scholarly journals Analysis of molecular dynamics simulations of 10-residue peptide, chignolin, using statistical mechanics: Relaxation mode analysis and three-dimensional reference interaction site model theory

2019 ◽  
Vol 16 (0) ◽  
pp. 407-429
Author(s):  
Yutaka Maruyama ◽  
Hiroshi Takano ◽  
Ayori Mitsutake
Keyword(s):  
Molecular Dynamics ◽  
Statistical Mechanics ◽  
Molecular Dynamics Simulations ◽  
Model Theory ◽  
Three Dimensional ◽  
Mode Analysis ◽  
Relaxation Mode ◽  
Interaction Site ◽  
Site Model ◽  
Dynamics Simulations

scholarly journals Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis

2015 ◽  
Vol 7 (17) ◽  
pp. 2317-2331 ◽  
Author(s):  
Gautier Moroy ◽  
Olivier Sperandio ◽  
Shakti Rielland ◽  
Saurabh Khemka ◽  
Karen Druart ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Virtual Screening ◽  
Molecular Dynamics Simulations ◽  
Normal Mode ◽  
Normal Mode Analysis ◽  
Mode Analysis ◽  
Conformational Ensemble ◽  
Dynamics Simulations

Pyrrolidine Derivatives as Plasmepsin Inhibitors: Binding Mode Analysis Assisted by Molecular Dynamics Simulations of a Highly Flexible Protein

ChemMedChem ◽  
2010 ◽  
Vol 5 (3) ◽  
pp. 443-454 ◽  
Author(s):  
Torsten Luksch ◽  
Andreas Blum ◽  
Nina Klee ◽  
Wibke E. Diederich ◽  
Christoph A. Sotriffer ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Mode ◽  
Mode Analysis ◽  
Flexible Protein ◽  
Dynamics Simulations

Molecular-Dynamics Simulations of Granular Axial Segregation in a Rotating Cylinder

1998 ◽  
Vol 12 (04) ◽  
pp. 115-122 ◽  
Author(s):  
Sakamoto Shoichi
Keyword(s):  
Molecular Dynamics ◽  
Diffusion Process ◽  
Molecular Dynamics Simulations ◽  
Three Dimensional ◽  
Rotating Cylinder ◽  
Axial Segregation ◽  
Cohesive Forces ◽  
Dynamics Simulations ◽  
Different Diameters ◽  
Narrow Bands

In order to investigate segregation of granular binary-mixtures in a horizontally rotating cylinder, three-dimensional molecular dynamics simulations are carried out. Two kinds of particles, which have different diameters and/or different roughness of surfaces, are segregated into three bands. It is found that particles receive averaged force cohesively at the boundaries of segregated bands. The present analysis shows that segregated narrow bands are formed by diffusion process and that the cohesive forces operating at the boundaries stabilize them.

Molecular Dynamics Simulations of Coupling between Flow and Heat Transfer in a Nanochannel

2012 ◽  
Vol 455-456 ◽  
pp. 155-160
Author(s):  
Zhi Hai Kou ◽  
Min Li Bai
Keyword(s):  
Heat Transfer ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Wall Temperature ◽  
Solid Wall ◽  
Slip Length ◽  
Three Dimensional ◽  
Flow And Heat Transfer ◽  
Kapitza Length ◽  
Dynamics Simulations

Simulation of microscale thermo-fluidic transport has attracted considerable attention in recent years owing to rapid advances in nanoscience and nanotechnology. The three-dimensional molecular dynamics simulations are performed for coupling between flow and heat transfer in a nanochannel. Effects of interface wettability, shear rate and wall temperature are discussed. It is found that there exist the relatively immobile solid-like layers adjacent to each solid wall with higher number density. Both slip length and Kapitza length at the solid-liquid interface increase linearly with the increasing wall temperature. The Kapitza length decreases monotonously with the increasing shear rates. The slip length is found to be overestimated by 5.10% to 10.27%, while Kapitza length is overestimated by 8.92% to 19.09% for the solid-solid interaction modeled by the Lennard-Jones potential.

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