scholarly journals Hybrid machine learning assisted quantification of the compound internal and external uncertainties of graphene: Towards inclusive analysis and design

2021 ◽  
Author(s):  
Kritesh K. Gupta ◽  
Tanmoy Mukhopadhyay ◽  
Lintu Roy ◽  
Sudip Dey
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Interatomic Potential ◽  
Md Simulations ◽  
First Principle ◽  
Reliability Of Results ◽  
Analysis And Design ◽  
Hybrid Machine ◽  
Inclusive Analysis

Reliability of results derived from molecular dynamics (MD) simulations depends on the adopted interatomic potential (IP), which is mathematically fitted to the data obtained from first principle approaches or experiments....

Na ion dynamics in P2-Nax[Ni1/3Ti2/3]O2: a combination of quasi-elastic neutron scattering and first-principles molecular dynamics study

2020 ◽  
Vol 8 (47) ◽  
pp. 25290-25297
Author(s):  
Qian Chen ◽  
Niina H. Jalarvo ◽  
Wei Lai
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
First Principles ◽  
Md Simulations ◽  
First Principle ◽  
Ion Dynamics ◽  
Elastic Neutron ◽  
Elastic Neutron Scattering ◽  
First Principles Molecular Dynamics

The Na dynamics in P2-Nax[Ni1/3Ti2/3]O2 were investigated through a combination of QENS experiments and first-principle MD simulations.

Molecular Dynamics Simulations of Diffusion of O2 and N2 Penetrants in Polydimethylsiloxane-Based Nanocomposites

2012 ◽  
Vol 134 (2) ◽  
Author(s):  
Douglas E. Spearot ◽  
Alex Sudibjo ◽  
Varun Ullal ◽  
Adam Huang
Keyword(s):  
Molecular Dynamics ◽  
Polymer Composites ◽  
Diffusion Coefficients ◽  
Metal Particle ◽  
Interatomic Potential ◽  
Md Simulations ◽  
Coarse Grained ◽  
Cu Nanoparticles ◽  
Cu Nanoparticle ◽  
Nanoparticle Inclusions

Recently, metal particle polymer composites have been proposed as sensing materials for micro corrosion sensors. To design the sensors, a detailed understanding of diffusion through metal particle polymer composites is necessary. Accordingly, in this work molecular dynamics (MD) simulations are used to study the diffusion of O2 and N2 penetrants in metal particle polymer nanocomposites composed of an uncross-linked polydimethylsiloxane (PDMS) matrix with Cu nanoparticle inclusions. PDMS is modeled using a hybrid interatomic potential with explicit treatment of Si and O atoms along the chain backbone and coarse-grained methyl side groups. In most models examined in this work, MD simulations show that diffusion coefficients of O2 and N2 molecules in PDMS-based nanocomposites are lower than that in pure PDMS. Nanoparticle inclusions act primarily as geometric obstacles for the diffusion of atmospheric penetrants, reducing the available porosity necessary for diffusion, with instances of O2 and N2 molecule trapping also observed at or near the PDMS/Cu nanoparticle interfaces. In models with the smallest gap between Cu nanoparticles, MD simulations show that O2 and N2 diffusion coefficients are higher than that in pure PDMS at the lowest temperatures studied. This is due to PDMS chain confinement at low temperatures in the presence of the Cu nanoparticles, which induces low-density regions within the PDMS matrix. MD simulations show that the role of temperature on diffusion can be modeled using the Williams–Landel–Ferry equation, with parameters influenced by nanoparticle content and spacing.

Physical properties of high-temperature solid alkali chlorides by molecular dynamics simulation using a recent EIM interatomic potential

2019 ◽  
Vol 33 (10) ◽  
pp. 1950088 ◽  
Author(s):  
Xiandai Cui ◽  
Jiaoqun Zhu ◽  
Hong Xu ◽  
Xiaomin Cheng ◽  
Weibing Zhou
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Specific Heat ◽  
Specific Heat Capacity ◽  
Interatomic Potential ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Experimental Values ◽  
Alkali Chlorides ◽  
Change Material

Thermophysical properties of phase change material NaCl and KCl were calculated using molecular dynamics (MD) simulations and a recent EIM interatomic potential. Density, thermal expansion coefficient, specific heat capacity were computed using equilibrium MD (EMD) simulations. The results are very close to the experimental values. The thermal conductivity was computed using two non-equilibrium MD (NEMD) methods and the results were compared with the experimental data. They appear to be relatively reasonable. Binary NaCl/KCl systems have also been investigated. The specific heat capacity with different compositions are calculated. They are very close with recent experimental results.

scholarly journals Structural Analysis and Design of Chionodracine-Derived Peptides Using Circular Dichroism and Molecular Dynamics Simulations

2020 ◽  
Vol 21 (4) ◽  
pp. 1401
Author(s):  
Stefano Borocci ◽  
Giulia Della Pelle ◽  
Francesca Ceccacci ◽  
Cristina Olivieri ◽  
Francesco Buonocore ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Lipid Membranes ◽  
Lipid Vesicles ◽  
Md Simulations ◽  
Structural Basis ◽  
Human Pathogens ◽  
Analysis And Design ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

Antimicrobial peptides have been identified as one of the alternatives to the extensive use of common antibiotics as they show a broad spectrum of activity against human pathogens. Among these is Chionodracine (Cnd), a host-defense peptide isolated from the Antarctic icefish Chionodraco hamatus, which belongs to the family of Piscidins. Previously, we demonstrated that Cnd and its analogs display high antimicrobial activity against ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species). Herein, we investigate the interactions with lipid membranes of Cnd and two analogs, Cnd-m3 and Cnd-m3a, showing enhanced potency. Using a combination of Circular Dichroism, fluorescence spectroscopy, and all-atom Molecular Dynamics (MD) simulations, we determined the structural basis for the different activity among these peptides. We show that all peptides are predominantly unstructured in water and fold, preferentially as α-helices, in the presence of lipid vesicles of various compositions. Through a series of MD simulations of 400 ns time scale, we show the effect of mutations on the structure and lipid interactions of Cnd and its analogs. By explaining the structural basis for the activity of these analogs, our findings provide structural templates to design minimalistic peptides for therapeutics.

Atomistic study of chemical effect on local structure in Mg-based metallic glasses

RSC Advances ◽  
2015 ◽  
Vol 5 (58) ◽  
pp. 46861-46868
Author(s):  
Q. Wang ◽  
J. H. Li ◽  
J. B. Liu ◽  
B. X. Liu
Keyword(s):  
Molecular Dynamics ◽  
Metallic Glasses ◽  
Local Structure ◽  
Interatomic Potential ◽  
Md Simulations ◽  
Chemical Effect ◽  
Chemical Effects ◽  
Atomistic Study

By applying a recently constructed interatomic potential, molecular dynamics (MD) simulations were performed to investigate the structural origin of chemical effects in Mg–Cu–Ni ternary metallic glasses.

scholarly journals Deep Reinforcement Learning of Transition States

2021 ◽  
Author(s):  
Jun Zhang ◽  
Yao-Kun Lei ◽  
Zhen Zhang ◽  
Xu Han ◽  
Maodong Li ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Reinforcement Learning ◽  
Transition State ◽  
Chemical Reaction ◽  
Reaction Mechanisms ◽  
Md Simulations ◽  
Learning Approach ◽  
Machine Learning Approach ◽  
Chemical Reaction Mechanisms

Combining reinforcement learning (RL) and molecular dynamics (MD) simulations, we propose a machine-learning approach, called RL‡, to automatically unravel chemical reaction mechanisms. In RL‡, locating the transition state of a...

scholarly journals Molecular Dynamics Study on Lubrication Mechanism in Crystalline Structure between Copper and Sulfur

2015 ◽  
Vol 2015 ◽  
pp. 1-13 ◽  
Author(s):  
Ken-ichi Saitoh ◽  
Tomohiro Sato ◽  
Masanori Takuma ◽  
Yoshimasa Takahashi ◽  
Ryuketsu Chin
Keyword(s):  
Molecular Dynamics ◽  
Shear Stress ◽  
Potential Function ◽  
Crystalline Structure ◽  
Interatomic Potential ◽  
Hexagonal Phase ◽  
Interatomic Interaction ◽  
Md Simulations ◽  
Shear Loading ◽  
Atomistic Modeling

To clarify the nanosized mechanism of good lubrication in copper disulfide (Cu2S) crystal which is used as a sliding material, atomistic modeling of Cu2S is conducted and molecular dynamics (MD) simulations are performed in this paper. The interatomic interaction between atoms and crystalline structure in the phase of hexagonal crystal of Cu2S are carefully estimated by first-principle calculations. Then, approximating these interactions, we originally construct a conventional interatomic potential function of Cu2S crystal in its hexagonal phase. By using this potential function, we perform MD simulation of Cu2S crystal which is subjected to shear loading parallel to the basal plane. We compare results obtained by different conditions of sliding directions. Unlike ordinary hexagonal metallic crystals, it is found that the easy-glide direction does not always show small shear stress for Cu2S crystal. Besides, it is found that shearing velocity affects largely the magnitude of averaged shear stress. Generally speaking, higher velocity results in higher resistance against shear deformation. As a result, it is understood that Cu2S crystal exhibits somewhat liquid-like (amorphous) behavior in sliding condition and shear resistance increases with increase of sliding speed.

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