###### Quantum Theory

###### Models, Molecular

###### Thermodynamics

A rigorously mathematical analysis of energy relationships (heat, work, temperature, and equilibrium). It describes systems whose states are determined by thermal parameters, such as temperature, in addition to mechanical and electromagnetic parameters. (From Hawley's Condensed Chemical Dictionary, 12th ed)

###### Computer Simulation

###### Models, Chemical

###### Radiometry

###### Mathematics

###### Algorithms

###### Monte Carlo Method

In statistics, a technique for numerically approximating the solution of a mathematical problem by studying the distribution of some random variable, often generated by a computer. The name alludes to the randomness characteristic of the games of chance played at the gambling casinos in Monte Carlo. (From Random House Unabridged Dictionary, 2d ed, 1993)

###### Software

###### Drug Dosage Calculations

###### Hydrogen Bonding

###### Models, Theoretical

###### Molecular Dynamics Simulation

###### Water

###### Protein Conformation

The characteristic 3-dimensional shape of a protein, including the secondary, supersecondary (motifs), tertiary (domains) and quaternary structure of the peptide chain. PROTEIN STRUCTURE, QUATERNARY describes the conformation assumed by multimeric proteins (aggregates of more than one polypeptide chain).

###### Electrons

Stable elementary particles having the smallest known negative charge, present in all elements; also called negatrons. Positively charged electrons are called positrons. The numbers, energies and arrangement of electrons around atomic nuclei determine the chemical identities of elements. Beams of electrons are called CATHODE RAYS.

###### Molecular Structure

###### Sample Size

###### Models, Biological

###### Radiotherapy Planning, Computer-Assisted

###### Reproducibility of Results

The statistical reproducibility of measurements (often in a clinical context), including the testing of instrumentation or techniques to obtain reproducible results. The concept includes reproducibility of physiological measurements, which may be used to develop rules to assess probability or prognosis, or response to a stimulus; reproducibility of occurrence of a condition; and reproducibility of experimental results.

###### Magnetic Resonance Spectroscopy

###### Radiation Dosage

The amount of radiation energy that is deposited in a unit mass of material, such as tissues of plants or animal. In RADIOTHERAPY, radiation dosage is expressed in gray units (Gy). In RADIOLOGIC HEALTH, the dosage is expressed by the product of absorbed dose (Gy) and quality factor (a function of linear energy transfer), and is called radiation dose equivalent in sievert units (Sv).

###### Protons

###### Solutions

###### Models, Statistical

###### Solvents

###### Crystallography, X-Ray

###### Mathematical Computing

###### Phantoms, Imaging

Devices or objects in various imaging techniques used to visualize or enhance visualization by simulating conditions encountered in the procedure. Phantoms are used very often in procedures employing or measuring x-irradiation or radioactive material to evaluate performance. Phantoms often have properties similar to human tissue. Water demonstrates absorbing properties similar to normal tissue, hence water-filled phantoms are used to map radiation levels. Phantoms are used also as teaching aids to simulate real conditions with x-ray or ultrasonic machines. (From Iturralde, Dictionary and Handbook of Nuclear Medicine and Clinical Imaging, 1990)

###### Entropy

###### Proteins

Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.

###### Binding Sites

###### Energy Transfer

The transfer of energy of a given form among different scales of motion. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed). It includes the transfer of kinetic energy and the transfer of chemical energy. The transfer of chemical energy from one molecule to another depends on proximity of molecules so it is often used as in techniques to measure distance such as the use of FORSTER RESONANCE ENERGY TRANSFER.

###### Ions

###### Electrochemistry

###### Chemistry, Physical

###### Gases

The vapor state of matter; nonelastic fluids in which the molecules are in free movement and their mean positions far apart. Gases tend to expand indefinitely, to diffuse and mix readily with other gases, to have definite relations of volume, temperature, and pressure, and to condense or liquefy at low temperatures or under sufficient pressure. (Grant & Hackh's Chemical Dictionary, 5th ed)

###### Sensitivity and Specificity

###### Nuclear Magnetic Resonance, Biomolecular

###### Hydrogen

The first chemical element in the periodic table. It has the atomic symbol H, atomic number 1, and atomic weight [1.00784; 1.00811]. It exists, under normal conditions, as a colorless, odorless, tasteless, diatomic gas. Hydrogen ions are PROTONS. Besides the common H1 isotope, hydrogen exists as the stable isotope DEUTERIUM and the unstable, radioactive isotope TRITIUM.

###### Protein Structure, Secondary

###### Protein Binding

###### Numerical Analysis, Computer-Assisted

###### Physicochemical Phenomena

###### Data Interpretation, Statistical

###### Relative Biological Effectiveness

###### Ligands

A molecule that binds to another molecule, used especially to refer to a small molecule that binds specifically to a larger molecule, e.g., an antigen binding to an antibody, a hormone or neurotransmitter binding to a receptor, or a substrate or allosteric effector binding to an enzyme. Ligands are also molecules that donate or accept a pair of electrons to form a coordinate covalent bond with the central metal atom of a coordination complex. (From Dorland, 27th ed)

###### Diffusion

###### Radioisotopes

###### Hydrogen-Ion Concentration

###### Film Dosimetry

###### Nucleic Acid Conformation

###### Computational Biology

A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets.

###### Optics and Photonics

###### Temperature

###### Computer Graphics

###### Molecular Sequence Data

Descriptions of specific amino acid, carbohydrate, or nucleotide sequences which have appeared in the published literature and/or are deposited in and maintained by databanks such as GENBANK, European Molecular Biology Laboratory (EMBL), National Biomedical Research Foundation (NBRF), or other sequence repositories.

###### Statistics as Topic

###### Stereoisomerism

###### Amino Acid Sequence

###### Motion

###### Photons

###### Scattering, Radiation

###### Biometry

###### Imaging, Three-Dimensional

The process of generating three-dimensional images by electronic, photographic, or other methods. For example, three-dimensional images can be generated by assembling multiple tomographic images with the aid of a computer, while photographic 3-D images (HOLOGRAPHY) can be made by exposing film to the interference pattern created when two laser light sources shine on an object.

###### Spectrum Analysis

###### Image Processing, Computer-Assisted

###### Models, Structural

###### Vibration

###### Fourier Analysis

Analysis based on the mathematical function first formulated by Jean-Baptiste-Joseph Fourier in 1807. The function, known as the Fourier transform, describes the sinusoidal pattern of any fluctuating pattern in the physical world in terms of its amplitude and its phase. It has broad applications in biomedicine, e.g., analysis of the x-ray crystallography data pivotal in identifying the double helical nature of DNA and in analysis of other molecules, including viruses, and the modified back-projection algorithm universally used in computerized tomography imaging, etc. (From Segen, The Dictionary of Modern Medicine, 1992)

###### Catalysis

###### Structure-Activity Relationship

###### Mathematical Concepts

###### DNA

A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine).

###### X-Ray Diffraction

The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

###### Crystallography

###### Lipid Bilayers

###### Peptides

Members of the class of compounds composed of AMINO ACIDS joined together by peptide bonds between adjacent amino acids into linear, branched or cyclical structures. OLIGOPEPTIDES are composed of approximately 2-12 amino acids. Polypeptides are composed of approximately 13 or more amino acids. PROTEINS are linear polypeptides that are normally synthesized on RIBOSOMES.

###### Oxidation-Reduction

A chemical reaction in which an electron is transferred from one molecule to another. The electron-donating molecule is the reducing agent or reductant; the electron-accepting molecule is the oxidizing agent or oxidant. Reducing and oxidizing agents function as conjugate reductant-oxidant pairs or redox pairs (Lehninger, Principles of Biochemistry, 1982, p471).

###### Research Design

###### Organometallic Compounds

###### Protein Structure, Tertiary

The level of protein structure in which combinations of secondary protein structures (alpha helices, beta sheets, loop regions, and motifs) pack together to form folded shapes called domains. Disulfide bridges between cysteines in two different parts of the polypeptide chain along with other interactions between the chains play a role in the formation and stabilization of tertiary structure. Small proteins usually consist of only one domain but larger proteins may contain a number of domains connected by segments of polypeptide chain which lack regular secondary structure.

###### Catalytic Domain

###### Spectrum Analysis, Raman

###### Models, Genetic

###### Spectrophotometry, Infrared

###### Iron Compounds

###### Surface Properties

###### Body Burden

###### Models, Anatomic

###### Nitrogen Isotopes

###### Likelihood Functions

###### Crystallization

###### Oxygen

###### Refractometry

###### Calibration

###### Ytterbium

###### Enzymes

###### Titrimetry

The determination of the concentration of a given component in solution (the analyte) by addition of a liquid reagent of known strength (the titrant) until an equivalence point is reached (when the reactants are present in stoichiometric proportions). Often an indicator is added to make the equivalence point visible (e.g., a change in color).

###### Particle Accelerators

###### Pressure

###### Image Interpretation, Computer-Assisted

###### Chemistry, Organic

###### Neutrons

Electrically neutral elementary particles found in all atomic nuclei except light hydrogen; the mass is equal to that of the proton and electron combined and they are unstable when isolated from the nucleus, undergoing beta decay. Slow, thermal, epithermal, and fast neutrons refer to the energy levels with which the neutrons are ejected from heavier nuclei during their decay.

###### Isomerism

###### Iridium Radioisotopes

###### Reference Values

###### Circular Dichroism

###### Hydrophobic and Hydrophilic Interactions

###### Gramicidin

###### User-Computer Interface

###### Electronics

###### Mechanics

###### Physics

###### Observer Variation

The failure by the observer to measure or identify a phenomenon accurately, which results in an error. Sources for this may be due to the observer's missing an abnormality, or to faulty technique resulting in incorrect test measurement, or to misinterpretation of the data. Two varieties are inter-observer variation (the amount observers vary from one another when reporting on the same material) and intra-observer variation (the amount one observer varies between observations when reporting more than once on the same material).

###### Amino Acids

###### Isotopes

###### Computer-Aided Design

###### Radiotherapy, Conformal

###### Biomechanical Phenomena

###### Calorimetry

The measurement of the quantity of heat involved in various processes, such as chemical reactions, changes of state, and formations of solutions, or in the determination of the heat capacities of substances. The fundamental unit of measurement is the joule or the calorie (4.184 joules). (McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed)

###### Uncertainty

###### Normal Distribution

###### Molecular Docking Simulation

###### X-Ray Absorption Spectroscopy

###### Internet

###### Electron Spin Resonance Spectroscopy

A technique applicable to the wide variety of substances which exhibit paramagnetism because of the magnetic moments of unpaired electrons. The spectra are useful for detection and identification, for determination of electron structure, for study of interactions between molecules, and for measurement of nuclear spins and moments. (From McGraw-Hill Encyclopedia of Science and Technology, 7th edition) Electron nuclear double resonance (ENDOR) spectroscopy is a variant of the technique which can give enhanced resolution. Electron spin resonance analysis can now be used in vivo, including imaging applications such as MAGNETIC RESONANCE IMAGING.

###### Muramidase

A basic enzyme that is present in saliva, tears, egg white, and many animal fluids. It functions as an antibacterial agent. The enzyme catalyzes the hydrolysis of 1,4-beta-linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in peptidoglycan and between N-acetyl-D-glucosamine residues in chitodextrin. EC 3.2.1.17.

###### Physicochemical Processes

###### Nuclear Physics

###### Radiotherapy, Computer-Assisted

###### Models, Cardiovascular

###### Cyclization

###### Microscopy, Scanning Tunneling

A type of scanning probe microscopy in which a very sharp conducting needle is swept just a few angstroms above the surface of a sample. The tiny tunneling current that flows between the sample and the needle tip is measured, and from this are produced three-dimensional topographs. Due to the poor electron conductivity of most biological samples, thin metal coatings are deposited on the sample.

###### Iodine Radioisotopes

###### Membranes, Artificial

###### Tomography, X-Ray Computed

###### Mutation

###### Transition Elements

###### Finite Element Analysis

###### Biocatalysis

###### Coordination Complexes

Neutral or negatively charged ligands bonded to metal cations or neutral atoms. The number of ligand atoms to which the metal center is directly bonded is the metal cation's coordination number, and this number is always greater than the regular valence or oxidation number of the metal. A coordination complex can be negative, neutral, or positively charged.

###### Predictive Value of Tests

In screening and diagnostic tests, the probability that a person with a positive test is a true positive (i.e., has the disease), is referred to as the predictive value of a positive test; whereas, the predictive value of a negative test is the probability that the person with a negative test does not have the disease. Predictive value is related to the sensitivity and specificity of the test.

###### Optical Rotatory Dispersion

###### Stress, Mechanical

###### Quantitative Structure-Activity Relationship

###### Linear Models

###### Carbon

###### Magnetic Resonance Imaging

###### Base Pairing

###### Carbon Isotopes

###### Statistical Distributions

The complete summaries of the frequencies of the values or categories of a measurement made on a group of items, a population, or other collection of data. The distribution tells either how many or what proportion of the group was found to have each value (or each range of values) out of all the possible values that the quantitative measure can have.

###### Regression Analysis

Procedures for finding the mathematical function which best describes the relationship between a dependent variable and one or more independent variables. In linear regression (see LINEAR MODELS) the relationship is constrained to be a straight line and LEAST-SQUARES ANALYSIS is used to determine the best fit. In logistic regression (see LOGISTIC MODELS) the dependent variable is qualitative rather than continuously variable and LIKELIHOOD FUNCTIONS are used to find the best relationship. In multiple regression, the dependent variable is considered to depend on more than a single independent variable.

###### Sequence Alignment

The arrangement of two or more amino acid or base sequences from an organism or organisms in such a way as to align areas of the sequences sharing common properties. The degree of relatedness or homology between the sequences is predicted computationally or statistically based on weights assigned to the elements aligned between the sequences. This in turn can serve as a potential indicator of the genetic relatedness between the organisms.

###### Anisotropy

A physical property showing different values in relation to the direction in or along which the measurement is made. The physical property may be with regard to thermal or electric conductivity or light refraction. In crystallography, it describes crystals whose index of refraction varies with the direction of the incident light. It is also called acolotropy and colotropy. The opposite of anisotropy is isotropy wherein the same values characterize the object when measured along axes in all directions.

###### Risk Assessment

###### Macromolecular Substances

###### Prospective Studies

###### Spectrometry, Mass, Electrospray Ionization

A mass spectrometry technique used for analysis of nonvolatile compounds such as proteins and macromolecules. The technique involves preparing electrically charged droplets from analyte molecules dissolved in solvent. The electrically charged droplets enter a vacuum chamber where the solvent is evaporated. Evaporation of solvent reduces the droplet size, thereby increasing the coulombic repulsion within the droplet. As the charged droplets get smaller, the excess charge within them causes them to disintegrate and release analyte molecules. The volatilized analyte molecules are then analyzed by mass spectrometry.

###### Radiation Monitoring

The observation, either continuously or at intervals, of the levels of radiation in a given area, generally for the purpose of assuring that they have not exceeded prescribed amounts or, in case of radiation already present in the area, assuring that the levels have returned to those meeting acceptable safety standards.

###### Artifacts

Any visible result of a procedure which is caused by the procedure itself and not by the entity being analyzed. Common examples include histological structures introduced by tissue processing, radiographic images of structures that are not naturally present in living tissue, and products of chemical reactions that occur during analysis.

###### X-Rays

Penetrating electromagnetic radiation emitted when the inner orbital electrons of an atom are excited and release radiant energy. X-ray wavelengths range from 1 pm to 10 nm. Hard X-rays are the higher energy, shorter wavelength X-rays. Soft x-rays or Grenz rays are less energetic and longer in wavelength. The short wavelength end of the X-ray spectrum overlaps the GAMMA RAYS wavelength range. The distinction between gamma rays and X-rays is based on their radiation source.

###### Physical Phenomena

###### Signal Processing, Computer-Assisted

###### Blood Flow Velocity

###### Poisson Distribution

###### Cations

###### Fast Neutrons

###### Absorption

###### Equipment Failure Analysis

###### Radiation Oncology

###### Radiopharmaceuticals

###### Mass Spectrometry

###### Chemical Processes

###### Dimerization

###### Radiotherapy, Intensity-Modulated

###### Cattle

###### Least-Squares Analysis

###### WeNMR

... iCing Structure

**Calculation**: CS-ROSETTA • CYANA • UNIO • Xplor-NIH**Molecular**Dynamics: AMBER • GROMACS**Modelling**: 3D-DART • ... Van Dijk, M.; Bonvin, A. M. J. J. (2009). "3D-DART: A DNA structure**modelling**server". Nucleic Acids Research. 37 (Web Server ... "The CCPN data**model**for NMR spectroscopy: Development of a software pipeline". Proteins: Structure, Function, and ... integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural**modelling**. ...###### Basis set (chemistry)

When

**molecular****calculations**are performed, it is common to use a basis composed of atomic orbitals, centered at each nucleus ... Leach, Andrew R. (1996).**Molecular****Modelling**: Principles and Applications. Singapore: Longman. pp. 68-77. ISBN 978-0-582-23933- ... Dunning, Thomas H. (1989). "Gaussian basis sets for use in correlated**molecular****calculations**. I. The atoms boron through neon ... Davidson, Ernest; Feller, David (1986). "Basis set selection for**molecular****calculations**". Chem. Rev. 86 (4): 681-696. doi: ...###### Carbocation

"Ab initio

**calculations**of ionic hydrocarbon compounds with heptacoordinate carbon". Journal of**Molecular****Modeling**. 24 (5): 116 ... "Ab initio MO**calculations**of isotope effects in**model**processes of neopentyl ester solvolysis". The Journal of Organic ... In order for a carbocation to be resonance-stabilized, the**molecular**orbital of the donating group must have the proper ... Aue, Donald H. (2011). "Carbocations". WIREs Computational**Molecular**Science. 1 (4): 487-508. doi:10.1002/wcms.12. ISSN 1759- ...###### Planar hexacoordinate carbon

Journal of

**Molecular****Modeling**. 24 (5): 116. doi:10.1007/s00894-018-3640-9. ISSN 1610-2940. PMID 29696384. S2CID 13960338.. ... Wang, George; Rahman, A. K. Fazlur; Wang, Bin (May 2018). "Ab initio**calculations**of ionic hydrocarbon compounds with ... Planar hexacoordinate carbon in chemistry describes a**molecular**geometry featuring a planar arrangement of carbon with six ...###### Electron density

Most

**molecular****modeling**software packages allow the user to choose a value for the electron density, often called the isovalue ... A Guide to**Molecular**Mechanics and Quantum Chemical**Calculations**. Irvine, California: Wavefunction, Inc. pp. 85-100. ISBN 978-1 ...**Molecular****modeling**software often provides graphical images of electron density. For example, in aniline (see image at right). ... Warren J. Hehre, Alan J. Shusterman, Janet E. Nelson (1998). The**Molecular****Modeling**Workbook for Organic Chemistry. Irvine, ...###### Bradford protein assay

Mathematical

**Modeling**with Excel, p. 60, ISBN 978-0763765668 Stephenson, Frank Harold (2003),**Calculations**for**molecular**... Stephenson, Frank Harold (2003).**Calculations**for**molecular**biology and biotechnology: a guide to mathematics in the laboratory ... These should not be included**calculations**, as the equation given cannot apply to numbers outside of its limitations. In a large ... Albright, Brian (2009). Mathematical**Modeling**with Excel. p. 60. ISBN 978-0763765668. ...###### Reaction rate constant

First-principle based

**models**should be used for such**calculation**. It can be done with the help of computer simulation software ... Since a reaction requires a change in**molecular**geometry, unimolecular rate constants cannot be larger than the frequency of a ... making the temperature dependence of k different from both the Arrhenius and Eyring**models**. All three theories**model**the ... Here, A has the same dimensions as an (m + n)-order rate constant (see Units below). Another popular**model**that is derived ...###### Extensible Computational Chemistry Environment

Support for building

**molecular****models**. Graphical user interface to a broad range of electronic structure theory types. ... Remote submission of**calculations**to UNIX and Linux workstations, Linux clusters, and supercomputers. Supported queue ...**Molecular**orbitals and vibrational frequencies are among the properties displayed. Support for importing results from NWChem, ... Three-dimensional visualization and graphical display of**molecular**data properties while jobs are running and after completion ...###### Spartan (chemistry software)

Quantum chemical

**calculations**, including Hartree-Fock method**molecular**orbital**calculations**, but especially**calculations**that ... force fields**calculation**, Semi-empirical**calculations**, MNDO/MNDO(D), Austin**Model**1 (AM1), PM3, Recife**Model**1 (RM1) PM6. ... Spartan is a**molecular****modelling**and computational chemistry application from Wavefunction. It contains code for**molecular**... Molecule editor Comparison of software for**molecular**mechanics**modeling**List of software for Monte Carlo**molecular****modeling**...###### William Lipscomb

1966). "

**Molecular**Orbitals for Boron Hydrides Parameterized from SCF**Model****Calculations**". J. Am. Chem. Soc. 88 (11): 2361-2366 ...**Calculations**by these methods produced accurate Hartree-Fock self-consistent field (SCF)**molecular**orbitals and were used to ... Under Lipscomb's direction the Extended Hückel method of**molecular**orbital**calculation**was developed by Lawrence Lohr and by ... The**calculations**provided the first accurate values for the constants that describe the behavior of several types of molecules ...###### Basis set (chemistry)

When

**molecular****calculations**are performed, it is common to use a basis composed of atomic orbitals, centered at each nucleus ... Leach, Andrew R. (1996).**Molecular****Modelling**: Principles and Applications. Singapore: Longman. pp. 68-77. ISBN 978-0-582-23933- ... Hehre, Warren J.. (2003). A Guide to**Molecular**Mechanics and Quantum Chemical**Calculations**. Irvine, California: Wavefunction, ... Davidson, Ernest; Feller, David (1986). "Basis set selection for**molecular****calculations**". Chem. Rev. 86 (4): 681-696. doi: ...###### Mulliken population analysis

Leach, Andrew R. (2001).

**Molecular****modelling**: principles and applications. Englewood Cliffs, N.J: Prentice Hall. ISBN 0-582- ... I. G. Csizmadia, Theory and Practice of MO**Calculations**on Organic Molecules, Elsevier, Amsterdam, 1976. ... If the coefficients of the basis functions in the**molecular**orbital are Cμi for the μ'th basis function in the i'th**molecular**... Mulliken, R. S. (1955). "Electronic Population Analysis on LCAO-MO**Molecular**Wave Functions. I". The Journal of Chemical ...###### Pablo G. Debenedetti

"Direct

**calculation**of ice homogeneous nucleation rate for a**molecular****model**of water." PNAS, 112, 10582 (2015). P.G. ... "Direct**calculation**of ice homogeneous nucleation rate for a**molecular****model**of water". Proceedings of the National Academy of ... "Metastable liquid-liquid transition in a**molecular****model**of water." Nature, 510, 385 (2014). A. Haji-Akbari and P.G. ... his group demonstrated computationally the existence of a metastable liquid-liquid phase transition in a**molecular****model**of ...###### Mechanism of action

Journal of

**Molecular**Graphics and**Modelling**. 40: 99-109. doi:10.1016/j.jmgm.2012.12.013. PMID 23384979. Sharma, S.; Sharma, S. ... "Mechanism of the irreversible inhibition of human cyclooxygenase-1 by aspirin as predicted by QM/MM**calculations**". ... A mechanism of action usually includes mention of the specific**molecular**targets to which the drug binds, such as an enzyme or ... ISBN 978-1-4390-5616-5. Grant, R.L.; Combs, A.B.; Acosta, D. (2010) "Experimental**Models**for the Investigation of Toxicological ...###### Mechanism of action of aspirin

Journal of

**Molecular**Graphics and**Modelling**. 40: 99-109. doi:10.1016/j.jmgm.2012.12.013. PMID 23384979. Sharma S, Sharma SC ( ... "Mechanism of the irreversible inhibition of human cyclooxygenase-1 by aspirin as predicted by QM/MM**calculations**". ...###### Frank Westheimer

All of his

**calculations**were worked out by hand. The work became a**model**for studies of other elements and is considered ... with Joseph Edward Mayer on the**calculation**of**molecular**mechanics; explored the mechanisms of enzyme catalysis with Birgit ... Applications of**molecular**mechanics**calculations**". Annu. Rep. Prog. Chem., Sect. B: Org. Chem. 75: 23-35. doi:10.1039/ ... Their Kirkwood-Westheimer**model**for an ellipsoid cavity reconciles the work of Niels Bjerrum on dibasic acids with that of ...###### DOCK

AutoDock

**Molecular****modeling**Comparison of software for**molecular**mechanics**modeling**Kuntz, ID; Blaney, JM; Oatley, SJ; ... This ability accounts for receptor flexibility and allows for rank ordering by energetic ensembles in the docking**calculations**... Ewing, TJ; Makino, S; Skillman, AG; Kuntz, ID (2001). "DOCK 4.0: search strategies for automated**molecular**docking of flexible ... 2009). "DOCK 6: Combining techniques to**model**RNA-small molecule complexes". RNA. 15 (6): 1219-30. doi:10.1261/rna.1563609. PMC ...###### Alignment-free sequence analysis

...

**model**-free selection and parameter-free sensitivity**calculation**of spaced seeds". Algorithms for**Molecular**Biology. 12 (1): 1. ... In the context**modeling**complexity the next-symbol predictions, of one or more statistical**models**, are combined or competing to ...**molecular**phylogeny and subtyping".**Molecular**Phylogenetics and Evolution. 65 (2): 510-22. doi:10.1016/j.ympev.2012.07.003. ...**Molecular**sequence and structure data of DNA, RNA, and proteins, gene expression profiles or microarray data, metabolic pathway ...###### Reaction rate constant

Rate constant

**calculations**[edit]. Rate constant can be calculated for elementary reactions by**molecular**dynamics simulations. ... First-principle based**models**should be used for such**calculation**. It can be done with the help of computer simulation software ... Daru, János; Stirling, András (2014). "Divided Saddle Theory: A New Idea for Rate Constant**Calculation**". J. Chem. Theory Comput ...**Calculation**of rate constants of the processes of generation and relaxation of electronically and vibrationally excited ...###### Force field (chemistry)

Comparison of force field implementations

**Molecular**dynamics**Molecular**mechanics**Molecular**design software**Molecular****modelling**... "**Molecular**mechanics with fluctuating atomic charges-a new force field with a semi-empirical charge**calculation**".**Molecular**... "Tinker**Molecular****Modeling**Package". dasher.wustl.edu. Liu C, Piquemal JP, Ren P (January 2020). "Implementation of Geometry- ... In the context of chemistry and**molecular****modelling**, a force field is a computational method that is used to estimate the ...###### MOLCAS

Combined QM and

**molecular**mechanics**calculations**for systems such as proteins and**molecular**clusters. The NEMO procedure for ... Solvent effects can be treated by the Onsager spherical cavity**model**or Polarizable continuum**model**(PCM). ... and exchange-repulsion terms and are based on**calculations**for individual molecules. Tully Surface Hopping**Molecular**Dynamics ... In 2001 MOLCAS 5 has been released, featuring a distributed**model**for code development. In September 2017 the bulk of the ...###### Methylaluminoxane

Polymerization Mechanism and Kinetic

**Model**from Ab Initio**Molecular**Dynamics and Electronic Structure**Calculations**". J. Am. ...###### Phosphorus

Computer

**modeling**of**molecular**orbital theory indicates that this bonding involves only s- and p-orbitals. All four symmetrical ... Before extensive computer**calculations**were feasible, it was thought that bonding in phosphorus(V) compounds involved d ... Neufcourt, L.; Cao, Y.; Nazarewicz, W.; Olsen, E.; Viens, F. (2019). "Neutron drip line in the Ca region from Bayesian**model**...###### Angular momentum diagrams (quantum mechanics)

**Calculations**with real quantum systems, such as multielectron atoms and

**molecular**systems. Physics portal Vector

**model**of the ... ISBN 978-3-540-16649-8. G.W.F. Drake (2006). Springer Handbook of Atomic,

**Molecular**, and Optical Physics (2nd ed.). springer. p ... ISBN 978-1-4020-9975-5. G.H.F. Diercksen; S. Wilson (1983). Methods in Computational

**Molecular**Physics. NATO Science Series C. ... P.E.T. Jorgensen (1987). Operators and Representation Theory: Canonical

**Models**for Algebras of Operators Arising in Quantum ...

###### Ascalaph Designer

The

**molecular**mechanics**calculations**cover**model**building, energy optimizations and**molecular**dynamics. Firefly (formerly named ... Ascalaph Designer is a computer program for general purpose**molecular****modelling**for**molecular**design and simulations. It ... properties of liquids Chemical force field development List of software for**molecular**mechanics**modeling****Molecular**design ... family Geometry optimization**Molecular**dynamics Quantum chemistry Flexible SPC water**model**Nucleic acids Proteins**Modeling**...###### Constantin Bălăceanu-Stolnici

Journal of

**Molecular****Modeling**. 12 (2): 146-151. doi:10.1007/s00894-005-0007-9. Kozma, Andrei; Glavce, Cristiana; Bălăceanu- ... comparative HF and DFT**calculations**of the electronic properties of a complex between DHEA and serotonin". ...###### Virial stress

"The nature of the

**calculation**of the pressure in**molecular**simulations of continuous**models**from volume perturbations". The ... The expression of the (local) virial stress can be derived as the functional derivative of the free energy of a**molecular**... "The stress tensor of a**molecular**system: An exercise in statistical mechanics." The Journal of chemical physics 125.3 (2006): ... and using scaled coordinates in the**calculation**. If the system is not homogeneous in a given volume the above (volume averaged ...###### Clathrate hydrate

"A comparison of different water

**models**for melting point**calculation**of methane hydrate using**molecular**dynamics simulations". ... Most low**molecular**weight gases, including O2, H2, N2, CO2, CH4, H2S, Ar, Kr, and Xe, as well as some higher hydrocarbons and ... Their**calculations**revealed that, under 1 atm pressure, sI and sII empty hydrates are metastable regarding the ice phases up to ... employed**molecular**dynamics to perform a thorough and systematic study of several ice polymorphs, namely space fullerene ices, ...###### Crotamine

... based on computational

**calculations**that were supported with intensive**molecular**dynamics simulations and homology**modeling**... A crotamine amino acid sequence was compared to that of cloned DNA of myotoxin a, (the myotoxin used to**model**how SBPMs work). ... The structure and the shape of the protein was proposed through a 3D**model**generated by Siqueira et al. (2002) ... The amino acid sequence, YKQCHKKGGHCFPKEKICLPPSSDFGKMDCRWRWKCCKKGS-0, and the 3D**molecular**structure of crotamine have already ...###### Steroid hormone

A simplex search with implicit solvent

**model****calculations**". Biophysical Journal. 87 (2): 768-79. doi:10.1529/biophysj. ... Rousseau G (2013). "Fifty years ago: The quest for steroid hormone receptors".**Molecular**and Cellular Endocrinology. 375 (1-2 ... Gupta BBP, Lalchhandama K (2002). "**Molecular**mechanisms of glucocorticoid action" (PDF). Current Science. 83 (9): 1103-1111. ... International Journal of**Molecular**Sciences. 15 (9): 15412-25. doi:10.3390/ijms150915412. PMC 4200746. PMID 25257522. Brook CG ...###### Alternative medicine

... and an incorrect

**model**of the anatomy and physiology of internal organs.[8][59][60][61][62][63] ... Trends in**Molecular**Medicine. 20 (9): 473-76. doi:10.1016/j.molmed.2014.06.007. PMID 25150944.. ... blind experiments and**calculation**of prior probability), providing invalid results. ...**molecular**biology, biophysics, and other natural sciences to clinical practice, using scientific methods to establish the ...###### Aluminijum arsenid - Википедија

Ertl P.; Rohde B.; Selzer P. (2000). „Fast

**calculation**of**molecular**polar surface area as a sum of fragment based contributions ...###### 4,4'-Metilendianilin - Википедија, слободна енциклопедија

Ertl P.; Rohde B.; Selzer P. (2000). „Fast

**calculation**of**molecular**polar surface area as a sum of fragment based contributions ...###### Alkali metal

Unit cell ball-and-stick

**model**of lithium nitride.[118] On the basis of size a tetrahedral structure would be expected, but ... Further**calculations**show that unhexpentium would follow the trend of increasing ionisation energy beyond caesium, having an ... in a**molecular**dynamics (MD) simulation study". Biophys. Chem. 120 (1): 1-9. doi:10.1016/j.bpc.2005.10.002. PMID 16253415.. ...**Molecular**Metal-Metal Bonds: Compounds, Synthesis, Properties. John Wiley and Sons. pp. 23-24. ISBN 978-3-527-33541-1. .. ...###### Etil 8'-apo-beta,psi-karotenoat - Википедија, слободна енциклопедија

Ertl P.; Rohde B.; Selzer P. (2000). „Fast

**calculation**of**molecular**polar surface area as a sum of fragment based contributions ...###### Brain tumor

"

**Molecular**Therapy. 12 (5): 842-51. doi:10.1016/j.ymthe.2005.03.017. PMID 16257382. Archived from the original on 12 September ... to in vivo**models**of cancer and in 2005 reported a long-term survival benefit in an experimental brain tumor animal**model**.[62][ ... Radiosurgery is a treatment method that uses computerized**calculations**to focus radiation at the site of the tumor while ... Hourigan CS (2006). "The**molecular**basis of coeliac disease". Clin Exp Med (Review). 6 (2): 53-59. doi:10.1007/s10238-006-0095- ...###### Quercetin

"primary).

**Molecular**Pharmacology. 60 (3): 595-602. PMID 11502892.. *^ van der Woude H, Ter Veld MG, Jacobs N, van der Saag PT, ... A colorful**model**for genetics, biochemistry, cell biology, and biotechnology". Plant Physiology. 126 (2): 485-93. doi:10.1104/ ... Justesen U, Knuthsen P (May 2001). "Composition of flavonoids in fresh herbs and**calculation**of flavonoid intake by use of ... "review).**Molecular**and Cellular Endocrinology. 389 (1-2): 71-83. doi:10.1016/j.mce.2014.02.002. PMC 4040308. PMID 24530924.. ...###### Tris(pentafluorophenyl)borane

This zwitterionic salt can be converted to a system that reversibly binds

**molecular**H2: (C6F5)2B(F)-C6F4-P(H)mes2 + Me2SiHCl ... as well as quantum-chemical**calculations**all indicate that the Lewis acidity of B(C6F5)3 is slightly lower than the one of BF3 ...###### Cold fusion

The

**calculation**of excess heat in electrochemical cells involves certain assumptions.[148] Errors in these assumptions have ... 6-7, 35-36 "[page 7] This well established experimental result is consistent with the Bohr**model**, which predicts that the ...**molecular**resonance excitation']", Huizenga 1993, pp. 6-7, 35-36, 75, 108-109, 112-114, 118-125, 130, 139, 173, 183, 217-218, ... There is currently no accepted theoretical**model**that would allow cold fusion to occur. ...###### Inbreeding

"Genetic

**calculation**applets and other programs. Genetics pages.. *^ García-Cortés LA, Martínez-Ávila JC, Toro MA (2010-05-16 ... "The Habsburg Lip", Topics in the History of Genetics and**Molecular**Biology, Fall 2000. Msu.edu. Retrieved on 2013-03-05. ... The inbreeding guarantees a consistent and uniform animal**model**for experimental purposes and enables genetic studies in ... allowing for these offspring to serve as animal**models**for genetic studies.[61] The use of inbred strains is also important for ...###### Chemical engineering

**Models**often involve separate considerations for macroscopic, microscopic and

**molecular**level phenomena.

**Modeling**of transport ... Advancements in computer science found applications designing and managing plants, simplifying

**calculations**and drawings that ... Demonstration

**model**of a direct-methanol fuel cell. The actual fuel cell stack is the layered cube shape in the center of the ...

**Modeling**and analysis of transport phenomena is essential for many industrial applications. Transport phenomena involve fluid ...

###### Super-Kamiokande

Beyond the Standard

**Model**. Simulated Large Hadron Collider CMS particle detector data depicting a Higgs boson produced by ... Theoretical**calculations**of supernova explosions suggest that neutrinos are emitted over a total time-scale of tens of seconds ... is introduced to remove particles whose minimum size corresponds to**molecular**weight approximately 10,000 (or about 10 nm ... The proton is assumed to be absolutely stable in the Standard**Model**. However, the Grand Unified Theories (GUTs) predict that ...###### Plutonijum(III) fluorid - Википедија, слободна енциклопедија

**calculation**of

**molecular**polar surface area as a sum of fragment based contributions ...

###### James Clerk Maxwell

In it he provided a conceptual

**model**for electromagnetic induction, consisting of tiny spinning cells of magnetic flux. Two ... In the kinetic theory, temperatures and heat involve only**molecular**movement. This approach generalised the previously ... "Bakerian Lecture: Experiments and**calculations**relative to physical optics". Philosophical Transactions of the Royal Society ... The paper presented a simplified**model**of Faraday's work and how electricity and magnetism are related. He reduced all of the ...###### Amyotrophic lateral sclerosis

... the SOD1G93A

**model**remains both the most widely used SOD1 mouse**model**[136] and the most widely used ALS mouse**model**overall.[23 ... "**Molecular**and Cellular Neurosciences. 66 (Pt B): 75-80. doi:10.1016/j.mcn.2015.03.001. PMC 4461453. PMID 25748121.. ... this**calculation**has been criticized for relying on an inappropriately low number of expected cases of ALS in the cohort.[67] ... As of 2018, there are about 20 TARDBP mouse**models**, a dozen FUS mouse**models**, and a number of C9orf72, PFN1, and UBQLN2 mouse ...###### Spectrophotometry

The last and most popular

**model**became**Model**D which is better recognized now as the DU spectrophotometer which contained the ... "Biochemistry and**Molecular**Biology Education. 41 (4): 242-50. doi:10.1002/bmb.20694. PMID 23625877.. ... what substances are present in a target and exactly how much through**calculations**of observed wavelengths. ... From there,**Model**C was born with an adjustment to the wavelength resolution which ended up having three units of it produced. ...###### Tetrahydrocannabinol

**Calculations**of the n-octanol-water partition coefficient (Ko/w) of Δ9-THC at neutral pH vary between 6,000, using the shake ... Morales, Paula; Hurst, Dow P.; Reggio, Patricia H. (2017). "

**Molecular**Targets of the Phytocannabinoids: A Complex Picture". In ... 3D

**model**(JSmol). *Interactive image. Specific rotation. −152° (ethanol). Boiling point. 155-157°C @ 0.05mmHg,[6] 157-160°C @ ...

###### 3-Heksin - Vikipedija, slobodna enciklopedija

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###### Hidrogen bahasa Indonesia, ensiklopedia bebas

Gambaran atom hidrogen yang menampakkan diameter atom dua kali lebih besar dari jari-jari

**model**Bohr(citra tidak berskala). ... Department of**Molecular**and Optical Physics, University of Freiburg. ... Inggris) Basic Hydrogen**Calculations**of Quantum Mechanics. *(Inggris) National Hydrogen Association. *(Inggris) Hydrogen phase ... Oleh karena diskretisasi momentum sudut yang dipostulatkan pada awal mekanika kuantum oleh Bohr, elektron pada**model**Bohr hanya ...###### Гольберг, Дмитрий Викторович - Википедия

... experiment and objective

**molecular**dynamics**calculations**» Phys. Rev. Lett. 109[2] (2012) 025504-1 DOI:10.1103/Phys.Rev.Lett. ... M DEMURA, D GOLBERG and T HIRANO : «An athermal deformation**model**of the yield stress anomaly in Ni3Al» Intermetallics 15[10] ( ... insights into bonding at the Al/BN interface from first-principles**calculations**» J. Phys. Chem. C 118[46] (2014) 26894-26901 ... structure energetics and dependence on mechanical strain from first-principles**calculation**» Phys. Status Solidi B-Basic Solid ...###### Radiation therapy

... high dose at the

**molecular**level using AT aims for in situ**molecular**modifications involving**molecular**breakages and**molecular**... "A genome-based**model**for adjusting radiotherapy dose (GARD): a retrospective, cohort-based study". The Lancet. Oncology. 18 (2 ... Verification of dose**calculations**in radiation therapy. *Radiation Safety in External Beam Radiotherapy (IAEA) ... Auger therapy (AT) makes use of a very high dose[62] of ionizing radiation in situ that provides**molecular**modifications at an ...###### Hydrogen isocyanide

**Molecular**properties[edit]. Hydrogen isocyanide (HNC) is a linear triatomic molecule with C∞v point group symmetry. It is a ... 3 and C+.[12][13] Rate

**calculations**were done at 3.16 × 105 years, which is considered early time, and at 20 K, which is a ... 2004). "Physical-chemical

**modeling**of the low-mass protostar IRAS 16293-2422". Astronomy and Astrophysics. 418: 1021-1034. ... A survey of the W 3 Giant

**Molecular**Cloud in 1997 showed over 24 different

**molecular**isotopes, comprising over 14 distinct ...

###### Ashkenazi Jews

Tony Nick Frudakis (2010-07-19).

**Molecular**Photofitting: Predicting Ancestry and Phenotype Using DNA. p. 383. ISBN 978- ... Sergio Della Pergola in a rough**calculation**of Sephardic and Mizrahi Jews, implies that Ashkenazi Jews make up less than 74% of ... in line with this**model**of origin, David Goldstein, now of Duke University, reported that unlike male Ashkenazi lineages, the ... while Sergio DellaPergola in a rough**calculation**of Sephardic and Mizrahi Jews, implies that Ashkenazi make up a notably lower ...###### International System of Units

The resultant

**calculations**enabled him to assign dimensions based on mass, length and time to the magnetic field.[Note 9][44] ... A mole of a substance has a mass that is its**molecular**mass expressed in units of grams; the mass of a mole of table salt is ... "an original on which something is**modelled**"). ...###### Kobalt(II) fluorid - Википедија

**calculation**of

**molecular**polar surface area as a sum of fragment based contributions ...

###### Uridine monophosphate synthase

Suchi M, Mizuno H, Kawai Y, Tsuboi T, Sumi S, Okajima K, Hodgson ME, Ogawa H, Wada Y (Mar 1997). "

**Molecular**cloning of the ... Deficiency of the enzyme can be studied in the**model**organism Caenorhabditis elegans. The rad-6 strain has a premature stop ... Transition state analyses have used isotopic effects and quantum**calculations**to reveal a completely dissociated dianionic ... Suchi M, Harada N, Tsuboi T, Asai K, Okajima K, Wada Y, Takagi Y (1990). "**Molecular**cloning of human UMP synthase". Purine and ...###### Mie scattering

Like Mie

**model**, the extended**model**can be applied to spheres with a radius close to the wavelength of the incident light. There ... The formalism allows the**calculation**of the electric and magnetic fields inside and outside a spherical object and is generally ... Mie scattering (sometimes referred to as a non-**molecular**scattering or aerosol particle scattering) takes place in the lower ... The Rayleigh scattering**model**breaks down when the particle size becomes larger than around 10% of the wavelength of the ...###### Polar organic chemical integrative sampler

Therefore, both laboratory and field data justify the use of a linear uptake

**model**for the**calculation**of sample rates. In ... The SPMD consist of a thin-walled, nonporous, polyethylene membrane tube that is filled with high**molecular**weight lipid. These ... These last two steps make the**modeling**, understanding, and prediction of accumulation by a POCIS device challenging. To date, a ...###### Enthalpy of vaporization

... such as Pitzer

**model**or TCPC**model**. The vaporization of metals is a key step in metal vapor synthesis, which exploits the ... Ge, Xinlei; Wang, Xidong (2009). "**Calculations**of Freezing Point Depression, Boiling Point Elevation, Vapor Pressure and ... estimation of the heat of vaporization at the normal boiling point from**molecular**structures Latent heat Ge, Xinlei; Wang, ... of vaporization of electrolyte solutions can be simply carried out using equations based on the chemical thermodynamic**models**, ...###### Delocalization errors in a hubbard- like **model** : Consequences for density- functional tight- binding **calculations** of...

###### Spectroscopic Characterization, **Molecular** **Modeling** and DFT/TD-DFT/PCM **Calculations** of Novel Hydrogen-Bonded Charge Transfer...

Complemented with experimental results,

**molecular****modelling**using the density functional theory (DFT)**calculations**was carried ... Finally, a good consistency between experimental and theoretical**calculations**was found confirming that the applied basis set ... Spectroscopic Characterization,**Molecular****Modeling**and DFT/TD-DFT/PCM**Calculations**of Novel Hydrogen-Bonded Charge Transfer ... Complemented with experimental results,**molecular****modelling**using the density functional theory (DFT)**calculations**was carried ...**Calculation** of Protein Heat Capacity From Replica-Exchange **Molecular** Dynamics Simulations With Different Implicit Solvent **Models**

Its

**calculation**by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of ...**Calculation**of Protein Heat Capacity From Replica-Exchange**Molecular**Dynamics Simulations With Different Implicit Solvent ... A reformulated GBMV2**model**of employing a smoother**molecular**-volume dielectric interface was the most accurate in reproducing ... Our**model**protein system is the src Homology 3 (SH3) domain of alpha-spectrin, and we report a series of 10 ns replica-exchange ...**Molecular** Dynamics of Water in Foods and Related **Model** Systems: Multinuclear Spin Relaxation Studies and Comparison with...

A review of recent studies of

**molecular**dynamics of water in foods and**model**systems is presented, and the theoretical results ... Multinuclear Spin Relaxation Studies and Comparison with Theoretical**Calculations**. In: Levine H., Slade L. (eds) Water ...**Molecular**Dynamics of Water in Foods and Related**Model**Systems: Multinuclear Spin Relaxation Studies and Comparison with ... A review of recent studies of**molecular**dynamics of water in foods and**model**systems is presented, and the theoretical results ...###### Workshop III: Density-Functional Theory **Calculations** for **Modeling** Materials and Bio-**Molecular** Properties and Functions - A...

Density-Functional Theory

**Calculations**for**Modeling**Materials and Bio-**Molecular**Properties and Functions - A Hands-On Computer ... Programs , Workshops , Workshop III: Density-Functional Theory**Calculations**for**Modeling**Materials and Bio-**Molecular**Properties ... Workshop III: Density-Functional Theory**Calculations**for**Modeling**Materials and Bio-**Molecular**Properties and Functions - A ... It is the aim of the workshop that participants gain a broad (and deep) understanding of what DFT**calculations**can provide. The ...**Calculation** of Diagnostic Parameters of Advanced Serological and **Molecular** Tissue-Print Methods for Detection of Citrus...

**Calculation**of Diagnostic Parameters of Advanced Serological and

**Molecular**Tissue-Print Methods for Detection of Citrus ... tristeza virus: A

**Model**for Other Plant Pathogens... ... The

**calculation**of diagnostic parameters is discussed, as a ...

**Calculation**of Diagnostic Parameters of Advanced Serological and

**Molecular**Tissue-Print Methods for Detection of Citrus ... validating the use of the

**molecular**technique for routine CTV-detection purposes. In addition, our results show that the ...

###### Periodicity of **molecular** clusters based on symmetry-adapted orbital **model** | Nature Communications

Here the authors propose a symmetry adapted orbital

**model**by quantum chemistry**calculations**for the prediction of stable ... The jellium**model**is effective to explain subglobular clusters such as icosahedral clusters. To broaden the scope of this**model**... Prediction of stable clusters based on the jellium**model**is limited because of the usual assumption of their spherical symmetry ... Many stable substances such as clusters have been predicted based on the jellium**model**, which usually assumes that their ...###### Reactivity of disulfide bonds is markedly affected by structure and environment: implications for protein modification and...

**Molecular**

**modelling**

**calculations**. Standard density functional theory

**calculations**were carried out using Gaussian 0961. ... Universal solvation

**model**based on solute electron density and on a continuum

**model**of the solvent defined by the bulk ... Computational

**modeling**of reactions. The variation in k2 for the acylic disulfides (~102), and between the acyclic species/6- ... Single-point energy

**calculations**were carried out with M06-2X/6-311 + G(3df,2p) + SMD solvation + thermal corrections65. ...

###### Frontiers | A Review of Solid-Solution **Models** of High-Entropy Alloys Based on Ab Initio **Calculations** | Materials

... and hybrid Monte Carlo/

**molecular**dynamics) and their applications and limits in single phase HEAs. ... The present review focuses on the available ab initio based solid-solution**models**(virtual lattice approximation, coherent ... The present review focuses on the available ab initio based solid-solution**models**(virtual lattice approximation, coherent ... and hybrid Monte Carlo/**molecular**dynamics) and their applications and limits in single phase HEAs. ...###### Extension of the Einstein molecule method for solid free energy **calculation** to non-periodic and semi-periodic systems(Journal...

Accuracy of free-energy perturbation

**calculations**in**molecular**simulation. I.**Modeling**journal, May 2001 * Lu, Nandou; Kofke, ... Monte Carlo**calculation**of the surface tension for two- and three-dimensional lattice-gas**models**journal, March 1982 * Binder, ... We have created a software package which interfaces with the LAMMPS**molecular**dynamics code to perform these**calculations**.},. ... Finally, our results have broad implications for the determination of solubilities of**molecular****models**of ionic systems« less ...###### Molecules | Free Full-Text | Therapeutic Use of Scoparia dulcis Reduces the Progression of Experimental Osteoarthritis | HTML

An in silico test and

**Molecular**Docking tests were performed. A histopathological evaluation was made on articular cartilage ... in an experimental**model**of osteoarthritis. The experiment was performed with Wistar rats divided into 4 groups with 5 animals ... 4.11.1. Predictive**Models**and Theoretical**Calculations**. The compounds identified in the crude extract of S. dulcis had their ... was used to obtain 3D structural**models**. Geometric optimization**calculations**were performed according to the functional density ...###### Functionality in single-molecule devices: **Model** **calculations** and applications of the inelastic electron tunneling signal in...

**Model**

**calculations**and applications of the inelastic electron tunneling signal in

**molecular**junctions. ... en] ab initio

**calculations**; Greens function methods ;

**molecular**electronics. Abstract :. [en] We analyze how functionality ... Second, we consider a realistic

**model**of a organic conjugated molecule. We use ab initio

**calculations**to study how the vibronic ... Reference : Functionality in single-molecule devices:

**Model**

**calculations**and applications of the .... ...

###### Computational Chemistry & **Molecular** **Modeling** | Chemistry | Subjects | Wiley

Rate Constant

**Calculation**for Thermal Reactions: Methods and Applications Herbert DaCosta, Maohong Fan ... Multiscale**Modeling**of Particle Interactions: Applications in Biology and Nanotechnology Michael King, David Gee ... Process**Modeling**and Simulation for Chemical Engineers: Theory and Practice Simant R. Upreti ... Chemically Reacting Flow: Theory,**Modeling**, and Simulation, 2nd Edition Robert J. Kee, Michael E. Coltrin, Peter Glarborg, ...###### Dicyanovinylnaphthalenes for neuroimaging of amyloids and relationships of electronic structures and geometries to binding...

We then use

**molecular**docking to study the binding modes of these molecules to the established tau steric zipper**model**. The ...**Molecular**Docking and QM/MM**Calculations**.. AutoDock Vina was used to perform the docking simulations (25) with the QM-optimized ... Amyloid Binding**Model**. A steric zipper pseudofibril of the VQIVYK tau sequence was built as a**model**in which to rationalize the ... they serve as excellent**models**for full-length fibrils (8, 11). Recently, the VQIVYK steric zipper**model**from tau has been used ...###### Antimicrobial Activity, DFT **Calculations**, and **Molecular** Docking of Dialdehyde Cellulose/Graphene Oxide Film Against Covid-19 |...

**Molecular**

**Modeling**and Docking. The

**molecular**

**modeling**of Pseudomonas aeruginosa (NCID-9016) as Gram-negative bacteria PDB ( ...

**Molecular**

**Modeling**and Docking. Figure 7a shows plausible interaction sites of DAC to bind in active pocket of protein. ... Antimicrobial Activity, DFT

**Calculations**, and

**Molecular**Docking of Dialdehyde Cellulose/Graphene Oxide Film Against Covid-19. * ... Antimicrobial Activity, DFT

**Calculations**, and

**Molecular**Docking of Dialdehyde Cellulose/Graphene Oxide Film Against Covid-19 ...

**Calculations** for **Molecular** Biology and Biotechnology - 2nd Edition

Purchase

**Calculations**for**Molecular**Biology and Biotechnology - 2nd Edition. Print Book & E-Book. ISBN 9780123756909, ... 9.10 The Pfaffl**Model**. Chapter Summary. References. Further Reading. Chapter 10 Recombinant DNA. Introduction. 10.1 Restriction ...**Calculations**for**Molecular**Biology and Biotechnology 2nd Edition. A Guide to Mathematics in the Laboratory. ...**Calculations**for**Molecular**Biology and Biotechnology: A Guide to Mathematics in the Laboratory, Second Edition, provides an ...###### Frontiers | In silico Guided Drug Repurposing: Discovery of New Competitive and Non-competitive Inhibitors of Falcipain-2 |...

Here, we report the development and validation of an ensemble of ligand-based computational

**models**capable of identifying ... we report the development and validation of an ensemble of ligand-based computational**models**capable of identifying falcipain-2 ...**Molecular**Descriptor**Calculation**and**Modeling**Procedure. 3,668 conformation-independent descriptors were computed with Dragon ... 85.8% of the individual**models**achieved an AUC ROC , 0.90 for the training set, whereas only one of the**models**(named**model**975 ...###### Chemical **Modelling** (RSC Publishing)

This book is the first stop for any materials scientist, biochemist, chemist or

**molecular**physicist wishing to acquaint ... chemical**modelling**of fluidics near surfaces and organic solar cells. ... Chemical**modelling**covers a wide range of disciplines and with the increase in volume, velocity and variety of information, ... themselves with major developments in the applications and theory of chemical**modelling**. Containing both comprehensive and ...###### Pharmacokinetic-directed dosing of vandetanib and docetaxel in a mouse **model** of human squamous cell carcinoma | **Molecular**...

Tumor Growth Rate

**Calculations**and Statistical Analysis. Tumor growth rates were calculated by liner regression of the tumor ... The resulting**model**simulation of 1 mg/kg delivered i.p. in mice daily is shown in Fig. 2C.**Model**simulations were generated ... Preclinical**models**have shown the utility of vandetanib as a single agent in numerous tumor**models**(12) as well as its ability ... The resulting**model**simulation is shown in Fig. 2B.**Model**simulations were generated using a dosing interval of 96 h for 28 ...###### Computational Chemistry & **Molecular** **Modeling** | Chemistry | Subjects | Wiley

###### A **model** of single-electron transport. **Calculation** of the thermodynamic parameters for electron capture by the bound proton of...

E. Illenberger and J. Momigny, Gaseous

**Molecular**Ions. An Introduction to Elementary Processes Induced by Ionization (Springer ... A**model**of single-electron transport.**Calculation**of the thermodynamic parameters for electron capture by the bound proton of ... Phosphate is one of the most important building units of biological molecules, whereas formic acid can serve as a**model**of the ... dissociative electron capture electron transport oxyacid quantum chemistry**modeling**bound proton hydrogen atom ...###### Molecules | Free Full-Text | New Cembranoid Diterpenes from the Cultured Octocoral Nephthea columnaris | HTML

Figure 2. The computer-generated

**model**of 1 using MM2 force field**calculations**and the calculated distance (Å) between selected ... 9.0, 2005) was used to calculate**molecular****models**.. 3.5. MTT Antiproliferative Assay. MOLT-4, SUP-T1, U-937, DLD-1, LNCaP and ... Figure 2. The computer-generated**model**of 1 using MM2 force field**calculations**and the calculated distance (Å) between selected ...**Molecular**Mechanics**Calculations**. Implementation of the MM2 force field [18] in CHEM3D PRO software from CambridgeSoft ...**Molecular** Vision: Meta-analysis of transcriptomic changes in optic nerve injury and neurodegenerative **models** reveals a...

Data normalization and fold change

**calculation**. Affymetrix CEL files were normalized using the RMA normalization method from ...**Molecular**clustering identifies complement and endothelin induction as early events in a mouse**model**of glaucoma. J Clin Invest ... Among the CONI**models**used for transcriptome analyses, the most commonly used are**models**of experimental or inherited glaucoma ... Biologic processes that are changed in multiple**models**and multiple species are less likely to be artifacts of a**model**and more ...###### Peptide bond distortions from planarity: new insights from quantum mechanical **calculations** and peptide/protein crystal...

Schematic representation of Pep

**model****molecular**orbitals.. The three highest energy occupied π orbitals (A, B mainly ... Δω vs. peptide conformation (A) Ala1**model**in solvent (B) high resolution protein structures (resolution better than 1.6 Å; Gly ... Results from**calculations**at the PBE0/6-31G(d) (•) level and MP2/6-31G(d) (▪) level for the conformer ϕ′i+1 = 60° (see ). On ... Pep**model**in vacuo: Minimized energy for the ψ′ = 150° conformer at different Δω′ values. Comparison of results from different ...###### An equilibrium thermodynamic **model** of the sequestration of calcium phosphate by casein micelles and its application to the...

An equilibrium thermodynamic

**model**of the interaction of calcium, phosphate and casein in milk is described in which the ... The use of the**model**is illustrated by**calculations**of the partition of salts in a standard milk and by comparison with ...**molecular**weight cut-off. OCP. octacalcium phosphate. PC. phosphate centre. TCC. tricalcium citrate ... An equilibrium thermodynamic**model**of the interaction of calcium, phosphate and casein in milk is described in which the ...###### Proceedings of MEST 2012: Exponential Type Orbitals for **Molecular** Electronic Structure Theory, Volume 67 - 1st Edition

Exponential Type Orbitals for

**Molecular**Electronic Structure Theory, Volume 67 - 1st Edition. Print Book & E-Book. ISBN ... 3 Examples of atomic**models**. *4 Examples of**molecular****calculations**. *5 Concluding remarks ... Chapter 3. A Basis Sets Composed of Only 1s Slater Orbitals and 1s Gaussian Orbitals to Perform**Molecular****Calculations**, SCF- ... Proceedings of MEST 2012: Exponential Type Orbitals for**Molecular**Electronic Structure Theory, Volume 67 1st Edition. Write a ...**Molecular** **Modeling** Techniques In Material Sciences - 1st Edition - Jö

...

**molecular****modeling**is a method that combines com ... Monte Carlo**Calculations****Molecular**Dynamics**Calculations**Grand ...**Molecular****Modeling**Techniques in Materials Science explores the impact of using**molecular****modeling**for various simulations in ... General Structure of**Molecular****Modeling**Programs Computer Hardware Software Related to Materials**Modeling**Metal Oxides. ...**Molecular****Modeling**Techniques in Materials Science presents the background and tools for chemists and physicists to perform in- ...###### Modellrechnungen zur Solvatation einatomiger Ionen (LCAO-MO-Untersuchungen von Molekülstrukturen VIII)<...

**Model**

**calculations**of the solvation of oneatomic ions (LCAO-MO-investigations of

**molecular**structures VIII). ...

**Model**

**calculations**of the solvation of oneatomic ions (LCAO-MO-investigations of

**molecular**structures VIII). ...

**Model**

**calculations**of the solvation of oneatomic ions (LCAO-MO-investigations of

**molecular**structures VIII). Together they ...

**Molecular** **Modeling** of Geochemical Reactions. An Introduction

**Molecular**processes in nature affect human health, the availability of resources and the Earth s climate.

**Molecular**

**modelling**... 8.2.1 Ab Initio

**Molecular**Dynamics and Density Functional Theory 275. 8.3

**Calculation**of the Surface Acidity from Reversible ...

**Molecular**processes in nature affect human health, the availability of resources and the Earth s climate.

**Molecular**

**modelling**...

**Molecular**

**Modeling**of Geochemical Reactions: An Introduction applies computational chemistry to geochemical problems. Chapters ...

###### RCSB PDB
- 173D: MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY, **MOLECULAR** **MODELING**, AND...

**Molecular**

**Modeling**, and Spectroscopic Studies of D(Gaagcttc)2-Actinomycin D Complexes and its Host DNA ... Type: Atomic

**model**, Database references, Derived

**calculations**, Non-polymer description, Structure summary ... MULTIPLE BINDING MODES OF ANTICANCER DRUG ACTINOMYCIN D: X-RAY,

**MOLECULAR**

**MODELING**, AND SPECTROSCOPIC STUDIES OF D(GAAGCTTC)2- ...

SimulationsComputational ChemistrySimulationMechanicsStructuralMoleculesMethodsDescriptorsMoleculeProteinOrbitalsSpectraAtomicStructuresProteinsThermodynamicsSolvationChemical calculationsPredictionChemistryBiochemistryEnergiesTheoretical calculationsUnited-atomDiffusionProcessesVisualizationDockingBiologyStochasticBiologicalElectronGenomicsOrbital calculationsDynamics CalculationsApplicationsConformationMathematicalLiquidsClustersVibrationalElectronic structure calculationsExperimentalBioinformaticsCentreMultiscaleInteractionsParametersReactionSurfaceReactivityResultsComparativeEnergy Calculations

###### Simulations22

- Our model protein system is the src Homology 3 (SH3) domain of alpha-spectrin, and we report a series of 10 ns replica-exchange molecular dynamics simulations performed at temperatures ranging from 298 to 550 K, starting from the SH3 native structure. (nih.gov)
- For the lower-resolution CHARMM19/GB model, the simulations failed to yield a bimodal energy distribution, yet the melting temperature was observed to be a good estimate of higher-resolution simulation models. (nih.gov)
- Molecular Modeling Techniques in Materials Science explores the impact of using molecular modeling for various simulations in industrial settings. (routledge.com)
- Molecular modeling on GPU is the technique of using a graphics processing unit (GPU) for molecular simulations. (wikipedia.org)
- mdcore - an open-source platform-independent library for molecular dynamics simulations on modern shared-memory parallel architectures. (wikipedia.org)
- Below, molecular dynamics simulations are performed on a lipid-protein complex. (nyu.edu)
- It uses concepts in free energy calculations, conformational analysis, reaction rates, and transition pathways to calculate and interpret biomolecular properties gleaned from computer-generated membrane simulations. (ebooks.com)
- Molecular Dynamics and Monte Carlo Simulations a. (bio.net)
- Molecular dynamics simulations c. (bio.net)
- Now we are thinking about buying a workstation to do some molecular graphics, modelling and molecular dynamics simulations. (bio.net)
- We would like to be able to visualize our proteins, to do some simple calculations (distances, angles, accesible surface area, radius of gyration, etc.) and modelling (for instance simulation of the effects of a mutation) and also (if possible) molecular dynamics simulations. (bio.net)
- Molecular dynamics simulations of the vacancy effect on the nickel self diffusion, oxygen diffusion and oxidation initiation in nickel using the ReaxFF reactive force field. (psu.edu)
- ReaxFF molecular dynamics simulations of intermediate species in dicyanamide anion and nitric acid hypergolic combustion. (psu.edu)
- Reactive molecular dynamics simulations of oxygen species in a liquid water layer of interest for plasma medicine. (psu.edu)
- Lately, a clear trend in the development and applications of line-broadening calculations is a significant increase in the computational results, in particular, using computer simulations [ 1 ]. (weizmann.ac.il)
- The scale of models being simulated by computer simulations today far exceeds anything possible (or perhaps even imaginable) using traditional paper-and-pencil mathematical modeling. (weizmann.ac.il)
- oxDNA - DNA and RNA coarse-grained simulations on GPUs PWmat - Plane-Wave Density Functional Theory simulations TeraChem - Quantum chemistry and ab initio Molecular Dynamics TINKER on GPUs. (wikipedia.org)
- BrianQC - has an open C level API for quantum chemistry simulations on GPUs, provides GPU-accelerated version of Q-Chem OpenMM - an API for accelerating molecular dynamics on GPUs, v1.0 provides GPU-accelerated version of GROMACS mdcore - an open-source platform-independent library for molecular dynamics simulations on modern shared-memory parallel architectures. (wikipedia.org)
- Workshop "Hybrid simulations of dynamical systems and applications to molecular dynamics" , Institut Henri Poincar , 27 septembre - 30 septembre 2010. (enpc.fr)
- The Mg2+ binding sites of the 5S rRNA loop E motif as investigated by molecular dynamics simulations. (currentprotocols.com)
- Molecular dynamics simulations on the hydration, structure and motions of DNA oligomers. (currentprotocols.com)
- The ABCs of molecular dynamics simulations on B‐DNA, circa 2012. (currentprotocols.com)

###### Computational Chemistry6

- Increasingly useful in materials research and development, molecular modeling is a method that combines computational chemistry techniques with graphics visualization for simulating and predicting the structure, chemical processes, and properties of materials. (routledge.com)
- Molecular Modeling of Geochemical Reactions: An Introduction applies computational chemistry to geochemical problems. (researchandmarkets.com)
- A basis set in theoretical and computational chemistry is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree-Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. (wikipedia.org)
- In modern computational chemistry , quantum chemical calculations are performed using a finite set of basis functions . (wikipedia.org)
- The scope of the journal includes all aspects of molecular modeling and computational chemistry , including. (elsevier.com)
- 1994: Wockhardt Ltd for Computer-aided molecular design and computational chemistry. (profeccoutinho.net.in)

###### Simulation17

- Its calculation by atomistic simulation methods remains a significant challenge due to the complex and dynamic nature of protein structures, their solvent environment, and configurational averaging. (nih.gov)
- To better understand these factors on calculating a protein heat capacity, we provide a comparative analysis of simulation models that differ in their implicit solvent description and force-field resolution. (nih.gov)
- We apply the all-atom CHARMM22 force field with different modified analytical generalized Born solvent models (GBSW and GBMV2) and compare these simulation models with the distance-dependent dielectric screening of charge-charge interactions. (nih.gov)
- Understanding and modeling biosystems requires simulation of biological behaviors and functions. (iaria.org)
- GPU Power Modeling of HPC Applications for the Simulation of Heterogeneous Clouds. (barnesandnoble.com)
- In this study, conventional molecular dynamics (MD) simulation and Gaussian accelerated MD (GaMD) simulation were performed to elucidate the resistance mechanisms of Cpd-5, a potent Mps1 inhibitor, induced by the four representative mutations I531M, I598F, C604Y, S611R. (peerj.com)
- Our results from conventional MD simulation combined with structural analysis and free energy calculation indicated that the four mutations weaken the binding affinity of Cpd-5 and the major variations in structural were the conformational changes of the P-loop, A-loop and αC-helix. (peerj.com)
- Modelling and Simulation in Materials Science and Engineering accepted for publication. (psu.edu)
- On the Lithium intercalation in Silicon Nanowires, Reactive Molecular Dynamics Simulation using ReaxFF Force Field. (psu.edu)
- Computer simulation is the discipline of designing an abstract model of an actual physical system, executing the model on a computer, and analyzing the execution output. (weizmann.ac.il)
- The first one is the molecular-dynamics N-body simulation that models the motion of plasma particles. (weizmann.ac.il)
- GPUGRID distributed supercomputing infrastructure [email protected] distributed computing project GPU GPU cluster GPGPU Molecular design software List of quantum chemistry and solid state physics software Comparison of software for molecular mechanics modeling Comparison of nucleic acid simulation software Molecule editor [email protected] Simulated reality John E. Stone, James C. Phillips, Peter L. Freddolino, David J. Hardy 1, Leonardo G. Trabuco, Klaus Schulten (2007). (wikipedia.org)
- Workshop "Numerical methods in molecular simulation" , Bonn, April 7-11th 2008. (enpc.fr)
- Modelling and simulation of complex systems: stochastic and deterministic approaches. (enpc.fr)
- Accelrys' Simulation Technologies Simulation/Modeling Methods (Mathematical representations of the real material) Quantum Mechanics Atomistic Simulation Mesoscale Modeling Analytical Instrument Simulation Statistical Correlations Properties Structure Solubility Activity Diversity Adhesion Stability Morphology Adsorption Diffusion Mechanical Energies Spectra. (slideserve.com)
- Amira is a software solution that satisfies your demanding needs to work with clinical or preclinical image data, nuclear data, optical or electron microscopy imagery, molecular models, vector and flow data, simulation data on finite element models, and all types of multidimensional image, vector, tensor, and geometry data. (wikibooks.org)
- Article Kondratyuk N. , Norman G. , Stegailov V. Rheology of liquid n-triacontane: Molecular dynamics simulation // Journal of Physics: Conference Series . (hse.ru)

###### Mechanics10

- Explain strengths and weaknesses of different models (molecular mechanics, semi-empirical, wavefunction based and density functional theory). (uio.no)
- The molecular geometry obtained using single crystal analysis is discussed along with results of the molecular mechanics modeling (MM), and the results showed the same cis conformation between benzoxazole nitrogen atom and the amino group. (hindawi.com)
- Molecular mechanics calculations are an efficient tool and an important aspect of molecular modeling, used for predicting structure and energy of molecules and heats of formation and used to compare different conformations of the same molecule, further reading in [ 7 , 8 ]. (hindawi.com)
- Herein, we report the crystal structure and conformation of 2-(4-amino-3-benzyl-2-thioxo-2,3-dihydrothiazol-5-yl)benzoxazole, comparing the results with its molecular mechanics modelling. (hindawi.com)
- We report a combined molecular dynamics and quantum mechanics (QM)/molecular mechanics (MM) analysis of the excitonic properties of the Fenna-Matthews-Olson (FMO) protein by using a polarizable MM model combined with a time-dependent density functional theory description. (nih.gov)
- In this new research, researchers first trained a neural network on a large set of density functional theory data, one the most popular quantum mechanics methods for studying molecular systems. (energy.gov)
- Next, they retrained the neural network on a smaller set of coupled‑cluster theory data, the gold standard for quantum mechanics calculations. (energy.gov)
- Using results from these calculations, the rate constants and thermodynamic properties of molecules can be calculated using statistical mechanics and (variational) transition state theory. (royalsocietypublishing.org)
- A thorough introduction to elementary quantum chemistry: angular momentum, quantum mechanical operators, interaction of radiation with matter, the many-electron atom, introduction to matrix mechanics, approximate methods, SCF calculations, electronic structure of polyatomic molecules, recent molecular orbital calculations. (luc.edu)
- molecular mechanics/dynamics force field development. (lifeboat.com)

###### Structural10

- To broaden the scope of this model, we propose the symmetry-adapted orbital model, which explicitly takes into account the level splittings of the electronic orbitals due to lower structural symmetries. (nature.com)
- Structural analysis of the data files from the BPBI calculations reveals that all of the analogues with good biological activity show the formation of a hydrogen bond between the ligand and the backbone nitrogen atom of lysine 103. (neb.com)
- By use of the structural results, two novel BPBI inhibitors have been designed and calculations have been carried out. (neb.com)
- It also demonstrates comparative protein structure modeling, outlines computer-aided drug design, discusses Bayesian statistics in molecular and structural biology, and examines the RISM-SCF/MCSCF approach to chemical processes in solution. (ebooks.com)
- Bayesian statistics in molecular and structural biology. (ebooks.com)
- Beyond simple one-to-one structural conversion, it is equally important to generate scientifically sound molecular models that enumerate the different structural and chemical possibilities a ligand could sample, as these variations could lead to dramatically different results in subsequent computations. (schrodinger.com)
- Overall, our results indicate that structural fluctuations, electrostatic interactions, and short-range quantum effects can significantly modulate the model Hamiltonian parameters (site energies and couplings). (nih.gov)
- However, in the structural bioinformatics community, Model Quality Assessment Programs (MQAPs) were developed, which predict the accuracy of protein structure models (i.e. without the knowledge of the true structure), both globally and for individual residues. (biomedcentral.com)
- WeNMR aims at bringing together complementary research teams in the structural biology and life science area into a virtual research community at a worldwide level and provide them with a platform integrating and streamlining the computational approaches necessary for NMR and SAXS data analysis and structural modelling. (wikipedia.org)
- We use structural modelling to reveal that the protein environment renders the 52Cys thiol a highly reactive functional group and we show its reactivity in vitro . (royalsocietypublishing.org)

###### Molecules15

- Phosphate is one of the most important building units of biological molecules, whereas formic acid can serve as a model of the −COOH group in amino acids, carboxylic acids, functional sites of enzymes, etc. (springer.com)
- Here, we describe a computational method to process molecular representations and classify molecules. (pnas.org)
- Several times faster rendering of large cellPACK models containing thousands of molecules. (ucsf.edu)
- New deep learning models predict the interactions between atoms in organic molecules. (energy.gov)
- Molecular dynamics is the study of how atoms and molecules move and interact based on traditional Newtonian physics. (energy.gov)
- This is the fastest and most accurate model of small organic molecules to date. (energy.gov)
- In nanoscience , it could advance modeling of how tiny structures grow and how molecules are arranged in self-assembled soft materials. (energy.gov)
- The result is the best-to-date empirical model of small organic molecules, in terms of both speed and accuracy. (energy.gov)
- For larger molecules and clusters of molecules, quantum calculations become unfeasible. (royalsocietypublishing.org)
- Ltd forSemi-empirical and forcefield calculations of organic molecules. (profeccoutinho.net.in)
- 1996: Alchemie Research Centre for Molecular modelling and quantum mechanical calculations of organic molecules. (profeccoutinho.net.in)
- Chemistry is now ready for the movies: an international team which includes researchers from the Max Planck Institute for the Structure and Dynamics of Matter in Hamburg has used a type of molecular camera to follow a fast-moving ballet performed by atoms in molecules as they change their structure. (mpg.de)
- A molecular movie: the individual frames show how each individual atom in Pt(dmit) 2 molecules moves within a few 100 femtoseconds (fs) while Me 4 P[Pt(dmit) 2 ] 2 is switched from the insulating state to the metallic, conducting state with the aid of laser light. (mpg.de)
- Theoretical models can describe at least the motions of small molecules during a chemical transformation. (mpg.de)
- Quantitative structure-activity relationship (QSAR) describes how a given biological activity can vary as a function of molecular descriptors derived from the chemical structure of a set of molecules. (biomedsearch.com)

###### Methods15

- The calculation of diagnostic parameters is discussed, as a necessary tool, to validate detection or diagnostic methods in plant pathology. (apsnet.org)
- Nearly all methods require accurate 3D molecular models as a starting point. (schrodinger.com)
- As the newest version, Exploring Chemistry with Electronic Structure Methods will provide you with the latest information about using electronic structure calculations to investigate various chemical problems. (gaussian.com)
- To develop these models one needs to proceed from rigorous theoretical methods to approximate ones by exploiting the potential of innovative architectural features of modern concurrent processors. (indigo.ca)
- Computational Reaction and Molecular Dynamics: from Simple Systems and Rigorous Methods to Large Systems and Approximate Methods. (indigo.ca)
- Considerable emphasis will be placed on practical use of modeling and an understanding of the methods which extends beyond purely operational skills. (uio.no)
- The aim is to give the students the sufficient background to independently evaluate choice of methods and reliability of results in molecular modeling. (uio.no)
- In an earlier work, that group reported that GDT_TS (Global Distance Test, see Methods for explanation of this measure) was a better indicator of the model utility for MR than RMSD. (biomedcentral.com)
- Transfer learning methods begin with a model trained on data from one task. (energy.gov)
- Ltd for Solution structure of the N-terminal sequence of a bacterial protein by 2D-NMR and molecular modelling methods. (profeccoutinho.net.in)
- Monte Carlo methods in molecular dynamics, expos , notes de cours . (enpc.fr)
- Monte Carlo methods in molecular dynamics part 1 part 2 . (enpc.fr)
- Minisymposium "Numerical Methods for Molecular Dynamics", ENUMATH 2011 conference , September 5-9th 2011, slides . (enpc.fr)
- Article Kondratyuk N. , Pisarev V. Calculation of viscosities of branched alkanes from 0.1 to 1000 MPa by molecular dynamics methods using COMPASS force field // Fluid Phase Equilibria . (hse.ru)
- Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target binding site . (wikipedia.org)

###### Descriptors4

- The energy terms and physical descriptors obtained from the calculations were correlated with their respective experimental EC(50) values, resulting in an r(2) value of 0.70 and a root-mean-square deviation (rms) of 0.53 kcal/mol. (neb.com)
- These are the same descriptors that were used for the TIBO compounds modeled in their own sites, where the r(2) value was 0.72. (neb.com)
- [9] These features may include molecular surface / complementary surface descriptors. (wikipedia.org)
- The PLS model presented six descriptors and three Latent Variables (LV) that cumulated 71.845% of variance. (biomedsearch.com)

###### Molecule13

- article{osti_1577597, title = {Extension of the Einstein molecule method for solid free energy calculation to non-periodic and semi-periodic systems}, author = {Pretti, Evan and Mittal, Jeetain}, abstractNote = {Free energy calculations on solid phases are important for understanding the phase behavior of various systems. (osti.gov)
- en] We analyze how functionality could be obtained within single-molecule devices by using a combination of non-equilibrium Green's functions and ab initio calculations to study the inelastic transport properties of single-molecule junctions. (uliege.be)
- We show that the features in the inelastic electron tunneling spectra (IETS) of the molecular junctions are virtually independent of the nature of the molecule-lead contacts. (uliege.be)
- Second, we consider a realistic model of a organic conjugated molecule. (uliege.be)
- We use ab initio calculations to study how the vibronic properties of the molecule can be controlled by an external electric field which acts as a gate voltage. (uliege.be)
- The movie above shows that the torsion bond energy of a molecule can be modeled by a periodic function. (nyu.edu)
- a ) shows the skeleton of a 2 F obs − F model map around a molecule, whereas ( b ) shows a portion of the region from the shadowed frame of the skeleton together with the map from which it was generated. (nih.gov)
- When molecular calculations are performed, it is common to use a basis composed of atomic orbitals , centered at each nucleus within the molecule ( linear combination of atomic orbitals ansatz ). (wikipedia.org)
- A minimal basis set is one in which, on each atom in the molecule, a single basis function is used for each orbital in a Hartree-Fock calculation on the free atom. (wikipedia.org)
- 20,000 molecule HIV model. (ucsf.edu)
- The reactivity of a molecule is determined by its electronic structure, and thus predictions of properties such as the vibrational frequencies, molecular dipole moments, and polarizability can be made. (uwosh.edu)
- Furthermore, the programs show three dimensional models of the molecule demonstrating the molecular orbitals. (uwosh.edu)
- In the field of molecular modeling , docking is a method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex . (wikipedia.org)

###### Protein15

- We observed that, for CHARMM22, the unfolding transition and energy probability density were quite sensitive to the implicit solvent description, in particular, the treatment of the protein-solvent dielectric boundary in GB models and their surface-area-based hydrophobic term. (nih.gov)
- The molecular docking of DAC shows binding energy interaction (− 4.1, − 4.0, and − 4.0) Kcal/mol against microbial protein of Pseudomonas aeruginosa as Gram-negative bacteria PDB (2W7Q), and Staphylococcus aureus as Gram-positive bacteria PDB (1BQB) as well as Covid-19 PDB (7BZ5) respectively. (springer.com)
- Also, molecular docking of DAC to show its interaction with microbial protein of Pseudomonas aeruginosa PDB (2W7Q), and Staphylococcus aureus PDB (1BQB) as well as with covid-19 PDB (7BZ5) was studied and compared with Hydroxychloroquine as a standard drug used against Covid-19. (springer.com)
- Peptide bond distortions from planarity: new insights from quantum mechanical calculations and peptide/protein crystal structures. (nih.gov)
- Conversely, if the TIBO compounds are modeled in a site constructed from the BPBI complex crystal coordinates, a correlation can be obtained using the drug-protein interaction energy and change in the total number of hydrogen bonds, giving an r(2) value of 0.63. (neb.com)
- Despite the several efforts made recently to elucidate the molecular basis for the anticancer activity of these natural products, little correlation has been found thus far between the putative protein targets of compounds found in tea extracts and levels found in plasma after tea consumption. (aacrjournals.org)
- protein models. (nih.gov)
- Computational models of protein structures were proved to be useful as search models in Molecular Replacement (MR), a common method to solve the phase problem faced by macromolecular crystallography. (biomedcentral.com)
- Traditionally, typical MR experiments involved homologous structures rather than theoretical models of the target protein. (biomedcentral.com)
- Anna Tramontano and coworkers tested the utility of theoretical models submitted to the Critical Assessment of Techniques for Protein Structure Prediction (CASP) experiment. (biomedcentral.com)
- Insights from the first Principles based large scale protein thermostability calculations. (mpg.de)
- The histogram based shape representation reduces the shape comparison problem of the flexible protein to a simple distance calculation between 1D feature vectors. (ebscohost.com)
- Simple Models of Protein Evolution and the Contribution of Structurally Viable Reconstructions to the Likelihood. (ebscohost.com)
- Most phylogenetic models of protein evolution assume that sites are independent and identically distributed. (ebscohost.com)
- Molecular docking may be defined as an optimization problem, which would describe the "best-fit" orientation of a ligand that binds to a particular protein of interest. (wikipedia.org)

###### Orbitals7

- The origin of electronic spectra and the composition of the frontier molecular orbitals will be studied using TD-DFT through the continuum polarizable solvation model PCM. (scirp.org)
- To obtain hands-on experience with such calculations the (full-potential) Augmented Plane Wave plus local orbitals (APW+lo) method as embodied in the WIEN2k code will be used. (ucla.edu)
- As described by the jellium model, molecular orbitals generated by valence electrons in highly symmetric clusters have shapes just like atomic orbitals. (nature.com)
- The single-particle states ( molecular orbitals ) are then expressed as linear combinations of the basis functions. (wikipedia.org)
- While hydrogen-like atoms lack many-electron interactions, it can be shown that the molecular orbitals of Hartree-Fock and density-functional theory also exhibit exponential decay. (wikipedia.org)
- This adds flexibility to the basis set, effectively allowing molecular orbitals involving the hydrogen atom to be more asymmetric about the hydrogen nucleus. (wikipedia.org)
- Also, for HCl, CH 3 OH, and aniline the log files were opened with Jmol to create the models of bond lengths, bond angles, and HOMO orbitals, for this webpage. (uwosh.edu)

###### Spectra2

- UV-Vis absorption spectra were measured in the range of 250-800 nm using a double beam UNICAM spectrophotometer model (He λ ios α ). (hindawi.com)
- Covers chemical thermodynamics, molecular structure and spectra, and chemical kinetics. (luc.edu)

###### Atomic7

- The present review focuses on the available ab initio based solid-solution models (virtual lattice approximation, coherent potential approximation, special quasirandom structure, similar local atomic environment, maximum-entropy method, and hybrid Monte Carlo/molecular dynamics) and their applications and limits in single phase HEAs. (frontiersin.org)
- Molecular Modeling Techniques in Materials Science presents the background and tools for chemists and physicists to perform in-silico experiments to understand relationships between the properties of materials and the underlying atomic structure. (routledge.com)
- Computational models of chemical and biological systems at the atomic scale are an important tool for chemists. (energy.gov)
- Analytically derived interaction energies, which are based on elasticity theory, are compared with interaction energies obtained from atomistic model using semi-empirical atomic potentials as physics basis. (diva-portal.org)
- pKa's of ionizable groups in proteins: Atomic detail from a continuum electrostatic model. (currentprotocols.com)
- Software for statistics-based fitting of atomic models into density maps of lower resolution such as those obtained by electron microscopy and image reconstruction. (wikibooks.org)
- Supports fitting atomic models in maps, interactive segmentation, coarse modeling, measuring and coloring of density maps for elucidating structures of large molecular assemblies. (wikibooks.org)

###### Structures9

- Many stable substances such as clusters have been predicted based on the jellium model, which usually assumes that their structures are approximately spherical. (nature.com)
- Many molecular structures have the same shape of familiar space figures. (nyu.edu)
- The unique and innovative sketcher is optimized for the touchscreen interface, and allows professional quality molecular structures to be drawn quickly and efficiently. (apple.com)
- However, many corporate and purchasable compound databases contain only 2D molecular structures. (schrodinger.com)
- LigPrep generates accurate, energy minimized 3D molecular structures. (schrodinger.com)
- Increase in data size and coverage: molecular structures, sequences, and density maps. (ucsf.edu)
- ChimeraX has new solvent excluded surface calculation works for all structures, 30x faster. (ucsf.edu)
- Using comparative models only marginally increases the MR success ratio in comparison to polyalanine structures of templates. (biomedcentral.com)
- This collection of 50 papers focuses on the theory and modeling of nanoscale materials and structures. (spie.org)

###### Proteins4

- Disulfides serve as (largely permanent) molecular "staples" that direct and stabilize the three-dimensional structure of proteins, and determine the distance and angle constraints between the joined cysteine residues, therefore stabilizing the folded state with respect to the unfolded form 2 . (nature.com)
- The proteins associated with amyotrophic lateral sclerosis also showed distinct differences between cell lines and primary motoneurons, providing a molecular basis for understanding fundamental alterations between cell lines and neurons with respect to neuronal pathways with relevance for disease mechanisms. (mcponline.org)
- In: Molecular Modeling of Proteins, S. 173 - 209 (Hg. (mpg.de)
- Hands-on activity that makes models of proteins and motifs such as beta pleated sheets and alpha helices and cyctochrome C. (netvouz.com)

###### Thermodynamics2

###### Solvation2

- Lithium Ion Solvation and Diffusion in Bulk Organic Electrolytes from First Principles Molecular Dynamics. (psu.edu)
- Generalized Born models of macromolecular solvation effects. (currentprotocols.com)

###### Chemical calculations1

- The Calculators & Predictors offer a wide range of chemical calculations that are available from multiple endpoints, combining great availability, consistency and integration options. (chemaxon.com)

###### Prediction5

- We have focused on the violation of the spherical jellium model to extend the theory for the prediction of clusters. (nature.com)
- Together, these models may find application in drug discovery for prediction of acyl glucuronide and glucoside metabolite behaviour. (rsc.org)
- Two concepts are key in the application of the model to the prediction of steady-state skin permeability coefficients: "effective diffusivity" and "effective path length," meaning the diffusivity and thickness of a homogeneous membrane having identical permeation properties as the stratum corneum. (cdc.gov)
- A new functionality was added to the GeneSilico Fold Prediction Metaserver in order to build models that are more useful for MR searches. (biomedcentral.com)
- Article Pisarev V. , Kondratyuk N. Prediction of viscosity-density dependence of liquid methane+n-butane+n-pentane mixtures using the molecular dynamics method and empirical correlations // Fluid Phase Equilibria . (hse.ru)

###### Chemistry8

- Exploring Chemistry will be helpful to most Gaussian users, from beginners who are just starting to use calculations to experienced users who want to become familiar with advanced modeling techniques and capabilities. (gaussian.com)
- JMGM is published in association with two of the largest and most active professional societies in the field: the Molecular Graphics and Modelling Society (MGMS) and the Computers in Chemistry (COMP) Division of the American Chemical Society . (elsevier.com)
- The course is designed to give students in chemistry and related subjects an introduction to the theory for molecular modeling, and use of modeling as a tool in chemical research. (uio.no)
- For example, it may simulate nature to advance research in chemistry, materials science, and molecular modeling. (intel.com)
- The method is central to many questions in modern chemistry, and computer models are a powerful tool for answering these questions. (energy.gov)
- Researchers have so far achieved these levels only with quantum chemistry calculations, which require much more computing power. (energy.gov)
- This model can capture a diversity of chemical processes, and it is broadly applicable to fields such as materials science, biology, and chemistry. (energy.gov)
- Gas-phase combustion chemistry can be investigated using detailed chemical models sometimes called mechanisms. (royalsocietypublishing.org)

###### Biochemistry1

- The name is 'Utopia' reversed: the software creates a utopia that simulates the genetics, biochemistry, molecular biology, and evolution of organisms in a biologically reasonable and pedagogically relevant way. (netvouz.com)

###### Energies3

- This allows for the calculation of exact absolute free energies of finite-sized crystals having specific shapes and surface geometries. (osti.gov)
- A UV-Vis spectrum for aniline was used as a comparison for calculations of the transitions energies of the two highest levels of theory for aniline. (uwosh.edu)
- Calculation of binding free energies. (mpg.de)

###### Theoretical calculations2

- Finally, a good consistency between experimental and theoretical calculations was found confirming that the applied basis set is the suitable one for the system under investigation. (scirp.org)
- The obtained results have been compared with theoretical calculations. (ebscohost.com)

###### United-atom1

- A further comparison is provided with the united-atom CHARMM19 plus a pairwise GB model. (nih.gov)

###### Diffusion4

- The rationale for this model is to represent diffusion by its fundamental molecular mechanism, i.e., random thermal motion. (cdc.gov)
- Diffusion is modeled as a twodimensional random walk through the biphasic (lipid and corneocyte) stratum corneum (SC). (cdc.gov)
- This approach permits calculations of diffusion phenomena in a morphologically realistic SC structure. (cdc.gov)
- Article Kondratyuk N. , Norman G. , Stegailov V. Self-consistent molecular dynamics calculation of diffusion in higher n-alkanes // Journal of Chemical Physics . (hse.ru)

###### Processes5

- Molecular processes in nature affect human health, the availability of resources and the Earth s climate. (researchandmarkets.com)
- This book will be of interest to graduate students and researchers looking to understand geochemical processes on a molecular level. (researchandmarkets.com)
- The amazing growth of computational resources has made possible the modeling of complex chemical processes. (indigo.ca)
- Inactivation of the endotoxic biomolecule lipid A by oxygen plasma species: a reactive molecular dynamics study Plasma Processes and Polymers 12, 162-171. (psu.edu)
- The behavior of drugs in the different biological processes of the human body is governed by the molecular structure. (chemaxon.com)

###### Visualization4

- The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. (nih.gov)
- The main purpose of this graphical model visualization is to explore structure-property relationships in depth by doing analysis of computational data. (hindawi.com)
- ChimeraX is our next generation molecular visualization software following Midas, MidasPlus and Chimera. (ucsf.edu)
- Ariadne Genomics is a bioinformatics company producing molecular networks databases and software for visualization and analysis of biological pathways and gene regulation networks. (netvouz.com)

###### Docking4

- An in silico test and Molecular Docking tests were performed. (mdpi.com)
- One can think of molecular docking as a problem of "lock-and-key" , in which one wants to find the correct relative orientation of the "key" which will open up the "lock" (where on the surface of the lock is the key hole, which direction to turn the key after it is inserted, etc. (wikipedia.org)
- Molecular docking research focuses on computationally simulating the molecular recognition process. (wikipedia.org)
- Two approaches are particularly popular within the molecular docking community. (wikipedia.org)

###### Biology4

- Calculations for Molecular Biology and Biotechnology: A Guide to Mathematics in the Laboratory, Second Edition , provides an introduction to the myriad of laboratory calculations used in molecular biology and biotechnology. (elsevier.com)
- Using bio-ontologies, biosemantics and special processing concepts, progress was achieved in dealing with genomics, biopharmaceutical and molecular intelligence, in the biology and microbiology domains. (iaria.org)
- The area brings a rich spectrum of informatics paradigms, such as epidemic models, pattern classification, graph theory, or stochastic models, to support special biocomputing applications in biomedical, genetics, molecular and cellular biology and microbiology. (iaria.org)
- There are double-major programs with the Departments of Physics, Chemical Engineering and Molecular Biology and Genetics. (boun.edu.tr)

###### Stochastic2

- Model reduction techniques for stochastic dynamics , pdf . (enpc.fr)
- Molecular dynamics with stochastic boundary conditions. (currentprotocols.com)

###### Biological4

- Reference: Molecular modeling calculations of HIV-1 reverse transcriptase nonnucleoside inhibitors: correlation of binding energy with biological activity for novel 2-aryl-substituted benzimidazole analogues. (neb.com)
- Subsequent synthesis and biological activity testing of these analogues have shown the validity of the predictive calculations. (neb.com)
- We used this resource to evaluate the suitability of murine in vitro model systems for cell biological and biochemical analysis of motoneuron disease mechanisms. (mcponline.org)
- There, molecular biological techniques are used to research causes, diagnosis and treatment of diseases such as cancer. (fh-campuswien.ac.at)

###### Electron4

- First, we apply a full non-equilibrium Green's function technique to a model system with electron-vibration coupling. (uliege.be)
- A model of single-electron transport. (springer.com)
- The spatial decay of the electron sharing indices in the course of transition has also been evaluated and compared with the results obtained for the Hubbard model and finite cluster calculations. (deepdyve.com)
- A comparison of the calculated bias factor with a model based on elasticity theory reveals around 30% discrepancy under conditions representative for electron irradiation at 600 degrees C. Possible reasons are discussed. (diva-portal.org)

###### Genomics1

- Heredity and Meiosis\n\nDNA and Genes\n\n * Genetics reference guide\n * U.S. Department of Energy Division of Science\n * G.A.M.E. (Genomics Analogy Model for Educators), University of Purdue\n * Genetic Animations (Dolan DNA Learning Center)\n * Genetics Education Center (University of Kansas Medical Center)\n * What the heck is a gene? (netvouz.com)

###### Orbital calculations1

- The surface chemical structure of [A-AM silane]/SiO 2 was characterized by Fourier transform infrared spectroscopy and molecular orbital calculations. (mdpi.com)

###### Dynamics Calculations1

- Article Stegailov V. , Dlinnova E. , Ismagilov T., Khalilov M. , Kondratyuk N. , Makagon D., Semenov A. , Simonov A., Smirnov G. , Timofeev A. Angara interconnect makes GPU-based Desmos supercomputer an efficient tool for molecular dynamics calculations // International Journal of High Performance Computing Applications . (hse.ru)

###### Applications5

- This book is the first stop for any materials scientist, biochemist, chemist or molecular physicist wishing to acquaint themselves with major developments in the applications and theory of chemical modelling. (rsc.org)
- applications of molecular modelling in NMR structure determination. (ebooks.com)
- Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. (elsevier.com)
- Evaluation of HCM: a New Model to Predict the Execution Time of Regular Parallel Applications on a Heterogeneous Cluster. (barnesandnoble.com)
- In addition to applications in the medical field, molecular biotechnology is also used in the development of vaccines and active pharmaceutical ingredients. (fh-campuswien.ac.at)

###### Conformation2

- Among the solvent models tested, the calculated melting temperature varied in the range 353-438 K and was higher than the experimental value near 340 K. A reformulated GBMV2 model of employing a smoother molecular-volume dielectric interface was the most accurate in reproducing the native conformation and a two-state folding landscape, although the melting transition temperature did not show the smallest deviation from experiment. (nih.gov)
- Organic compounds natural or synthetic are the main source of medical agents and drugs, so knowledge of their molecular structure and conformation is important because it has a direct correlation with their activity. (hindawi.com)

###### Mathematical2

###### Liquids1

- Journal of Molecular Liquids , 266 , 467-471. (tue.nl)

###### Clusters2

- The jellium model is effective to explain subglobular clusters such as icosahedral clusters. (nature.com)
- In such clusters, the validity of the spherical jellium model decreases relatively due to the split and shift of the superatomic orbital levels. (nature.com)

###### Vibrational1

- The dipole moments were found by opening the file in TextEditor and searching for the last occurrence of "/D/". For the calculation of the vibrational frequencies of HCl, CH 3 OH, and aniline, MacMolPlt was used along with the highest level of theory, DZV and 6311-G. The categories for the vibrational calculation in MacMolPlt were selected and the file written. (uwosh.edu)

###### Electronic structure calculations1

- However, now electronic structure calculations by computers with software packages can be made by non specialists. (uwosh.edu)

###### Experimental7

- Complemented with experimental results, molecular modelling using the density functional theory (DFT) calculations was carried out in the gas, chloroform and methanol phases where the existence of charge and hydrogen transfers. (scirp.org)
- In order to confirm the experimental results, a theoretical computations using the density functional theory (DFT) at the basis set B3LYP/6-31 G(d,p) will be carried out to study the ground-state properties as optimization the structure, geometrical parameters, reactivity parameters, Fukui functions and molecular electrostatic potential maps (MEP). (scirp.org)
- A review of recent studies of molecular dynamics of water in foods and model systems is presented, and the theoretical results are compared with experimental data obtained by several techniques. (springer.com)
- The objective of the study is to evaluate the analgesic and anti-inflammatory effect of the crude extract of S. dulcis , in an experimental model of osteoarthritis. (mdpi.com)
- Among the CONI models used for transcriptome analyses, the most commonly used are models of experimental or inherited glaucoma. (molvis.org)
- Molecular modelling is a powerful and versatile toolbox that complements experimental data and provides insights where direct observation is not currently possible. (researchandmarkets.com)
- The use of the model is illustrated by calculations of the partition of salts in a standard milk and by comparison with experimental data on the partition of salts in the milk of individual cows. (springer.com)

###### Bioinformatics2

- Bioinformatics deals with the system-level study of complex interactions in biosystems providing a quantitative systemic approach to understand them and appropriate tool support and concepts to model them. (iaria.org)
- Bioinformatics itself constitutes a vast area of research and specialization, as many classical domains such as databases, modeling, and regular expressions are used to represent, store, retrieve and process a huge volume of knowledge. (iaria.org)

###### Centre1

- Pendant l'ann e 2004-2005, j' tais en post-doc au Centre de Recherches Math matiques l'Universit de Montr al, dans le cadre d'une ann e th matique sur les math matiques de la mod lisation multi chelle et stochastique . (enpc.fr)

###### Multiscale1

- A multiscale modelling framework and an experiment campaign are used to study void swelling and Cu precipitation under irradiation. (diva-portal.org)

###### Interactions3

- Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. (nih.gov)
- Molecular dynamics investigation of the effects of tip-substrate interactions during nanoindentation. (psu.edu)
- Interactions of plasma species on nickel catalysts: a reactive molecular dynamics study on the influence of temperature and surface structure. (psu.edu)

###### Parameters3

- These diagnostic parameters show that TP real-time RT-PCR was the most sensitive technique, whereas TP-ELISA showed the highest specificity, validating the use of the molecular technique for routine CTV-detection purposes. (apsnet.org)
- Discussing the advantages and disadvantages of various approaches, the authors develop a framework for identifying objectives, defining design parameters, measuring accuracy/accounting for error, validating and assessing various data collected, supporting software needs, and other requirements for planning a modeling project. (routledge.com)
- Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. (elsevier.com)

###### Reaction8

- Although it's distinctive properties, cellulose is insoluble in conventional solvents and it owing to inter and intra-molecular hydrogen bonds which obstacle it's direct reaction. (springer.com)
- This book reviews some of the most advanced theoretical approaches in the field of molecular reaction dynamics in order to cope as rigorously as possible with the complexity of real systems. (indigo.ca)
- Direct Calculation of Reaction rates. (indigo.ca)
- Ab Initio Calculations on the Harpooning Reaction in BA. (indigo.ca)
- Here we report detailed kinetic models of each transacylation and hydrolysis reaction for a series of phenylacetic acid acyl glucuronides and their analogous acyl glucosides. (rsc.org)
- The transacylation reaction was modelled using density functional theory and the calculated activation energy for this reaction showed a close correlation with the degradation rate of the 1-β anomer. (rsc.org)
- In this paper, we outline the future of modelling in reaction engineering. (royalsocietypublishing.org)
- The reaction rate constants can be obtained from either parameter fitting to specially designed experiments, or directly from quantum calculations. (royalsocietypublishing.org)

###### Surface4

- Chimera 1 molecular surface and area calculations fail on many structure over 10000 atoms. (ucsf.edu)
- Surface and area calculation can use multiple cores. (ucsf.edu)
- Comparative molecular dynamics study of fcc-Ni nanoplate stress corrosion in water Surface Science 633, 94-101. (psu.edu)
- In this case, the receptor's molecular surface is described in terms of its solvent-accessible surface area and the ligand's molecular surface is described in terms of its matching surface description. (wikipedia.org)

###### Reactivity1

- Ab-Initio MD Calculations on Dynamics and Reactivity in Confined and Disordered Systems. (indigo.ca)

###### Results7

- As a typical solid-solution material, the large degree of uncertainty of high-entropy alloys (HEAs) results in the difficulty of ab initio calculations application to HEAs. (frontiersin.org)
- Therefore, we compared the expression results from heterogeneous studies of optic nerve injury and neurodegenerative models. (molvis.org)
- For individual models, the results are shown as a probability estimate, and a molecular overlay showing the atoms that contributed (ECFP6) fingerprints to the better/worse features. (apple.com)
- The last two are expected to yield similar results to the hypothetical RAO model, but with a different timescale. (creation.com)
- The alternative approach to molecular dynamics-i.e., models based on quantum mechanical physics-yields more complete results but is complex and time-consuming. (energy.gov)
- To view the results for the models and calculations of Hydrogen Chloride, Methanol, and Aniline click on molcules below. (uwosh.edu)
- Cutoff size need not strongly influence molecular dynamics results for solvated polypeptides. (currentprotocols.com)

###### Comparative3

- Fast display of hundreds of medium size models helps comparative modeling. (ucsf.edu)
- However, the situation changes dramatically once comparative models are used together with their predicted local accuracy. (biomedcentral.com)
- Comparative molecular dynamics study of fcc-Al hydrogen embrittlement Corrosion Science Published online. (psu.edu)

###### Energy Calculations4

- This hands-on course focuses on the application of density-functional theory (DFT) to electronic-structure and total-energy calculations in different scientific fields. (ucla.edu)
- Free energy calculations on solid phases are important for understanding the phase behavior of various systems. (osti.gov)
- They use the computer analysis to improve geometry and energy calculations, thus predicting if reactions will work. (uwosh.edu)
- Free energy calculations , expos . (enpc.fr)