scholarly journals Variable time domain discretization methodology for molecular dynamics simulation of metallic compounds

Author(s):  
Jamal Zeinalov

The present work proposes a methodology to improve the computational requirements of molecular dynamics simulations while maintaining or improving the fidelity of the obtained results. The most common method of molecular dynamics simulation at present is the multi-force, constant time-step, explicit computation, which advances a single time step at a time to determine the next state of the system. The present work proposes a variable time-step strategy, where a single large simulation is subdivided into multiple time domains which redistribute computational resources where they are needed the most: in areas of higher than average potential or kinetic energy or highly dynamic areas around impurity clusters, void formations and crack propagations. The research focuses on the simulation of metallic compounds, as these form the basis of most common molecular dynamics simulations, and have been very thoroughly investigated over the years, thus providing a very extensive body of work for the purpose of comparison and validation of the proposed methodology. The novel methodology presented in this work allows to alleviate some of the limitations associated with the molecular dynamics methodologies and go beyond traditional scales of simulation. The proposed method has been observed to deliver 5 to 20 percent increase in simulation size domain while maintaining or improving the accuracy and computational cycle time. The benefits were observed to be greater for large simulations with one or more areas of higher than average kinetic or potential energy levels, such as those found during crack initiation and propagation, coating-substrate interface, localized pressure application or large thermal gradient. The large difference allows for very clear prioritization of computational resources for high energy areas and as a result provides for faster and more accurate simulation even with increased domain size. Conversely, this method has been observed to provide little to no benefit when simulating stable systems that are undergoing very slow change, such as (relatively) slow change in ambient temperature or pressure, or otherwise homogeneous internal and external boundary conditions. However, for the majority of applications described above, including coating deposition and additive manufacturing, the proposed methodology will yield substantial increase in both simulation size and accuracy, since in the aforementioned processes kinetic and potential energy gradients across the simulation are typically very significant

2021 ◽  
Author(s):  
Jamal Zeinalov

The present work proposes a methodology to improve the computational requirements of molecular dynamics simulations while maintaining or improving the fidelity of the obtained results. The most common method of molecular dynamics simulation at present is the multi-force, constant time-step, explicit computation, which advances a single time step at a time to determine the next state of the system. The present work proposes a variable time-step strategy, where a single large simulation is subdivided into multiple time domains which redistribute computational resources where they are needed the most: in areas of higher than average potential or kinetic energy or highly dynamic areas around impurity clusters, void formations and crack propagations. The research focuses on the simulation of metallic compounds, as these form the basis of most common molecular dynamics simulations, and have been very thoroughly investigated over the years, thus providing a very extensive body of work for the purpose of comparison and validation of the proposed methodology. The novel methodology presented in this work allows to alleviate some of the limitations associated with the molecular dynamics methodologies and go beyond traditional scales of simulation. The proposed method has been observed to deliver 5 to 20 percent increase in simulation size domain while maintaining or improving the accuracy and computational cycle time. The benefits were observed to be greater for large simulations with one or more areas of higher than average kinetic or potential energy levels, such as those found during crack initiation and propagation, coating-substrate interface, localized pressure application or large thermal gradient. The large difference allows for very clear prioritization of computational resources for high energy areas and as a result provides for faster and more accurate simulation even with increased domain size. Conversely, this method has been observed to provide little to no benefit when simulating stable systems that are undergoing very slow change, such as (relatively) slow change in ambient temperature or pressure, or otherwise homogeneous internal and external boundary conditions. However, for the majority of applications described above, including coating deposition and additive manufacturing, the proposed methodology will yield substantial increase in both simulation size and accuracy, since in the aforementioned processes kinetic and potential energy gradients across the simulation are typically very significant


RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5507-5515
Author(s):  
Liang Song ◽  
Feng-Qi Zhao ◽  
Si-Yu Xu ◽  
Xue-Hai Ju

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


2015 ◽  
Vol 17 (45) ◽  
pp. 30307-30317 ◽  
Author(s):  
Sathish Kumar Mudedla ◽  
Ettayapuram Ramaprasad Azhagiya Singam ◽  
Kanagasabai Balamurugan ◽  
Venkatesan Subramanian

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


CrystEngComm ◽  
2018 ◽  
Vol 20 (25) ◽  
pp. 3569-3580 ◽  
Author(s):  
Xiaoxiao Sui ◽  
Yongjian Cheng ◽  
Naigen Zhou ◽  
Binbing Tang ◽  
Lang Zhou

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


RSC Advances ◽  
2018 ◽  
Vol 8 (23) ◽  
pp. 13008-13017 ◽  
Author(s):  
Jun Liu ◽  
Haixiao Wan ◽  
Huanhuan Zhou ◽  
Yancong Feng ◽  
Liqun Zhang ◽  
...  

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


2020 ◽  
Vol 22 (3) ◽  
pp. 1154-1167 ◽  
Author(s):  
Khair Bux ◽  
Syed Tarique Moin

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.


1998 ◽  
Vol 53 (8) ◽  
pp. 655-658
Author(s):  
Masanori Sakurai ◽  
Ryuzo Takagi ◽  
Ashok K. Adyaa ◽  
Marcelle Gaune-Escard

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.


1992 ◽  
Vol 278 ◽  
Author(s):  
A.M. Mazzone

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.


2014 ◽  
Vol 16 (39) ◽  
pp. 21706-21716 ◽  
Author(s):  
Manoj Mandal ◽  
Chaitali Mukhopadhyay

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


2021 ◽  
Vol 23 (37) ◽  
pp. 21262-21271
Author(s):  
L. Dai ◽  
P. P. Rutkevych ◽  
S. Chakraborty ◽  
G. Wu ◽  
J. Ye ◽  
...  

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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