scholarly journals Hydrogenation Dynamics of Biphenylene Carbon (Graphenylene) Membranes

MRS Advances ◽  
2017 ◽  
Vol 2 (29) ◽  
pp. 1571-1576
Author(s):  
Vinicius Splugues ◽  
Pedro Alves da Silva Autreto ◽  
Douglas S. Galvao
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Md Simulations ◽  
Structural Transformations ◽  
Extensive Study ◽  
Massively Parallel ◽  
Porous Membranes ◽  
Two Dimensional ◽  
Reactive Force

ABSTRACTThe advent of graphene created a revolution in materials science. Because of this there is a renewed interest in other carbon-based structures. Graphene is the ultimate (just one atom thick) membrane. It has been proposed that graphene can work as impermeable membrane to standard gases, such argon and helium. Graphene-like porous membranes, but presenting larger porosity and potential selectivity would have many technological applications. Biphenylene carbon (BPC), sometimes called graphenylene, is one of these structures. BPC is a porous two-dimensional (planar) allotrope carbon, with its pores resembling typical sieve cavities and/or some kind of zeolites. In this work, we have investigated the hydrogenation dynamics of BPC membranes under different conditions (hydrogenation plasma density, temperature, etc.). We have carried out an extensive study through fully atomistic molecular dynamics (MD) simulations using the reactive force field ReaxFF, as implemented in the well-known Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) code. Our results show that the BPC hydrogenation processes exhibit very complex patterns and the formation of correlated domains (hydrogenated islands) observed in the case of graphene hydrogenation was also observed here. MD results also show that under hydrogenation BPC structure undergoes a change in its topology, the pores undergoing structural transformations and extensive hydrogenation can produce significant structural damages, with the formation of large defective areas and large structural holes, leading to structural collapse.

Anomalous Effect on the Phononic Thermal Conductivity of Silicene Nanoribbon by Hydrogenation

2015 ◽  
Vol 1105 ◽  
pp. 110-114 ◽  
Author(s):  
Emmanuel Dioresma Monterola ◽  
Naomi Tabudlong Paylaga ◽  
Giovanni Jariol Paylaga ◽  
Rolando Viño Bantaculo
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Silicon Nanowires ◽  
Large Scale ◽  
Massively Parallel ◽  
Two Dimensional ◽  
Phonon Modes ◽  
Anomalous Effect ◽  
Hydrogenated Silicon ◽  
Out Of Plane

Silicene is a two-dimensional (2D) allotrope of silicon known to have a lower thermal conductivity than graphene; thus, more suitable for thermoelectric applications. This paper investigates the effect of hydrogenation on the thermal conductivity of silicene nanoribbon (SiNR) using equilibrium molecular dynamics (EMD) simulations. The simulations were carried out in Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) using a modified Tersoff potential that considers both Si-Si and Si-H interactions. The thermal conductivity of fully hydrogenated silicene nanoribbon (H-SiNR), also known as silicane nanoribbon, was found to be higher than that of pristine SiNR in all the temperatures and dimensions considered here. This anomalous enhancement in the thermal conductivity is similar to that found in hydrogenated silicon nanowires (H-SiNWs). A mechanism for this anomalous effect has been proposed relating the hydrogenation of SiNR with the stiffening and increase of the acoustic out-of-plane flexural (ZA) phonon modes. Also, for both SiNR and H-SiNR, the thermal conductivities generally increase as the dimensions are increased while they generally decrease as the temperatures are increased, in agreement to other reports.

Large-Scale Molecular Dynamics Simulations of Interstitial Defect Diffusion in Silicon

2002 ◽  
Vol 731 ◽  
Author(s):  
David A. Richie ◽  
Jeongnim Kim ◽  
Richard Hennig ◽  
Kaden Hazzard ◽  
Steve Barr ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Tight Binding ◽  
Md Simulations ◽  
Binding Potential ◽  
Interstitial Defect ◽  
Long Time ◽  
Computational Materials ◽  
Dynamics Simulations

AbstractThe simulation of defect dynamics and evolution is a technologicaly relevant challenge for computational materials science. The diffusion of small defects in silicon unfolds as a sequence of structural transitions. The relative infrequency of transition events requires simulation over extremely long time scales. We simulate the diffusion of small interstitial clusters (I1, I2, I3) for a range of temperatures using large-scale molecular dynamics (MD) simulations with a realistic tight-binding potential. A total of 0.25 μ sec of simulation time is accumulated for the study. A novel real-time multiresolution analysis (RTMRA) technique extracts stable structures directly from the dynamics without structural relaxation. The discovered structures are relaxed to confirm their stability.

scholarly journals High-Performance Modeling of Carbon Dioxide Sequestration by Coupling Reservoir Simulation and Molecular Dynamics

SPE Journal ◽  
2016 ◽  
Vol 21 (03) ◽  
pp. 0853-0863 ◽  
Author(s):  
Kai Bao ◽  
Mi Yan ◽  
Rebecca Allen ◽  
Amgad Salama ◽  
Ligang Lu ◽  
...  
Keyword(s):  
Experimental Data ◽  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Reservoir Simulation ◽  
Co2 Sequestration ◽  
High Performance ◽  
Large Scale ◽  
Md Simulations ◽  
Massively Parallel ◽  
Geological Conditions

Summary The present work describes a parallel computational framework for carbon dioxide (CO2) sequestration simulation by coupling reservoir simulation and molecular dynamics (MD) on massively parallel high-performance-computing (HPC) systems. In this framework, a parallel reservoir simulator, reservoir-simulation toolbox (RST), solves the flow and transport equations that describe the subsurface flow behavior, whereas the MD simulations are performed to provide the required physical parameters. Technologies from several different fields are used to make this novel coupled system work efficiently. One of the major applications of the framework is the modeling of large-scale CO2 sequestration for long-term storage in subsurface geological formations, such as depleted oil and gas reservoirs and deep saline aquifers, which has been proposed as one of the few attractive and practical solutions to reduce CO2 emissions and address the global-warming threat. Fine grids and accurate prediction of the properties of fluid mixtures under geological conditions are essential for accurate simulations. In this work, CO2 sequestration is presented as a first example for coupling reservoir simulation and MD, although the framework can be extended naturally to the full multiphase multicomponent compositional flow simulation to handle more complicated physical processes in the future. Accuracy and scalability analysis are performed on an IBM BlueGene/P and on an IBM BlueGene/Q, the latest IBM supercomputer. Results show good accuracy of our MD simulations compared with published data, and good scalability is observed with the massively parallel HPC systems. The performance and capacity of the proposed framework are well-demonstrated with several experiments with hundreds of millions to one billion cells. To the best of our knowledge, the present work represents the first attempt to couple reservoir simulation and molecular simulation for large-scale modeling. Because of the complexity of subsurface systems, fluid thermodynamic properties over a broad range of temperature, pressure, and composition under different geological conditions are required, although the experimental results are limited. Although equations of state can reproduce the existing experimental data within certain ranges of conditions, their extrapolation out of the experimental data range is still limited. The present framework will definitely provide better flexibility and predictability compared with conventional methods.

Evolution of Metastable Structures in Bimetallic Catalysts from Microscopy and Machine-Learning Molecular Dynamics

2020 ◽  
Author(s):  
Jin Soo Lim ◽  
Jonathan Vandermause ◽  
Matthijs A. van Spronsen ◽  
Albert Musaelian ◽  
Christopher R. O’Connor ◽  
...  
Keyword(s):  
Machine Learning ◽  
Molecular Dynamics ◽  
Large Scale ◽  
Materials Science ◽  
Complete Characterization ◽  
Layer By Layer ◽  
Surface Restructuring ◽  
Metastable Structures ◽  
Mechanistic Investigation ◽  
Underlying Mechanisms

Restructuring of interface plays a crucial role in materials science and heterogeneous catalysis. Bimetallic systems, in particular, often adopt very different composition and morphology at surfaces compared to the bulk. For the first time, we reveal a detailed atomistic picture of the long-timescale restructuring of Pd deposited on Ag, using microscopy, spectroscopy, and novel simulation methods. Encapsulation of Pd by Ag always precedes layer-by-layer dissolution of Pd, resulting in significant Ag migration out of the surface and extensive vacancy pits. These metastable structures are of vital catalytic importance, as Ag-encapsulated Pd remains much more accessible to reactants than bulk-dissolved Pd. The underlying mechanisms are uncovered by performing fast and large-scale machine-learning molecular dynamics, followed by our newly developed method for complete characterization of atomic surface restructuring events. Our approach is broadly applicable to other multimetallic systems of interest and enables the previously impractical mechanistic investigation of restructuring dynamics.

Molecular Dynamics Simulation of a Pullout Test on a Carbon Nanotube in a Polymer Matrix

2014 ◽  
Vol 1700 ◽  
pp. 61-66
Author(s):  
Guttormur Arnar Ingvason ◽  
Virginie Rollin
Keyword(s):  
Molecular Dynamics ◽  
Polymer Matrix ◽  
Large Scale ◽  
Md Simulations ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Polymer Molecules ◽  
Molecular Potential ◽  
Pull Out ◽  
Walled Carbon Nanotubes

ABSTRACTAdding single walled carbon nanotubes (SWCNT) to a polymer matrix can improve the delamination properties of the composite. Due to the complexity of polymer molecules and the curing process, few 3-D Molecular Dynamics (MD) simulations of a polymer-SWCNT composite have been run. Our model runs on the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS), with a COMPASS (Condensed phase Optimized Molecular Potential for Atomistic Simulations Studies) potential. This potential includes non-bonded interactions, as well as bonds, angles and dihedrals to create a MD model for a SWCNT and EPON 862/DETDA (Diethyltoluenediamine) polymer matrix. Two simulations were performed in order to test the implementation of the COMPASS parameters. The first one was a tensile test on a SWCNT, leading to a Young’s modulus of 1.4 TPa at 300K. The second one was a pull-out test of a SWCNT from an originally uncured EPON 862/DETDA matrix.

scholarly journals Antimicrobial action of the cationic peptide, chrysophsin-3: a coarse-grained molecular dynamics study

Soft Matter ◽  
2018 ◽  
Vol 14 (15) ◽  
pp. 2796-2807 ◽  
Author(s):  
Andrea Catte ◽  
Mark R. Wilson ◽  
Martin Walker ◽  
Vasily S. Oganesyan
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
Antimicrobial Action ◽  
Coarse Grained ◽  
Cationic Peptide ◽  
Coarse Grained Molecular Dynamics

Antimicrobial action of a cationic peptide is modelled by large scale MD simulations.

scholarly journals Molecular dynamics simulations for genetic interpretation in protein coding regions: where we are, where to go and when

2019 ◽  
Author(s):  
Juan J Galano-Frutos ◽  
Helena García-Cebollada ◽  
Javier Sancho
Keyword(s):  
Molecular Dynamics ◽  
Amino Acid ◽  
Large Scale ◽  
Binary Classification ◽  
Chemical Properties ◽  
Md Simulations ◽  
Single Amino Acid ◽  
Medical Decision ◽  
Evolutionary Information ◽  
Protein Variants

Abstract The increasing ease with which massive genetic information can be obtained from patients or healthy individuals has stimulated the development of interpretive bioinformatics tools as aids in clinical practice. Most such tools analyze evolutionary information and simple physical–chemical properties to predict whether replacement of one amino acid residue with another will be tolerated or cause disease. Those approaches achieve up to 80–85% accuracy as binary classifiers (neutral/pathogenic). As such accuracy is insufficient for medical decision to be based on, and it does not appear to be increasing, more precise methods, such as full-atom molecular dynamics (MD) simulations in explicit solvent, are also discussed. Then, to describe the goal of interpreting human genetic variations at large scale through MD simulations, we restrictively refer to all possible protein variants carrying single-amino-acid substitutions arising from single-nucleotide variations as the human variome. We calculate its size and develop a simple model that allows calculating the simulation time needed to have a 0.99 probability of observing unfolding events of any unstable variant. The knowledge of that time enables performing a binary classification of the variants (stable-potentially neutral/unstable-pathogenic). Our model indicates that the human variome cannot be simulated with present computing capabilities. However, if they continue to increase as per Moore’s law, it could be simulated (at 65°C) spending only 3 years in the task if we started in 2031. The simulation of individual protein variomes is achievable in short times starting at present. International coordination seems appropriate to embark upon massive MD simulations of protein variants.

scholarly journals Indentation-induced plastic behaviour of nanotwinned Cu/high entropy alloy FeCoCrNi nanolaminate: an atomic simulation

RSC Advances ◽  
2020 ◽  
Vol 10 (16) ◽  
pp. 9187-9192 ◽  
Author(s):  
Hui Feng ◽  
Jingwen Tang ◽  
Haotian Chen ◽  
Yuanyuan Tian ◽  
Qihong Fang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Md Simulations ◽  
High Entropy Alloy ◽  
High Entropy ◽  
Atomic Simulation ◽  
Layer Number ◽  
Plastic Behaviour

Using large-scale molecular dynamics (MD) simulations, the effects of interface and layer number in the nanoindentation response of experimentally observed nanotwinned Cu/high entropy alloy (HEA) FeCoCrNi nanolaminate are studied.

Shear Flows in Two Dimensional Strongly Coupled Yukawa Liquids: A Large Scale Molecular Dynamics Study

2011 ◽  
Author(s):  
R. Ganesh ◽  
J. Ashwin ◽  
Vladimir Yu. Nosenko ◽  
Padma K. Shukla ◽  
Markus H. Thoma ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Shear Flows ◽  
Two Dimensional ◽  
Strongly Coupled

IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers

1997 ◽  
Vol 08 (05) ◽  
pp. 1131-1140 ◽  
Author(s):  
J. Stadler ◽  
R. Mikulla ◽  
H.-R. Trebin
Keyword(s):  
Molecular Dynamics ◽  
Software Package ◽  
Large Scale ◽  
Md Simulation ◽  
Parallel Computers ◽  
Massively Parallel ◽  
Massively Parallel Computers ◽  
Communication Scheme ◽  
And Performance ◽  
Dynamics Simulations

We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After a short explanation of the cell-based algorithm, its extension to parallel computers as well as two variants of the communication scheme are discussed. We provide performance numbers for simulations of different sizes and compare them with values found in the literature. Finally we describe two applications, namely a very large scale simulation with more than 1.23×109 atoms, to our knowledge the largest published MD simulation up to this day and a simulation of a crack propagating in a two-dimensional quasicrystal.

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