scholarly journals Relaxation of Phonons in Classical MD Simulation

2007 ◽  
Author(s):  
Mitsuhiro Matsumoto ◽  
Tomohisa Kunisawa ◽  
Peng Xiao
Keyword(s):  
Relaxation Time ◽  
Power Spectrum ◽  
Md Simulation ◽  
Silicon Crystal ◽  
Dynamics Simulation ◽  
Novel Technique ◽  
Lennard Jones ◽  
Model Crystal ◽  
Specific Frequency ◽  
Single Exponential Function

We propose a novel technique of molecular dynamics simulation to evaluate the relaxation time of phonons in solids for investigation of solid heat conductivity. The basic idea is to observe relaxation behavior of the power spectrum of atomic velocities after energetically stimulating modes in a specific frequency region. The transient entropy S(t) is defined with the power spectrum based on non-equilibrium statistical mechanics to quantitatively evaluate the relaxation speed. In this paper, two example systems are shown: a Lennard-Jones model crystal and a silicon crystal. For both systems, we found that the observed S(t) is well fitted to a single exponential function, from which we can obtain a frequency-dependent relaxation time.

Structure prediction of SPAK C-terminal domain and analysis of its binding to RFXV/I motifs by homology modelling, docking, and molecular dynamics simulation studies

2020 ◽  
Vol 16 ◽  
Author(s):  
Mubarak A. Alamri ◽  
Ahmed D. Alafnan ◽  
Obaid Afzal ◽  
Alhumaidi B. Alabbas ◽  
Safar M. Alqahtani
Keyword(s):  
Molecular Dynamic ◽  
Dynamic Stability ◽  
Md Simulation ◽  
Homology Modelling ◽  
Antihypertensive Agents ◽  
Structure And Function ◽  
Dynamics Simulation ◽  
Dimensional Structure ◽  
Terminal Domain ◽  
And Function

Background: The STE20/SPS1-related proline/alanine-rich kinase (SPAK) is a component of WNKSPAK/OSR1 signaling pathway that plays an essential role in blood pressure regulation. The function of SPAK is mediated by its highly conserved C-terminal domain (CTD) that interacts with RFXV/I motifs of upstream activators, WNK kinases, and downstream substrate, cation-chloride cotransporters. Objective: To determine and validate the three-dimensional structure of the CTD of SPAK and to study and analyze its interaction with the RFXV/I motifs. Methods: A homology model of SPAK CTD was generated and validated through multiple approaches. The model was based on utilizing the OSR1 protein kinase as a template. This model was subjected to 100 ns molecular dynamic (MD) simulation to evaluate its dynamic stability. The final equilibrated model was used to dock the RFQV-peptide derived from WNK4 into the primary pocket that was determined based on the homology sequence between human SPAK and OSR1 CTDs. The mechanism of interaction, conformational rearrangement and dynamic stability of the binding of RFQV-peptide to SPAK CTD were characterized by molecular docking and molecular dynamic simulation. Results: The MD simulation suggested that the binding of RFQV induces a large conformational change due to the distribution of salt bridge within the loop regions. These results may help in understanding the relation between the structure and function of SPAK CTD and to support drug design of potential SPAK kinase inhibitors as antihypertensive agents. Conclusion: This study provides deep insight into SPAK CTD structure and function relationship.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Molecular dynamics simulation of sI methane hydrate under compression and tension

2020 ◽  
Vol 18 (1) ◽  
pp. 69-76
Author(s):  
Qiang Wang ◽  
Qizhong Tang ◽  
Sen Tian
Keyword(s):  
Molecular Dynamics ◽  
Methane Hydrate ◽  
Fracture Process ◽  
Md Simulation ◽  
Maximum Stress ◽  
Dynamics Simulation ◽  
Tensile Fracture ◽  
Maximum Compressive Stress ◽  
Motion State ◽  
Stress States

AbstractMolecular dynamics (MD) analysis of methane hydrate is important for the application of methane hydrate technology. This study investigated the microstructure changes of sI methane hydrate and the laws of stress–strain evolution under the condition of compression and tension by using MD simulation. This study further explored the mechanical property and stability of sI methane hydrate under different stress states. Results showed that tensile and compressive failures produced an obvious size effect under a certain condition. At low temperature and high pressure, most of the clathrate hydrate maintained a stable structure in the tensile fracture process, during which only a small amount of unstable methane broke the structure, thereby, presenting a free-motion state. The methane hydrate cracked when the system reached the maximum stress in the loading process, in which the maximum compressive stress is larger than the tensile stress under the same experimental condition. This study provides a basis for understanding the microscopic stress characteristics of methane hydrate.

Molecular Dynamics Simulation of AFM-Based Nanomachining Processes

2011 ◽  
Author(s):  
Rapeepan Promyoo ◽  
Hazim El-Mounayri ◽  
Kody Varahramyan ◽  
Ashlie Martini
Keyword(s):  
Molecular Dynamics ◽  
Friction Coefficient ◽  
Md Simulation ◽  
Computational Models ◽  
Dynamics Simulation ◽  
Radius Of Curvature ◽  
Force Microscopy ◽  
Indentation Force ◽  
Atomic Force ◽  
Development And Validation

Recently, atomic force microscopy (AFM) has been widely used for nanomachining and fabrication of micro/ nanodevices. This paper describes the development and validation of computational models for AFM-based nanomachining (nanoindentation and nanoscratching). The Molecular Dynamics (MD) technique is used to model and simulate mechanical indentation and scratching at the nanoscale in the case of gold and silicon. The simulation allows for the prediction of indentation forces and the friction force at the interface between an indenter and a substrate. The effects of tip curvature and speed on indentation force and friction coefficient are investigated. The material deformation and indentation geometry are extracted based on the final locations of atoms, which are displaced by the rigid tool. In addition to modeling, an AFM was used to conduct actual indentation at the nanoscale, and provide measurements to validate the predictions from the MD simulation. The AFM provides resolution on nanometer (lateral) and angstrom (vertical) scales. A three-sided pyramid indenter (with a radius of curvature ∼ 50 nm) is raster scanned on top of the surface and in contact with it. It can be observed from the MD simulation results that the indentation force increases as the depth of indentation increases, but decreases as the scratching speed increases. On the other hand, the friction coefficient is found to be independent of scratching speed.

Molecular dynamics simulation of homogeneous nucleation of supersaturated potassium chloride (KCl) in aqueous solutions

CrystEngComm ◽  
2019 ◽  
Vol 21 (48) ◽  
pp. 7507-7518 ◽  
Author(s):  
Soroush Ahmadi ◽  
Yuanyi Wu ◽  
Sohrab Rohani
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulation ◽  
Aqueous Solutions ◽  
Potassium Chloride ◽  
Homogeneous Nucleation ◽  
Md Simulation ◽  
Crystal Nucleation ◽  
Dynamics Simulation

Molecular dynamics (MD) simulation is used to investigate the mechanism of crystal nucleation of potassium chloride (KCl) in a supersaturated aqueous solution at 293 K and 1 atm.

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