the atomic-level structure of dislocations, is not suitable for prediction of its thermal conductivity. (osti.gov)
  • Molecular Dynamics Computer simulation of objects and materials at the atomic scale is becoming an increasingly important tool for physicists. (cnki.net)
  • A molecular dynamics trajectory is accessed through the trajectory attribute, which is an instance of a Reader class. (nih.gov)
  • Additionally, molecular dynamics simulation trajectory showed that the stereo-specific localization of glutathione moiety in the hydrophobic groove across the globin subunit interface of tetrameric HbS might contribute to inhibition in polymerization. (biochemj.org)
  • The in situ observations, combined with large-scale reactive molecular dynamics simulations, reveal the details of the transformation from solid metal nanoparticles to hollow metal oxide nanoshells via a nanoscale Kirkendall process-for example, coalescence of voids as they grow and reversal of mass diffusion direction depending on crystallinity. (phys.org)
  • Here, we have been able to quantitatively reconstruct the complete binding process of the enzyme-inhibitor complex trypsin-benzamidine by performing 495 molecular dynamics simulations of free ligand binding of 100 ns each, 187 of which produced binding events with an rmsd less than 2 Å compared to the crystal structure. (pnas.org)
  • The simulations also allowed us to elucidate the local side-chain dynamical variations in ligand-bound mutant receptors. (nih.gov)
  • The library was subjected to rigid receptor docking, quantum polarized ligand docking, and induced fit docking followed by molecular mechanics-generalized born and surface area calculations resulted in two compounds possess the best scoring functions (XP GScore). (ijpsonline.com)
  • Using MD simulation techniques at the atomistic level allows for the exploration of ligand positioning and the initialization of protein activation. (pubmedcentralcanada.ca)
  • In recent years, it has become possible to perform simulations on time scales of the order of milliseconds using special hardware. (springer.com)
  • Recently, it has become possible to perform simulations at the millisecond scale by using special hardware such as Anton (Lindorff-Larsen et al. (springer.com)
  • The method makes possible to perform simulations of either very large cluster hypervelocity impacts on amorphous targets or small displacements induced by low energy ion impacts in silicon. (harvard.edu)
  • Snapshots of the 3-D structure of iron nanoparticles in the course of the oxidation process, captured through large-scale reactive molecular dynamic simulations. (phys.org)
  • Journal of Molecular Biology, 376(1), 13-22. (scirp.org)
  • Protein folding is an important subject not only for basic research in molecular biology but also for understanding folding diseases and designing new polymeric materials ( Dill and MacCallum, 2012 ). (elifesciences.org)
  • We go beyond previous MD simulations of interfacial systems by considering also stationary nonequilibrium situations, which are technically more challenging to implement. (tu-darmstadt.de)
  • Based on molecular dynamics simulations, an analysis of structure and dynamics is performed on interfacial water at a liquid crystalline dipalmitoylphosphatidycholine/water system. (diva-portal.org)
  • Miao Y, McCammon JA (2016) G-protein coupled receptors: advances in simulation and drug discovery. (springer.com)
  • There is an exciting opportunity to apply for a PhD studentship in the area of protein NMR and molecular dynamics simulations methodologies to support chemical probes development. (weizmann.ac.il)
  • Available estimated literature values based on calculations (scaling laws, a modified Sutherland equation and classical molecular dynamics) will be used to compare the results in a first instance. (diva-portal.org)
  • This orientation has changed during first 50 ns of classical molecular dynamics simulation for both of studied cytotoxins. (scientific.net)
  • We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. (nature.com)
  • The effect of the length in the simulations results was also observed where shorter bilayers showed lower strain for pore formation compared to longer bilayers. (diva-portal.org)
  • Molecular dynamics simulations of hydrophilic pores in lipid bilayers. (semanticscholar.org)
  • article{Leontiadou2004MolecularDS, title={Molecular dynamics simulations of hydrophilic pores in lipid bilayers. (semanticscholar.org)
  • Simulation of the spontaneous aggregation of phospholipids into bilayers. (semanticscholar.org)
  • Simulation of pore formation in lipid bilayers by mechanical stress and electric fields. (semanticscholar.org)
  • We present MDMap, a system designed to summarize long-running molecular dynamics (MD) simulations. (umd.edu)
  • With the description of the algorithms and the presentation of the results of various simulations from the areas material science, nanotechnology, biochemistry and astrophysics, the reader of this book will be able to write his own programs for molecular dynamics step by step and to run successful experiments. (springer.com)
  • Of course, experiments play an essential role in validating the simulation methodology: comparisons of simulation and experimental data serve to test the accuracy of the calculated results and to provide criteria for improving the methodology. (psu.edu)
  • The results from such simulations are then often compared with experimental results. (springer.com)
  • Our results show that the breaking dynamics is strongly temperature dependent, giving rise to remarkable changes in the computed histograms. (environmental-expert.com)
  • A slight difference in strain for pore formation between single and parallel bilayer was found which showed the bilayer structure can play a role in simulation results. (diva-portal.org)
  • The results from the present AIMD simulations could be shown to be in good agreement with the literature. (diva-portal.org)
  • Although the results from those simulations are not available to this date. (diva-portal.org)
  • The two approaches of the diffusion simulations in the binary and multicomponent system are giving matching results. (diva-portal.org)
  • MD and BCA simulation results for crystalline W are found to be in a good agreement even at small displacements, while in crystalline Si there is some difference due to displacements in amorphous pockets. (harvard.edu)
  • The repulsion term is constructed using hard sphere molecular dynamics computer simulation results with a modified Carnahan-Starling function. (cnki.net)
  • Here, we present the results of unbiased molecular dynamics simulations of the HAMP domain from the archaeal phototaxis signal transducer NpHtrII. (inria.fr)
  • The observed features are in good agreement with recent experimental results and allow us to propose that the states detected in the simulations are the resting state and the signaling state of the NpHtrII HAMP domain. (inria.fr)
  • Our results highlight the complex interplay between defect chemistry and defect dynamics in determining nanoparticle transformation and formation. (phys.org)
  • The bulk thermal conductivity of Stillinger-Weber (SW) wurtzite GaN in the [0001] direction at a temperature of 300 K is calculated using equilibrium molecular dynamics (EMD), non-equilibrium MD (NEMD), and lattice dynamics (LD) methods. (osti.gov)
  • In the first methodology, non-equilibrium constant velocity-steered simulations are combined with Jarzynski's identity to derive the free energy profiles for the passage of a polynucleotide molecule through the pore. (bl.uk)
  • Employing both equilibrium and Steered MD (SMD) simulations, the pathway and mechanism of substrate unbinding from the IF state of the vSGLT have been investigated. (illinois.edu)
  • During a 200-ns equilibrium simulation, repeated spontaneous unbinding events of the substrate from its binding site have been observed. (illinois.edu)
  • Now, Zhaoxuan Wu and co-workers at the A*STAR Institute of High Performance Computing in Singapore and the University of Pennsylvania, United States, have used large-scale molecular dynamics simulations to demonstrate the main deformation mechanisms in nanocrystalline nickel nanowires. (phys.org)
  • Analyzing molecular dynamics (MD) simulations is a key aspect to understand protein dynamics and function. (muni.cz)
  • Protein dynamics connect protein structure to function. (umich.edu)
  • The long term goal of the Nam research lab is to understand how large-scale protein dynamics and local fluctuations determine protein function at the molecular level. (umich.edu)
  • The two examples highlight the central role of protein dynamics on the control of protein activity. (umich.edu)
  • It is important to extract the characteristic degrees of freedom (order parameters) from the complex protein movements obtained from simulations, which are good indicators for analyzing trajectories. (springer.com)
  • MDMap automatically determines potential intermediate conformations and the transitions amongst them by analyzing the conformational space explored by the MD simulation. (umd.edu)
  • This is most graphically demonstrated by the use of 'computer alchemy' -transmuting the potential from that representing one system to another during a simulation -in the calculation of free energy differences There are three types of applications of simulation methods in the macromolecular area, as well as in other areas involving mesoscopic systems. (psu.edu)
  • Although some analysis methods for protein systems have been developed using increasing simulation times, many of these methods are static in nature (i.e., no information on time). (springer.com)
  • Investigation of Ribosomes Using Molecular Dynamics Simulation Methods. (umassmed.edu)
  • Non-adiabatic molecular dynamics methods have been developed for the calculation of charge carrier dynamics, with a focus on large molecular and materials systems. (washington.edu)
  • In this dissertation we first give an overview of two of the most popular methods for non-adiabatic molecular dynamics: Ehrenfest dynamics and fewest switches surface hopping (FSSH). (washington.edu)
  • These parallel methods are based on a spatial decomposition of the simulation box, that takes advantage of a linked-cell list. (spie.org)
  • 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. (spie.org)
  • and (e) performing accurate all-atom dynamics simulations by tracking their output energies, temperature, pressure, etc. (simtk.org)
  • The situation is even more complicated since the shape and the chemical properties of the catalyst itself depend on the molecular composition as well as the thermodynamic state (determined by temperature and pressure) of the surrounding gas phase [1,2]. (gauss-centre.eu)
  • A molecular dynamics simulation of water (TIP4P model) at 298 K and 1 atm pressure. (wikimedia.org)
  • Qian L, Tu C, Bao F, Zhang Y. Virtual-Wall Model for Molecular Dynamics Simulation. (mdpi.com)
  • Dynamics of a nonlocal SIS epidemic model with free boundary. (aimsciences.org)
  • Dokhoylan NV, Buldyrev SV, Stanley HE, Shakhnovich EI (1998) Discrete molecular dynamics studies of the folding of a protein-like model. (springer.com)
  • Bykhovskaia M, Jagota A, Gonzalez A, Vasin A, Littleton JT (2013) Interaction of the complexin accessory helix with the C-terminus of the SNARE complex: molecular-dynamics model of the fusion clamp. (springer.com)
  • Molecular dynamics simulations (50 ns) in the solvated model system determined consistency nature of AroB-lead 1 over the AroB-carbaphosphonate complex. (ijpsonline.com)
  • MD simulations over 400 μs led to an initial Markov state model (MSM), which was then "refined" using single-molecule Förster resonance energy transfer (FRET) data through hidden Markov modeling. (elifesciences.org)
  • Thus, this work is aimed to provide insight into them by using a molecular dynamics approximation to the problems. (scirp.org)
  • Such a simulation could be considered as a numerical experiment, since the underlying assumptions are so fundamental that the system should, depending on their approximation of reality, also behave realistic on a larger scale in many situations. (tu-darmstadt.de)
  • We construct an analytical approximation (i.e. a surrogate or emulator) of the simulations, treating the input structure energy and size as adjustable calibration parameters. (nanohub.org)
  • Duan Y, Kollman PA (1998) Pathways to a protein folding intermediate observed in a 1-microsecond simulation in aqueous solution. (springer.com)
  • In addition, I will discuss our recent progress on elucidating the catalytic mechanism of protein tyrosine kinase by multiscale quantum mechanical and molecular mechanical simulations. (umich.edu)
  • Our expressions for the nonlinear time-dependent response are tested against nonequilibrium molecular dynamics computer simulation of two simple nonautonomous systems. (cnki.net)
  • Here, we performed independently small-angle neutron and X-ray scattering experiments and unbiased molecular dynamics simulations to probe the solution structure of an IDP. (pnas.org)
  • The a-Si_3N_4 structure can be reproduced by our MD simulation. (nii.ac.jp)
  • Valinomycin's molecular structure efficiently surrounds the K+ ion, as this structure has to exactly correspond to the K+ ion in size. (scirp.org)
  • Journal of Molecular Structure: THEOCHEM, 487,117-125. (scirp.org)
  • Journal of Molecular Structure: THEOCHEM, 867, 39-46. (scirp.org)
  • Leidner F, Kurt Yilmaz N, Paulsen J, Muller YA, Schiffer CA. Hydration Structure and Dynamics of Inhibitor-Bound HIV-1 Protease. (umassmed.edu)
  • dynamics on cisplatin/DNA adducts in the free from and complexed to the HMG protein domain A. Since this method allows for a parameter free treatment of the Pt-moiety and includes as well the DNA environment, we gain accurate insight into the structure of the drug/DNA complex. (epfl.ch)
  • By applying molecular simulation techniques, we have trapped an intermediate state structure of F1-ATPase, which has eluded its experimental determination despite biophysical evidence for its existence, and showed how the release of ATP hydrolysis product is coupled to large-scale conformational changes of the enzyme. (umich.edu)
  • Moreover, the methodology is directly applicable to other molecular systems and thus of general interest in biomedical and pharmaceutical research. (pnas.org)
  • The MD/OPX code is designed for the simulation of nanoscale systems with all-atom resolution over milliseconds or longer. (simtk.org)
  • Then 25 ns steered molecular dynamics simulation has been done for both of systems. (scientific.net)
  • The Molecular Simulations and Design group is a Max Planck Research Group at the Max Planck Institute for Dynamics of Complex Technical Systems. (mpg.de)
  • The 7th Summer School on Applied Mathematics and Mechanics will be held from 27 to 31 July 2020 at the Max Planck Institute for Dynamics of Complex Technical Systems in Magdeburg. (mpg.de)
  • Marcus Wenzel, former scientist at the Max Planck Institute for Dynamics of Complex Technical Systems Magdeburg, received the Otto Hahn Medal, awarded by the Max Planck Society. (mpg.de)
  • There are three difficulties in current approaches for protein simulations (Freddolino et al. (springer.com)
  • M. P. Allen and D. J. Tildesley, Computer Simulation of Liquids , Clarendon Press, 1987. (hindawi.com)
  • Journal of Molecular Liquids, 110(13), 36. (scirp.org)
  • However, it is still a challenge to achieve quantitative agreement between simulation and experimental data during the entire folding process, owing not only to simulation time limitations but also to inherent force-field biases. (elifesciences.org)
  • To this end, a coarse time stepper for the macroscopic variables can be constructed, based on appropriately initialized microscopic simulations. (aimsciences.org)
  • With respect to the folding mechanism, simulation at the millisecond scale is necessary. (springer.com)
  • However, the molecular mechanism of this damage is not yet completely cleared. (scientific.net)
  • The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation. (nature.com)
  • The dimensions of the pore fluctuate over the course of the simulation revealing it to be flexible, but only wide enough to allow transport of the passenger domain in an unfolded or extended conformation. (soton.ac.uk)
  • The simulations help us to understand the role of the central helix in plugging the pore and in maintaining the width of the barrel, and show that the NalP monomer is sufficient for the transport of the passenger domain in an unfolded or extended conformation. (soton.ac.uk)
  • Molecular dynamics simulations of pore formation dynamics during the rupture process of a phospholipid bilayer caused by high-speed equibiaxial stretching. (semanticscholar.org)
  • In the second methodology, the free energy profiles are calculated from a biasing force which varies in response to energy barriers encountered during the simulation. (bl.uk)
  • We review the basics of MD simulation methodology, the successes achieved through MD simulation in animal PKs, and current work on plant PKs using MD simulation. (biochemj.org)

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