Molecular Simulations
Molecular simulations and visualization: introduction and overview
... three-dimensional molecular structures, a notable milestone along this path goes back to the early 40s when Roger Hayward depicted the arrangement of atomic assemblies in collaboration with Linus Pauling in both a ...
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Promoting transparency and reproducibility in enhanced molecular simulations
... The success of the open-source PLUMED library is due not only to the contributions of the core developers but also to the efforts of an entire community of users and developers. To acknowledge this working model, here we ...
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Molecular Simulations of Protein-Induced Membrane Remodeling
... In order to quantify protein-induced bilayer curvatures, we extract two types of data from our coarse-grained simulations. First, lipid centers of mass from both mono- layers are interpolated and then averaged to ...
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Stochastic quasi-Newton molecular simulations
... surface information and varies. Langevin dynamics, however, is a coarse-grained description for the purely diffu- sive motion of n particles on a time scale that is large enough to integrate out the rapid modes and ...
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Polymer Nanocomposites: Insights from Theory and Molecular Simulations.
... The molecular electrostatic potential for thiophene chains and fullerene molecules was calculated using the AM1-BCC charge model that emulates the Hartree-Fock level of theory with a 6-31G* basis set ...
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A stochastic quasi Newton method for molecular simulations
... Many simulations of protein conformational changes or dynamics begin at the native crystal structure using the atomic coordinates measured from electron density maps obtained by X-ray diffraction ...Other ...
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Visual cavity analysis in molecular simulations
... As a next step, we perform a cavity based analysis, which classifies the samples into potential cavity sam- ples. Note that there is no exact cavity definition with respect to any of aforementioned molecular ...
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Molecular dynamics pre simulations for nanoscale computational fluid dynamics
... and molecular simulations show that the continuum-fluid assumptions ...MD simulations have been used to show that Lennard–Jones (LJ) fluids confined to geometries of *2–3 nm still show continuum ...
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Molecular dynamics pre-simulations for nanoscale computational fluid dynamics
... and molecular simulations show that the continuum-fluid assumptions ...MD simulations have been used to show that Lennard–Jones (LJ) fluids confined to geometries of *2–3 nm still show continuum ...
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Throughput Improvement of Molecular Dynamics Simulations Using Reconfigurable Computing
... Since the performance of the FPGA devices are increasing at a much faster rate than commodity micro- processors [43, 44] and the SRC-6E contains relatively old FPGA devices (two generations old), we developed a ...
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Temperature control in molecular dynamic simulations of non equilibrium processes
... MD simulations of non-equilibrium processes? We give several arguments in favour of the SBC which is a stochastic thermostat with only border atoms experiencing additional random and friction forces to control the ...
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Protocol for classical molecular dynamics simulations of nano junctions in solution
... classical molecular dynamics for water confined in the ...classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N ...
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Chemical evolution of giant molecular clouds in simulations of galaxies
... A final caveat to note is that these conclusions depend on how the cloud age is defined. We have defined the cloud age from the time when half of the particles currently in the cloud were in a cloud progenitor. However, ...
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Nitrogenation of Amorphous Silicon : Reactive Molecular Dynamics Simulations
... In this simulation, Reactive Force Field (ReaxFF) made by Van Duin et.al was used due to its capability to handle forming and breaking of atomic bonding as well as its ability to represent charge transfer [13]. ...
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Quantum Molecular Dynamics Simulations of Warm Dense Li Plasma
... the molecular dynamics (MD) in which the atoms (ions) are followed individually through their interactions and trajectory in space, time and ...quantum molecular dynamics (QMD) the electrons are given an ...
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Exploiting molecular dynamics in Nested Sampling simulations of small peptides
... In the original algorithm, simulations are initialised by choosing samples uniformly throughout the whole of configuration space. As we are only interested in thermodynamics at relatively low temperatures, we ...
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Mechanical characterization of nanoindented graphene via molecular dynamics simulations
... The mechanical behavior of graphene under various indentation depths, velocities, and temperatures is studied using molecular dynamics analysis. The results show that the load, elastic and plastic energies, and ...
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Molecular Dynamics Simulations of Charged Nanodroplets
... Choosing a proper water model for computer simulations of charged droplets plays a significant role in the final results. The literature serves as a vast repository of various water models designed over the course ...
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Molecular dynamics simulations of liquid flow in and around carbon nanotubes
... both simulations are shown in ...flow simulations of confined liquids in nanoscale channels and pores [8, 17, ...both simulations that the fluid density close to the CNT walls is zero, which is in ...
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Machine Learning Molecular Dynamics Simulations for Enhanced Student Learning
... mentioned simulations of ionic systems ...fastest simulations took about 10 minutes to provide the converged ionic densities while the slowest ones (generally associated with larger system sizes) took over ...
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