scholarly journals Structural, dynamic, and electrostatic properties of fully hydrated DMPC bilayers from molecular dynamics simulations accelerated with graphical processing units (GPUs)

2011 ◽  
Vol 32 (14) ◽  
pp. 2958-2973 ◽  
Author(s):  
Narayan Ganesan ◽  
Brad A. Bauer ◽  
Timothy R. Lucas ◽  
Sandeep Patel ◽  
Michela Taufer
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Dynamic ◽  
Electrostatic Properties ◽  
Graphical Processing Units ◽  
Graphical Processing ◽  
Dynamics Simulations

Salt-in-water and water-in-salt electrolytes: The effects of the asymmetry in cation and anion valence on its properties

2021 ◽  
Author(s):  
Andresa Messias ◽  
Débora Ariana Corrêa da Silva ◽  
Eudes E. Fileti
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ion Pairs ◽  
Structural Dynamic ◽  
Electrostatic Properties ◽  
The Asymmetry ◽  
Dynamics Simulations

We investigated the structural, dynamic, energetic, and electrostatic properties of electrolytes based on the ion pairs LiCl and Li2SO4. Atomistic molecular dynamics simulations were used to simulate these aqueous electrolytic...

Ecological Impact of Green Computing Using Graphical Processing Units in Molecular Dynamics Simulations

2018 ◽  
Vol 9 (1) ◽  
pp. 35-48 ◽  
Author(s):  
Izabele Marquetti ◽  
Jhonatam Rodrigues ◽  
Salil S. Desai
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ecological Impact ◽  
Green Computing ◽  
Processing Unit ◽  
Central Processing ◽  
Computational Performance ◽  
Graphical Processing Units ◽  
Graphical Processing ◽  
Dynamics Simulations

Molecular dynamics (MD) models require comprehensive computational power to simulate nanoscale phenomena. Traditionally, central processing unit (CPU) clusters have been the standard method of performing these numerically intensive computations. This article investigates the use of graphical processing units (GPUs) to implement large-scale MD models for exploring nanofluidic-substrate interactions. MD models of water nanodroplets over flat silicon substrate are tracked wherein the simulation attains a steady state computational performance. Different classes of GPU units from NVIDIA (C2050, K20, and K40) are evaluated for energy efficiency performance with respect to three green computing measures: simulation completion time, power consumption, and CO2 emissions. The CPU+K40 configuration displayed the lowest energy consumption profile for all the measures. This research demonstrates the use of energy efficient graphical computing versus traditional CPU computing for high-performance molecular dynamics simulations.

scholarly journals Molecular dynamics simulations of tubulin structure and calculations of electrostatic properties of microtubules

2005 ◽  
Vol 41 (10) ◽  
pp. 1055-1070 ◽  
Author(s):  
J.A. Tuszyński ◽  
J.A. Brown ◽  
E. Crawford ◽  
E.J. Carpenter ◽  
M.L.A. Nip ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electrostatic Properties ◽  
Dynamics Simulations ◽  
Tubulin Structure

scholarly journals Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1

RSC Advances ◽  
2019 ◽  
Vol 9 (36) ◽  
pp. 20901-20916 ◽  
Author(s):  
Budheswar Dehury ◽  
Ning Tang ◽  
Tom L. Blundell ◽  
Kasper P. Kepp
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Presenilin 1 ◽  
Structural Dynamic ◽  
Structure And Dynamics ◽  
Presenilin 2 ◽  
Dynamics Simulations

We constructed a model of presenilin-2 γ-secretase in the membrane and studied it by all-atom molecular dynamics simulations. The study provides the first structural-dynamic comparison of presenilin 1 and 2 relevant to Alzheimer's disease.

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