scholarly journals GENESIS: a hybrid-parallel and multi-scale molecular dynamics simulator with enhanced sampling algorithms for biomolecular and cellular simulations

2015 ◽  
Vol 5 (4) ◽  
pp. 310-323 ◽  
Author(s):  
Jaewoon Jung ◽  
Takaharu Mori ◽  
Chigusa Kobayashi ◽  
Yasuhiro Matsunaga ◽  
Takao Yoda ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enhanced Sampling ◽  
Multi Scale ◽  
Sampling Algorithms ◽  
Genesis A

scholarly journals GENESIS 1.1: A hybrid-parallel molecular dynamics simulator with enhanced sampling algorithms on multiple computational platforms

2017 ◽  
Vol 38 (25) ◽  
pp. 2193-2206 ◽  
Author(s):  
Chigusa Kobayashi ◽  
Jaewoon Jung ◽  
Yasuhiro Matsunaga ◽  
Takaharu Mori ◽  
Tadashi Ando ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enhanced Sampling ◽  
Sampling Algorithms ◽  
Parallel Molecular Dynamics

Toward an Enhanced Sampling Molecular Dynamics Method for Studying Ligand-Induced Conformational Changes in Proteins

2015 ◽  
Vol 119 (46) ◽  
pp. 14594-14603 ◽  
Author(s):  
Ole Juul Andersen ◽  
Julie Grouleff ◽  
Perri Needham ◽  
Ross C. Walker ◽  
Frank Jensen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Molecular Dynamics Method ◽  
Enhanced Sampling ◽  
Dynamics Method

SPONGE : A GPU‐Accelerated Molecular Dynamics Package with Enhanced Sampling and AI‐Driven Algorithms

2021 ◽  
Author(s):  
Yu‐Peng Huang ◽  
Yijie Xia ◽  
Lijiang Yang ◽  
Jiachen Wei ◽  
Yi Isaac Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Enhanced Sampling ◽  
Accelerated Molecular Dynamics

Simulating Surface Forces Between Iron Oxide Surfaces Immersed in Methyl Oleate Using Molecular Dynamics

2018 ◽  
Author(s):  
William W. F. Chong ◽  
Hedong Zhang
Keyword(s):  
Molecular Dynamics ◽  
Iron Oxide ◽  
Methyl Oleate ◽  
Md Simulation ◽  
Surface Forces ◽  
Oxide Surfaces ◽  
Load Bearing ◽  
Multi Scale ◽  
Molecular Potentials ◽  
Solvation Forces

Using Molecular Dynamics (MD) simulation, the current study determined the surface forces between iron oxide surfaces when immersed in methyl oleate. Condensed-phase Optimized Molecular Potentials for Atomistic Simulation Studies (COMPASS) force field was used to model the methyl oleate molecules. For the nano-confinement simulation, the iron oxide wall was modelled from its crystal structure. The nano-confinement simulation model was setup in a manner where the confined methyl oleate molecules were in contact with the bulk molecules surrounding each side of the iron oxide walls. Through the simulation, the load-separation gap profile was obtained by reducing the separation gap between the ferric oxide walls. When the separation gap was reduced from 2.75 nm to 1.88 nm, the load is shown to increase monotonically. Such increase in load bearing ability of the contact is observed to correspond to a more densely packed methyl oleate molecules, reflected by four well-formed layers across the separation gap. As the gap is dropped from 1.88 nm to 1.63 nm, the load instead reduces, indicating deteriorating load bearing ability of the contact. However, the load bearing ability of the contact is then shown to recover when the gap was further reduced till 1.38 nm. This oscillatory load trend is shown to be as a result of a layer of methyl oleate molecules being squeezed out of contact, corroborated by the density profile change where four well-formed layers were reduced to only three layers from 1.88 nm to 1.38 nm gap. This also indicates that the simulated contact exhibits structural forces, known as solvation forces. Thus, the MD simulation discussed in this study is demonstrated to be capable of providing a foundation to allow for a multi-scale simulation, integrating various force laws at different length scales, to study larger scale tribological contacts.

A multi-scale molecular dynamics simulation of PMAL facilitated delivery of siRNA

RSC Advances ◽  
2015 ◽  
Vol 5 (83) ◽  
pp. 68227-68233 ◽  
Author(s):  
Jipeng Li ◽  
Yiyun Ouyang ◽  
Xian Kong ◽  
Jingying Zhu ◽  
Diannan Lu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Lipid Bilayer ◽  
Dynamics Simulation ◽  
Lipid Bilayer Membranes ◽  
Bilayer Membranes ◽  
Multi Scale

PMAL as a novel carrier for the delivery of siRNA into lipid bilayer membranes.

scholarly journals Multi-Scale Modeling of Aqueous-Phase Methane Diffusion in Silicate Channels

2021 ◽  
Author(s):  
Tom Pace ◽  
Hadi Rahmaninejad ◽  
Bin Sun ◽  
Peter Kekenes-Huskey
Keyword(s):  
Molecular Dynamics ◽  
Multi Scale ◽  
Relative Contribution ◽  
Kinetic Information ◽  
Two Factors ◽  
Molecule Transport ◽  
Potentials Of Mean Force ◽  
Methane Diffusion ◽  
Dynamics Simulations ◽  
Small Molecule Transport

Silica-based materials including zeolites are commonly used for wide ranging applications including separations and catalysis.<br>Substrate transport rates in these materials often significantly influence the efficiency of such applications.<br>Two factors that contribute to transport rates include<br>1) the porosity of the silicate matrix and<br>2) non-bonding interactions between the diffusing species and the silicate surface.<br>Here, we utilize computer simulation to resolve the relative contribution of these factors to effective methane transport rates in a silicate channel.<br>Specifically, we develop a `homogenized' model of methane transport valid at micron and longer length scales that incorporates atomistic-scale kinetic information.<br>The atomistic-scale data are obtained from extensive molecular dynamics simulations that yield local diffusion coefficients and potentials of mean force.<br>With this model, we demonstrate how nuances in silicate hydration and silica/methane interactions impact 'macroscale' methane diffusion rates in bulk silicate materials.<br>This hybrid homogenization/molecular dynamics approach will be of general use for describing small molecule transport in materials with detailed molecular interactions.<br><br>

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