Results 221 to 230 of about 321,840 (265)
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Molecular dynamics simulation and steered molecular dynamics simulation on irisin dimers
Journal of Molecular Modeling, 2018Irisin is found closely associated with promoting the browning of beige fat cells in white adipose tissue. The crystal structure reveals that irisin forms a continuous inter-subunit β-sheet dimer. Here, molecular dynamics (MD) simulation and steered molecular dynamics (SMD) simulation were performed to investigate the dissociation process and the ...
Qi, Gao +5 more
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Accounting for polarization in molecular simulation
Computer Physics Communications, 2005Abstract Polarization plays an important role in the energetics of molecular systems, not the least in biomolecular systems. Most computer simulation studies of such systems do not treat electronic polarizability explicitly, but only implicitly using effective charges, dielectric permittivities or continuum electrostatics methods.
Haibo Yu 0003, Wilfred F. van Gunsteren
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Molecular Simulation – A Primer
1997Quantum chemistry allows us to calculate molecular properties with arbitrary accuracy: potential surface, geometry, moments, spectra, etc. However, there are properties which do not depend on a single molecule alone but can only be defined for an ensemble of many molecules: melting point, diffusion coefficient, density, for example.
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Molecular dynamics simulations of xDNA
Biopolymers, 2009AbstractxDNA is a modified DNA, which contains natural as well as expanded bases. Expanded bases are generated by the addition of a benzene spacer to the natural bases. A set of AMBER force‐field parameters were derived for the expanded bases and the structural dynamics of the xDNA decamer (xT5′ G xT A xC xG C xA xG T3′) · (xA5′ C T xG C G xT A xC A3′)
Mathew K, Varghese +3 more
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Molecular dynamics simulation and visualization
1999 IEEE International Conference on Information Visualization (Cat. No. PR00210), 2003We have developed atomic-scale material models capable of simulating melting, crystallization and amorphization. These models feature molecular dynamics governed by Langevin equations of motion in which particles interact through attractive covalent forces and short-range repulsion forces.
Roman Durikovic, Teruaki Motooka
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Molecular simulation as an aid to experimentalists
Current Opinion in Structural Biology, 2008Computer-based molecular simulation techniques are increasingly used to interpret experimental data on biomolecular systems at an atomic level. Direct comparison between experiment and simulation is, however, seldom straightforward. The available experimental data are limited in scope and generally correspond to averages over both time and space.
van Gunsteren, W.F. +2 more
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Hybrid approaches to molecular simulation
Current Opinion in Structural Biology, 2012Molecular dynamics (MD) simulation is an established method for studying the conformational changes that are important for protein function. Recent advances in hardware and software have allowed MD simulations over the same timescales as experiment, improving the agreement between theory and experiment to a large extent.
Bosco K, Ho +2 more
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Integrating Molecular Docking and Molecular Dynamics Simulations
2019Computational methods, applied at the early stages of the drug design process, use current technology to provide valuable insights into the understanding of chemical systems in a virtual manner, complementing experimental analysis. Molecular docking is an in silico method employed to foresee binding modes of small compounds or macromolecules in contact
Lucianna H S, Santos +2 more
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Molecular Simulations of Interacting Nanocrystals
Nano Letters, 2008We compute the potential of mean force for two gold nanocrystals capped by alkylthiols from atomistic simulations and show how variables such as temperature, capping molecule length, and the presence of solvent affect these interactions. Our main findings are (1) the equilibrium distance in vacuum always equals approximately 1.25 times the core ...
Philipp, Schapotschnikow +2 more
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Visualization of Molecular Dynamics by Simulation
Annals of the New York Academy of Sciences, 2002Abstract: The mechanism of formation of methane hydrate is investigated here at a molecular level. The key to whether or not methane hydrates can be formed is the stability of the hydrate structure. This paper deals with a computer simulation of methane hydrate type 1 formation by a molecular dynamics method and an accurate description of the crystal ...
Masahiro, Ota, Yingxia, Qi
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