scholarly journals Improving productivity while managing extensive molecular dynamics simulation data

2018 ◽  
Author(s):  
Avimanyu Bandyopadhyay
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Experimental Analysis ◽  
Dynamics Simulation ◽  
Limited Resources ◽  
Simulation Data ◽  
New Approach ◽  
Extensive Data ◽  
Dynamics Simulations

This paper discusses the difficulties experienced by bioinformaticians while working with extensive data generated from extended molecular dynamics simulations. For better experimental analysis, it often becomes crucial to conduct simulations up to extended periods of time. When with limited resources, running a complete simulation up to a desired length of time can become quite difficult to be performed at one go. So, a new approach is proposed to simplify handling such data for better productivity.

scholarly journals Improving productivity while managing extensive molecular dynamics simulation data

2018 ◽  
Author(s):  
Avimanyu Bandyopadhyay
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Experimental Analysis ◽  
Dynamics Simulation ◽  
Limited Resources ◽  
Simulation Data ◽  
New Approach ◽  
Extensive Data ◽  
Dynamics Simulations

This paper discusses the difficulties experienced by bioinformaticians while working with extensive data generated from extended molecular dynamics simulations. For better experimental analysis, it often becomes crucial to conduct simulations up to extended periods of time. When with limited resources, running a complete simulation up to a desired length of time can become quite difficult to be performed at one go. So, a new approach is proposed to simplify handling such data for better productivity.

scholarly journals Reactive molecular dynamics simulation of the high-temperature pyrolysis of 2,2′,2′′,4,4′,4′′,6,6′,6′′-nonanitro-1,1′:3′,1′′-terphenyl (NONA)

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju
Keyword(s):  
Molecular Dynamics ◽  
High Temperature ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Reactive Molecular Dynamics ◽  
Ring Compounds ◽  
Fused Ring ◽  
Dynamics Simulations

The bimolecular and fused ring compounds are found in the high-temperature pyrolysis of NONA using ReaxFF molecular dynamics simulations.

Influence of the size and charge of gold nanoclusters on complexation with siRNA: a molecular dynamics simulation study

2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Simulation Study ◽  
Gold Nanoclusters ◽  
Dynamics Simulation ◽  
Classical Molecular Dynamics ◽  
Dynamics Simulations ◽  
Positively Charged

The complexation of siRNA with positively charged gold nanoclusters has been studied using classical molecular dynamics simulations.

Molecular dynamics simulation of the solidification process of multicrystalline silicon from homogeneous nucleation to grain coarsening

CrystEngComm ◽  
2018 ◽  
Vol 20 (25) ◽  
pp. 3569-3580 ◽  
Author(s):  
Xiaoxiao Sui ◽  
Yongjian Cheng ◽  
Naigen Zhou ◽  
Binbing Tang ◽  
Lang Zhou
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Homogeneous Nucleation ◽  
Solidification Process ◽  
Dynamics Simulation ◽  
Multicrystalline Silicon ◽  
Solidification Processes ◽  
Dynamics Simulations ◽  
Weber Potential

Based on the Stillinger–Weber potential, molecular dynamics simulations of the solidification processes of multicrystalline silicon were carried out.

scholarly journals Formation mechanism of bound rubber in elastomer nanocomposites: a molecular dynamics simulation study

RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Formation Mechanism ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Bound Rubber ◽  
Dynamics Simulations ◽  
Coarse Grained Molecular Dynamics

The formation mechanism of the bound rubber in elastomer nanocomposites using the coarse-grained molecular-dynamics simulations.

Solvation of cholesterol in different solvents: a molecular dynamics simulation study

2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dimethyl Sulfoxide ◽  
Simulation Study ◽  
Dynamics Simulation ◽  
Dynamical Properties ◽  
Dynamics Simulations

Molecular dynamics simulations were applied to an isolated cholesterol immersed in four different solvents of varying polarity, such as water, methanol, dimethyl sulfoxide and benzene, to gain insights into the structural and dynamical properties.

Estimation of the Chemical Potential and the Activity of NaCl in Molten DyCl3-NaCl by Molecular Dynamics Simulation

1998 ◽  
Vol 53 (8) ◽  
pp. 655-658
Author(s):  
Masanori Sakurai ◽  
Ryuzo Takagi ◽  
Ashok K. Adyaa ◽  
Marcelle Gaune-Escard
Keyword(s):  
Molecular Dynamics ◽  
Phase Diagram ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Chemical Potential ◽  
Dynamics Simulation ◽  
Dynamics Simulations ◽  
Positional Data ◽  
Liquidus Temperatures

Abstract Molecular dynamics simulations of molten DyCl3-NaCl were carried out at liquidus temperatures of the phase diagram. The chemical potential and the activity of NaCl was successfully estimated with the method proposed by Powles et al., which requires only positional data of the ions at the temperatures in question.

Molecular Dynamics Simulations of Hot Electrons and Lattice Relaxation in Realistic Cascade Volumes

1992 ◽  
Vol 278 ◽  
Author(s):  
A.M. Mazzone
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Classical Mechanics ◽  
Lattice Relaxation ◽  
Simulation Method ◽  
High Energy ◽  
Hot Electrons ◽  
Dynamics Simulation ◽  
Dynamics Simulations

AbstractThis work presents a molecular dynamics simulation method designed to describe the processes of electron and lattice relaxation taking place in typical cascade volumes formed by high-energy implants. The simulation method is based on classical mechanics and includes the motions of electrons and nuclei. The results are in agreement with experiments.

Microsecond molecular dynamics simulation of guanidinium chloride induced unfolding of ubiquitin

2014 ◽  
Vol 16 (39) ◽  
pp. 21706-21716 ◽  
Author(s):  
Manoj Mandal ◽  
Chaitali Mukhopadhyay
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Dynamics Simulation ◽  
Guanidinium Chloride ◽  
Dynamics Simulations

All atom molecular dynamics simulations have been used to explore the atomic detail mechanism of guanidinium induced unfolding of the protein ubiquitin.

scholarly journals Molecular dynamics simulation of octacosane for phase diagrams and properties via the united-atom scheme

2021 ◽  
Vol 23 (37) ◽  
pp. 21262-21271
Author(s):  
L. Dai ◽  
P. P. Rutkevych ◽  
S. Chakraborty ◽  
G. Wu ◽  
J. Ye ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Molecular Dynamics Simulations ◽  
Phase Diagrams ◽  
Dynamics Simulation ◽  
Crystalline Structures ◽  
Dynamics Simulations ◽  
Phase Properties

We used the united-atom scheme to build three types of crystalline structures for octacosane (C28H58) and carried out molecular dynamics simulations to investigate their phase properties.

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