MD simulations
MD Simulations of the P53 oncoprotein structure: the effect of the Arg273→His mutation on the DNA binding domain
... The MD simulations have been performed using computing facilities, software, and clusters at JINR, Russia (CICC); RIKEN, Japan (RICC); RIKEN-Yokohama (MDGARPE-3); and the Yasuoka Laboratory at Keio ...
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A Dynamic View of Proton-Coupled Electron Transfer in Photocatalytic Water Splitting
... through nonadiabatic dynamics. On the other hand the dynamical description of the first catalytic water splitting step is obtained with adiabatic ab initio constrained MD simulations performed for the ...
21
Collective dynamics of glass-forming polymers at intermediate length scales - A synergetic combination of neutron scattering, atomistic simulations and theoretical modelling
... atomistic MD-simulations to try to shed some light on the collective dynamics of a glass-forming polymer, polyisobutylene (PIB), in the intermediate length scales ...computer simulations, the ...
10
Targeting amyloid aggregation: an overview of strategies and mechanisms
... with MD simulations, Wang and coworkers demonstrated that high-throughput-based strategies hold a remarkable potential for the development of peptide inhibitors sharing no sequence relationship with natural ...
26
Mechanical Properties and Failure Behavior of Hexagonal Boron Nitride–Graphene van der Waals Heterostructures through Molecular Dynamics Simulation
... dynamics(MD) simulations are carried out to characterize the mechanical properties and failure behavior of van der Waals heterostructures composed of graphene and hexagonal boron nitride(hBN) single layer ...
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Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells
... Comparative MD simulations of HiGom, AgGomKR, SpGom, AgGomL5A, AgGomR3A, and AgGomV12A with AgGom determined that amino acid substitutions in gomesin analogues do not confer structural modi fi cations and ...
11
on quorum sensing in Chromobacterium violaceum
... Molecular dynamics simulations and binding free energy calculations 629. MD simulations of the CviR-ligand systems were conducted with the PMEMD module[r] ...
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Investigating the molecular orientation of Ir(ppy)3 and Ir(ppy)2(acac) emitter complexes by X ray diffraction
... performed molecular density MD simulations of CBP films comprising Irppy3 and Irppy2acac as emitters, respectively.[28] For both emitters they found a preferential orientation of the emi[r] ...
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Effective mean free path and viscosity of confined gases
... both the direct simulation Monte Carlo (DSMC) and molecular dynamics (MD) simulations. The[r] ...
31
Different interface orientations of pentacene and PTCDA induce different degrees of disorder
... (MD) simulations of the interfaces between PTCDA and pentacene have been performed with the atomistic molecular dynamics package GROMACS (Stockholm Center for Biomem- brane Research, Stockholm, Sweden and ...
5
Investigations of ion channel structure function relationships using molecular modeling and experimental biochemistry
... utilized MD simulations of MscS similar to those performed on MscL to structurally verify the supposed voltage sensitivity of the channel and to identify specific amino acid residues likely to be important ...
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Effect of Intrinsic Ripples on Elasticity of the Graphene Monolayer
... Recently, DFT calculations showed that strain- induced hardening in the out-of-plane acoustic phonon mode explains the absence of rippling in graphene under a biaxial strain [37, 38]. In the study, the vari- ation of the ...
9
Self assembly of decoupled borazines on metal surfaces : the role of the peripheral groups
... (MD) simulations suggesting that a very effective decoupling of the central borazine core from the substrate occurs for both molecules, whereas a pro- nounced molecule–substrate interaction through its ...
8
Surface Effect on Oil Transportation in Nanochannel: a Molecular Dynamics Study
... using MD simulations and demonstrate that the surface inter- action between oil molecules and channel surface, roughness of channel surface, and the interaction among oil molecules all have great effects on ...
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In Silico Analysis of the Apolipoprotein E and the Amyloid β Peptide Interaction: Stabilizing a Molten Globule by Frustration of the Salt Bridges Network
... Our computational approach assumes a direct interaction between ApoE and Ab. Although the docking was plausible for ApoE2 and ApoE3, the interactions did not generate any conformational transition in the 10 ns time ...
7
Computational and Experimental Analyses of Detachment Force at the Interface between Carbon Fibers and Epoxy Resin
... and MD simulations to determine the inter- molecular interaction energy for each epoxy monomer in bulk epoxy compound, observing a correlation between the simulated interaction energy and the shear strength ...
7
Study of Materials Deformation in Nanometric Cutting by Large scale Molecular Dynamics Simulations
... the MD simulation of nanometric cutting is compute-intensive, small simulation models with a few thousands to tens of thousands of atoms were used in the reported studies to reduce the computing ...in MD ...
8
Large-scale atomistic simulations of nanostructured materials based on divide-and-conquer density functional theory
... in MD simulations to study atomic motions and chemical ...The MD simulations are carried out at temperature 2000 K in the canonical ...
6
Gomesin peptides prevent proliferation and lead to the cell death of devil facial tumour disease cells
... Comparative MD simulations of HiGom, AgGomKR, SpGom, AgGomL5A, AgGomR3A, and AgGomV12A with AgGom determined that amino acid substitutions in gomesin analogues do not confer structural modi fi cations and ...
11
Molecular dynamics simulations reveal disruptive self-assembly in dynamic peptide libraries
... During the last few years, an e ff ort has been made to search for the sequence space for minimalistic unmodified self- assembling peptides. 2a,b,8 Frederix et al. employed coarse grained molecular dynamics (CG-MD) ...
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