نتایج جستجو برای: md simulation

تعداد نتایج: 596938  

2006
V. P. Carey A. P. Wemhoff

The concept of disjoining pressure, developed from thermodynamic and hydrodynamic analysis, has been widely used as a means of modeling the liquid-solid molecular force interactions in an ultra-thin liquid film on a solid surface. In particular, this approach has been extensively used in models of thin film transport in passages in micro evaporators and micro heat pipes. In this investigation, ...

Journal: :The Journal of chemical physics 2015
Philipp Schierz Johannes Zierenberg Wolfhard Janke

Molecular Dynamics (MD) and Monte Carlo (MC) simulations are the most popular simulation techniques for many-particle systems. Although they are often applied to similar systems, it is unclear to which extent one has to expect quantitative agreement of the two simulation techniques. In this work, we present a quantitative comparison of MD and MC simulations in the microcanonical ensemble. For t...

Journal: :Protein science : a publication of the Protein Society 2014
Yi Xue Nikolai R Skrynnikov

Currently, the best existing molecular dynamics (MD) force fields cannot accurately reproduce the global free-energy minimum which realizes the experimental protein structure. As a result, long MD trajectories tend to drift away from the starting coordinates (e.g., crystallographic structures). To address this problem, we have devised a new simulation strategy aimed at protein crystals. An MD s...

2000
Dušanka Janežič Matej Praprotnik

Molecular dynamics (MD) simulation, in which the classical equations of motion for all particles of a system are integrated over finite period of time, is one of the theoretical methods to investigate dynamical properties of molecular systems [1]. The problem which arises in performing MD simulations of such systems is that only short simulations can be performed due to the high-frequency motio...

F. Kaveh H. Pasdar

The interaction between proteins and membranes has an important role in biological pro-cesses.We have calculated energies of interaction between Melittin and DMPC bilayer in differenttemperatures. We have used the CHARMM software for MD simulation under the canonical (N,V, E) ensemble at different temperatures. The computations have shown that water moleculeshave more penetration into the bilay...

2011
Sara E. Nichols Riccardo Baron Anthony Ivetac James Andrew McCammon

Molecular dynamics (MD) simulation is a well-established method for understanding protein dynamics. Conformations from unrestrained MD simulations have yet to be assessed for blind virtual screening (VS) by docking. This study presents a critical analysis of the predictive power of MD snapshots to this regard, evaluating two well-characterized systems of varying flexibility in ligand-bound and ...

A. Kazemi Babaheydari M. Khaleghian M. Monajjemi N. Dalili Mansour

Serum Albumin is the most aboundant protein in blood plasma. Its two major roles aremaintaining osmotic pressure and depositing and transporting compounds. In this paper,Albumin-methanol solution simulation is carried out by three techniques including MonteCarlo (MC), Molecular Dynamic (MD) and Langevin Dynamic (LD) simulations. Byinvestigating energy changes by time and temperature (between 27...

2014
James A. Mckinnell Sarah M. Bartsch Bruce Lee Susan S. Huang Loren Miller

for Methicillin-resistant Staphylococcus aureus: A Monte Carlo Simulation of the Economic Impact to the Individual Hospital James A. Mckinnell, MD; Sarah M. Bartsch, MPH; Bruce Lee, MD, MBA; Susan S. Huang, MD, MPH, FIDSA; Loren Miller, MD, MPH; Torrance Memorial Medical Center, Torrance, CA; Infectious Disease Clinical Outcomes Research Unit at Los Angeles Biomedical Research Institute, Torran...

Journal: :The Journal of chemical physics 2006
Wenzhong Tang Suresh G Advani

In this work, nonequilibrium molecular dynamics (MD) simulations were performed to investigate uniform liquid argon flow past a carbon nanotube. In the simulation, nanotubes were modeled as rigid cylinders of carbon atoms. Both argon-argon and argon-carbon interactions were calculated based on Lennard-Jones potential. Simulated drag coefficients were compared with (i) published empirical equati...

M. Shariaty-Niassar

The overall aim of this study is to calculate some water properties in the single wall carbon naotubes (SWCNT) and compare them to the bulk water properties to investigate the deviation of water properties inside the SWCNT from those in the bulk. Here some physical and transport properties of water molecules in the single wall carbon nanotube were reported by performing molecular dynamics (MD) ...

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