Effective Molecular Dynamics Model of Ionic Solutions for Large-Scale Calculations

Abstract Titanium alloys’ excellent mechanical and physical properties make it the most popular material widely used in aerospace, medical, nuclear and other significant industries. The study of titanium alloys mainly focused on the macroscopic mechanical mechanism. However, very few researches addressed the nanostructure of titanium alloys and its mechanical response in Nano-machining due to the difficulty to perform and characterize nano-machining experiment. Compared with nano-machining, nano-indentation is easier to characterize the microscopic plasticity of titanium alloys. This research presents a nano-indentation molecular dynamics model in titanium to address its microstructure alteration, plastic deformation and other mechanical response at the atomistic scale. Based on the molecular dynamics model, a complete nano-indentation cycle, including the loading and unloading stages, is performed by applying Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS). The plastic deformation mechanism of nano-indentation of titanium with a rigid diamond ball tip was studied under different indentation velocities. At the same time, the influence of different environment temperatures on the nano-plastic deformation of titanium is analyzed under the condition of constant indentation velocity. The simulation results show that the Young’s modulus of pure titanium calculated based on nano-indentation is about 110GPa, which is very close to the experimental results. The results also show that the mechanical behavior of titanium can be divided into three stages: elastic stage, yield stage and plastic stage during the nano-indentation process. In addition, indentation speed has influence on phase transitions and nucleation of dislocations in the range of 0.1–1.0 Å/ps.

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Dissipative particle dynamics model of homogalacturonan based on molecular dynamics simulations

Scientific Reports ◽

10.1038/s41598-020-71820-2 ◽

2020 ◽

Vol 10 (1) ◽

Cited By ~ 1

Author(s):

P. M. Pieczywek ◽

W. Płaziński ◽

A. Zdunek

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Large Scale ◽

Dissipative Particle Dynamics ◽

Three Dimensional ◽

Structural Features ◽

Particle Dynamics ◽

Distribution Functions ◽

Coarse Grained ◽

Dynamics Model

Abstract In this study we present an alternative dissipative particle dynamics (DPD) parametrization strategy based on data extracted from the united-atom molecular simulations. The model of the homogalacturonan was designed to test the ability of the formation of large-scale structures via hydrogen bonding in water. The extraction of coarse-grained parameters from atomistic molecular dynamics was achieved by means of the proposed molecule aggregation algorithm based on an iterative nearest neighbour search. A novel approach to a time-scale calibration scheme based on matching the average velocities of coarse-grained particles enabled the DPD forcefield to reproduce essential structural features of homogalacturonan molecular chains. The successful application of the proposed parametrization method allowed for the reproduction of the shapes of radial distribution functions, particle velocities and diffusivity of the atomistic molecular dynamics model using DPD force field. The structure of polygalacturonic acid molecules was mapped into the DPD force field by means of the distance and angular bond characteristics, which closely matched the MD results. The resulting DPD trajectories showed that randomly dispersed homogalacturonan chains had a tendency to aggregate into highly organized 3D structures. The final structure resembled a three-dimensional network created by tightly associated homogalacturonan chains organized into thick fibres.

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Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

10.26434/chemrxiv.11462160.v1 ◽

2019 ◽

Author(s):

Liqun Cao ◽

Jinzhe Zeng ◽

Mingyuan Xu ◽

Chih-Hao Chin ◽

Tong Zhu ◽

...

Keyword(s):

Molecular Dynamics ◽

Ab Initio ◽

Large Scale ◽

Methane Combustion ◽

Combustion Method ◽

Dynamics Simulation ◽

Ab Initio Molecular Dynamics ◽

Computational Time ◽

Combustion Mechanism ◽

Daily Lives

Combustion is a kind of important reaction that affects people's daily lives and the development of aerospace. Exploring the reaction mechanism contributes to the understanding of combustion and the more efficient use of fuels. Ab initio quantum mechanical (QM) calculation is precise but limited by its computational time for large-scale systems. In order to carry out reactive molecular dynamics (MD) simulation for combustion accurately and quickly, we develop the MFCC-combustion method in this study, which calculates the interaction between atoms using QM method at the level of MN15/6-31G(d). Each molecule in systems is treated as a fragment, and when the distance between any two atoms in different molecules is greater than 3.5 Å, a new fragment involved two molecules is produced in order to consider the two-body interaction. The deviations of MFCC-combustion from full system calculations are within a few kcal/mol, and the result clearly shows that the calculated energies of the different systems using MFCC-combustion are close to converging after the distance thresholds are larger than 3.5 Å for the two-body QM interactions. The methane combustion was studied with the MFCC-combustion method to explore the combustion mechanism of the methane-oxygen system.

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

10.26434/chemrxiv.11811660.v1 ◽

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.

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