Results 221 to 230 of about 291,774 (264)

Molecular dynamics simulation and steered molecular dynamics simulation on irisin dimers

Journal of Molecular Modeling, 2018
Irisin 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, Chao, Lu, Xiao-Wen, Wang, Jun-Wei, Zhang, Youtao, Song, You-Lin, Xue   +5 more
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Accounting for polarization in molecular simulation

Computer Physics Communications, 2005
Abstract 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

1997
Quantum 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, 2009
AbstractxDNA 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, Renjith, Thomas, N V, Unnikrishnan, C, Sudarsanakumar   +3 more
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Molecular dynamics simulation and visualization

1999 IEEE International Conference on Information Visualization (Cat. No. PR00210), 2003
We 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, 2008
Computer-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., Dolenc, J., Mark, A.E.   +2 more
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Hybrid approaches to molecular simulation

Current Opinion in Structural Biology, 2012
Molecular 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, David, Perahia, Ashley M, Buckle   +2 more
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Molecular Dynamics Simulation of Colchicinoids

Journal of Biomolecular Structure and Dynamics, 1998
Colchicine, a tricyclic alkaloid, has a remarkable range of biological activities. It binds with tubulin and prevents the formation of microtubules. This compound consists of a six membered aromatic ring (A ring), a seven membered troponoid ring (C ring) and another seven membered aliphatic ring (B ring).
A K, Bothra, S, Roy, B, Bhattacharyya, C, Mukhopadhyay   +3 more
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Integrating Molecular Docking and Molecular Dynamics Simulations

2019
Computational 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, Rafaela S, Ferreira, Ernesto R, Caffarena   +2 more
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Molecular Dynamics simulation of the microregion

International Journal of Thermal Sciences, 2012
As evaporation occurs in microchannels, most heat transfer takes place in the region where the evaporation meniscus is in contact with the channel wall. This microregion has been studied before, using continuum methods. Experimental results have shown the existence of this microregion but its internal structure can not be verified experimentally ...
Akker, van den, E.A.T., Frijns, A.J.H., Kunkelmann, C., Hilbers, P.A.J., Stephan, P., Steenhoven, van, A.A.   +5 more
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