scholarly journals Simulation Algorithm That Conserves Energy and Momentum for Molecular Dynamics of Systems Driven by Switching Potentials

2009 ◽  
Vol 2009 ◽  
pp. 1-14
Author(s):  
Christopher G. Jesudason
Keyword(s):  
Molecular Dynamics ◽  
Md Simulation ◽  
Reactive Systems ◽  
Extreme Temperature ◽  
Hysteresis Loops ◽  
Reaction Model ◽  
Equilibrium System ◽  
Particle Potential ◽  
Temperature And Pressure ◽  
Energy And Momentum

Whenever there exists a crossover from one potential to another, computational problems are introduced in Molecular Dynamics (MD) simulation. These problem are overcome here by an algorithm, described in detail. The algorithm is applied to a 2-body particle potential for a hysteresis loop reaction model. Extreme temperature conditions were applied to test for algorithm effectiveness by monitoring global energy, pressure and temperature discrepancies in an equilibrium system. No net rate of energy and other flows within experimental error should be observed, in addition to invariance of temperature and pressure along the MD cell for the said system. It is found that all these conditions are met only when the algorithm is applied. It is concluded that the method can easily be extended to Nonequilibrium MD (NEMD) simulations and to reactive systems with reversible, non-hysteresis loops.

Effects of pressure and temperature on sp3 fraction in diamondlike carbon materials

2007 ◽  
Vol 22 (10) ◽  
pp. 2770-2775 ◽  
Author(s):  
Zhanrong Zhong ◽  
Xinwei Wang ◽  
Xuhui Feng
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Radial Distribution Function ◽  
Large Scale ◽  
Md Simulation ◽  
Carbon Materials ◽  
Diamond Coating ◽  
Coating Structure ◽  
Diamondlike Carbon ◽  
Temperature And Pressure

In this work, formation of diamond coating is studied using large-scale molecular dynamics (MD) simulation. The diamond coating is studied to explore how and to what extent the temperature and pressure affects the deposition structure. To analyze the coating results, the radial distribution function and the fraction of diamond (sp3 bonds) is calculated. It is found that the sp3 fraction in the deposition structure increases with the temperature and pressure. When the pressure becomes large enough (10 GPa), the effect of the pressure on the coating structure is quite small and the sp3 fraction tends to be constant.

Design of potential IKK-β inhibitors using molecular docking and molecular dynamics techniques for their anti-cancer potential

2020 ◽  
Vol 16 ◽  
Author(s):  
Salam Pradeep Singh ◽  
Iftikar Hussain ◽  
Bolin Kumar Konwar ◽  
Ramesh Chandra Deka ◽  
Chingakham Brajakishor Singh
Keyword(s):  
Molecular Dynamics ◽  
Molecular Docking ◽  
Md Simulation ◽  
Inflammatory Diseases ◽  
Binding Free Energy ◽  
Anti Cancer ◽  
Dietary Phytochemicals ◽  
Toxicity Analysis ◽  
The Stability ◽  
Stable Trajectory

Aim and Objective: To evaluate a set of seventy phytochemicals for their potential ability to bind the inhibitor of nuclear factor kappaB kinase beta (IKK-β) which is a prime target for cancer and inflammatory diseases. Materials and Methods: Seventy phytochemicals were screened against IKK-β enzyme using DFT-based molecular docking technique and the top docking hits were carried forward for molecular dynamics (MD) simulation protocols. The adme-toxicity analysis was also carried out for the top docking hits. Results: Sesamin, matairesinol and resveratrol were found to be the top docking hits with a total score of -413 kJ/mol, -398.11 kJ/mol and 266.73 kJ/mol respectively. Glu100 and Gly102 were found to be the most common interacting residues. The result from MD simulation observed a stable trajectory with a binding free energy of -107.62 kJ/mol for matairesinol, -120.37 kJ/mol for sesamin and -40.56 kJ/mol for resveratrol. The DFT calculation revealed the stability of the compounds. The ADME-Toxicity prediction observed that these compounds fall within the permissible area of Boiled-Egg and it does not violate any rule for pharmacological criteria, drug-likeness etc. Conclusion: The study interprets that dietary phytochemicals are potent inhibitors of IKK-β enzyme with favourable binding affinity and less toxic effects. In fact, there is a gradual rise in the use of plant-derived molecules because of its lesser side effects compared to chemotherapy. The study has also provided an insight by which the phytochemicals inhibited the IKK-β enzyme. The investigation would also provide in understanding the inhibitory mode of certain dietary phytochemicals in treating cancer.

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.

scholarly journals Fully Atomistic Molecular Dynamics Computation of Physico-Mechanical Properties of PB, PS, and SBS

Nanomaterials ◽  
2019 ◽  
Vol 9 (8) ◽  
pp. 1088 ◽  
Author(s):  
Yang Kang ◽  
Dunhong Zhou ◽  
Qiang Wu ◽  
Fuyan Duan ◽  
Rufang Yao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Strain Rate ◽  
Strain Hardening ◽  
Md Simulation ◽  
Md Simulations ◽  
Strain Rates ◽  
Young’S Moduli ◽  
Plastic Modulus ◽  
Styrene Butadiene ◽  
Butadiene Styrene

The physical properties—including density, glass transition temperature (Tg), and tensile properties—of polybutadiene (PB), polystyrene (PS) and poly (styrene-butadiene-styrene: SBS) block copolymer were predicted by using atomistic molecular dynamics (MD) simulation. At 100 K, for PB and SBS under uniaxial tension with strain rate ε ˙ = 1010 s−1 and 109 s−1, their stress–strain curves had four features, i.e., elastic, yield, softening, and strain hardening. At 300 K, the tensile curves of the three polymers with strain rates between 108 s−1 and 1010 s−1 exhibited strain hardening following elastic regime. The values of Young’s moduli of the copolymers were independent of strain rate. The plastic modulus of PS was independent of strain rate, but the Young’s moduli of PB and SBS depended on strain rate under the same conditions. After extrapolating the Young’s moduli of PB and SBS at strain rates of 0.01–1 s−1 by the linearized Eyring-like model, the predicted results by MD simulations were in accordance well with experimental results, which demonstrate that MD results are feasible for design of new materials.

Molecular Dynamics Study of Microscopic Mechanism of Diffusion in Li2SiO3 System

1991 ◽  
Vol 46 (7) ◽  
pp. 616-620 ◽  
Author(s):  
Junko Habasaki
Keyword(s):  
Molecular Dynamics ◽  
Coordination Number ◽  
Md Simulation ◽  
Mean Square Displacement ◽  
Mean Square ◽  
Lithium Ions ◽  
Microscopic Mechanism ◽  
Trapping Model ◽  
The Mean

MD simulation has been performed to learn the microscopic mechanism of diffusion of ions in the Li2SiO3 system. The motion of lithium ions can be explained by the trapping model, where lithium is trapped in the polyhedron and moves with fluctuation of the coordination number. The mean square displacement of lithium was found to correlate well with the net changes in coordination number.

Self-diffusion of lignite/water under different temperatures and pressure: A molecular dynamics study

2016 ◽  
Vol 30 (01) ◽  
pp. 1550253 ◽  
Author(s):  
Xinjian Liu ◽  
Yu Jin ◽  
Congliang Huang ◽  
Jingfeng He ◽  
Zhonghao Rao ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Water System ◽  
Simulation Method ◽  
The Self ◽  
Dynamics Simulation ◽  
Low Rank ◽  
Self Diffusion ◽  
Change Mechanism ◽  
Different Temperatures ◽  
Temperature And Pressure

Temperature and pressure have direct and remarkable implications for drying and dewatering effect of low rank coals such as lignite. To understand the microenergy change mechanism of lignite, the molecular dynamics simulation method was performed to study the self-diffusion of lignite/water under different temperatures and pressure. The results showed that high temperature and high pressure can promote the diffusion of lignite/water system, which facilitates the drying and dewatering of lignite. The volume and density of lignite/water system will increase and decrease with temperature increasing, respectively. Though the pressure within simulation range can make lignite density increase, the increasing pressure showed a weak impact on variation of density.

scholarly journals Contributions of Molecular Dynamics Simulations to Elastohydrodynamic Lubrication

2021 ◽  
Vol 69 (1) ◽  
Author(s):  
James P. Ewen ◽  
Hugh A. Spikes ◽  
Daniele Dini
Keyword(s):  
Molecular Dynamics ◽  
Shear Rate ◽  
Experimental Design ◽  
Md Simulation ◽  
Elastohydrodynamic Lubrication ◽  
Quantitative Agreement ◽  
Coupling Methods ◽  
Fundamental Understanding ◽  
Shear Heating ◽  
Dynamics Simulations

AbstractThe prediction of friction under elastohydrodynamic lubrication (EHL) conditions remains one of the most important and controversial areas of tribology. This is mostly because the pressure and shear rate conditions inside EHL contacts are particularly severe, which complicates experimental design. Over the last decade, molecular dynamics (MD) simulation has played an increasingly significant role in our fundamental understanding of molecular behaviour under EHL conditions. In recent years, MD simulation has shown quantitative agreement with friction and viscosity results obtained experimentally, meaning that they can, either in isolation or through the use of multiscale coupling methods, begin to be used to test and inform macroscale models for EHL problems. This is particularly useful under conditions that are relevant inside machine components, but are difficult to obtain experimentally without uncontrollable shear heating.

Atomistic Level Molecular Dynamics Analysis and its Integrity in the Interim of Irradiation

2021 ◽  
Vol 318 ◽  
pp. 39-47
Author(s):  
Ahli K.D. Willie ◽  
Hong Tao Zhao ◽  
M. Annor-Nyarko
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Mixed Oxide ◽  
Md Simulation ◽  
Lattice Thermal Conductivity ◽  
Gas Diffusion ◽  
Mixed Oxide Fuel ◽  
Fission Gas ◽  
Increasing Temperature ◽  
End Members

In this work, molecular dynamics (MD) simulation was utilized in relation to access the thermal conductivity of UO2, PuO2 and (U, Pu)O2 in temperature range of 500–3000 K. Diffusion study on mixed oxide (MOX) was also performed to assess the effect of radiation damage by heavy ions at burnup temperatures. Analysis of the lattice thermal conductivity of irradiated MOX to its microstructure was carried out to enhance the irradiation defects with how high burnup hinders fuel properties and its pellet-cladding interaction. Fission gas diffusion as determined was mainly modelled by main diffusion coefficient. Degradation of diffusivity is predicted in MOX as composition deviate from the pure end members. The concentration of residual anion defects is considerably higher than that of cations in all oxides. Depending on the diffusion behavior of the fuel lattice, there was decrease in the ratio of anion to cation defects with increasing temperature. Besides, the modern mixed oxide fuel releases fission gas compared to that of UO2 fuel at moderate burnups.

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