scholarly journals Fast Nosé–Hoover thermostat: molecular dynamics in quasi-thermodynamic equilibrium

2019 ◽  
Vol 21 (11) ◽  
pp. 6059-6070
Author(s):  
Dominik Sidler ◽  
Sereina Riniker
Keyword(s):  
Molecular Dynamics ◽  
Thermodynamic Equilibrium ◽  
Degrees Of Freedom ◽  
Md Simulation ◽  
Average Temperature ◽  
System P

An extension of the Nosé–Hoover thermostat equation for molecular dynamics (MD) simulation is introduced, which perturbs fast degrees of freedom out of canonical equilibrium, while preserving the average temperature of the system.

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.

Unraveling cGAS catalytic mechanism upon DNA activation through molecular dynamics simulations

2021 ◽  
Author(s):  
Jordi Soler ◽  
Pedro Paiva ◽  
Maria Joao Joao Ramos ◽  
Pedro Alexandrino Fernandes ◽  
Marie Brut
Keyword(s):  
Molecular Dynamics ◽  
Dna Binding ◽  
Molecular Dynamics Simulations ◽  
Cyclic Gmp ◽  
Catalytic Mechanism ◽  
System P ◽  
Dynamics Simulations ◽  
Cyclic Dinucleotide

Cyclic GMP-AMP Synthase (cGAS) is activated upon DNA binding and catalyzes the synthesis of 2’,3’-cGAMP from GTP and ATP. This cyclic dinucleotide is a messenger that triggers the autoimmune system...

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.

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.

All-atomistic molecular dynamics study of the glass transition of amorphous polymers

2021 ◽  
Author(s):  
Zhiye Tang ◽  
Susumu Okazaki
Keyword(s):  
Molecular Dynamics ◽  
Glass Transition ◽  
Spatial Scale ◽  
Degrees Of Freedom ◽  
Main Chain ◽  
Polymer Materials ◽  
Coarse Grained ◽  
Mode Analysis ◽  
Radius Of Gyration ◽  
Chemical Structures

Glass transition is an important phenomenon of polymer materials and it has been intensively studied over the past a few decades. However, the influencing factors arising from the chemical structures of the polymers are often ignored due to a continuous or coarse-grained description of the polymer. Here, we approached this phenomenon using all-atomistic molecular dynamics (MD) simulations and two conventionally used polymer materials, polycarbonate (PC) and poly-(methyl methacrylate) (PMMA). We reproduced the glass transition temperatures (Tg) of the two materials reasonably well. Then we characterized and investigated the glass transition process by looking at the changes of potential energy, dihedral transition, and thermal fluctuation of the individual degrees of freedom in the systems, over the entire temperature range of glass transition. As previously reported, the dihedral angles stop their conformational changes gradually at the Tg, especially for the main chain dihedrals, and sidechain rotations immediately rooting from the main chain. The volumetric change during the temperature decrease is confirmed to be because of conformational adjustment, probably due to the tendency of chain stretching for the maintenance of the radius of gyration, and the loss of thermal energy. The strength of motions of single degrees of freedom and polymer chains, and overall slow motions obtained by normal mode analysis (NMA) shows that different motions at different spatial scale may gradually stop at distinct temperature in the MD simulation temporal and spatial scales. Presumably, the small spatial scale do not contribute to the glass transition at the experimental scale since the timescale is much longer than their relaxation time.

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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