Analysis of a one-billion atom simulation of work-hardening in ductile materials

2004 ◽  
Vol 821 ◽  
Author(s):  
Markus J. Buehler ◽  
Alexander Hartmaier ◽  
Mark Duchaineau ◽  
Farid F. Abraham ◽  
Huajian Gao
Keyword(s):  
Molecular Dynamics ◽  
Work Hardening ◽  
Large Scale ◽  
Pair Potential ◽  
Model Material ◽  
Dynamics Simulation ◽  
Ductile Materials ◽  
Lennard Jones ◽  
Cutting Processes ◽  
First Time

AbstractWe analyze a large-scale molecular dynamics simulation of work hardening in a ductile model material comprising of 500 million atoms interacting with a Lennard-Jones pair potential within a classical molecular dynamics scheme. With tensile loading, we observe emission of thousands of dislocations from two sharp cracks. The dislocations interact in a complex way, revealing three fundamental mechanisms of work-hardening. These are (1) dislocation cutting processes, jog formation and generation of point defects; (2) activation of secondary slip systems by cross-slip; and (3) formation of sessile Lomer-Cottrell locks. The dislocations self-organize into a complex sessile defect topology. Our analysis illustrates mechanisms formerly only known from textbooks and observed indirectly in experiment. It is the first time that such a rich set of fundamental phenomena has been seen in a single computer simulation.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

scholarly journals Molecular Dynamics Simulation of Tolman Length and Interfacial Tension of Symmetric Binary Lennard–Jones Liquid

Symmetry ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1376
Author(s):  
Hideki Kanda ◽  
Wahyudiono ◽  
Motonobu Goto
Keyword(s):  
Molecular Dynamics ◽  
Interfacial Tension ◽  
Large Scale ◽  
Interfacial Area ◽  
Dynamics Simulation ◽  
Continuum Approximation ◽  
Lennard Jones ◽  
Partially Miscible ◽  
Tolman Length ◽  
Dividing Surface

The Tolman length and interfacial tension of partially miscible symmetric binary Lennard–Jones (LJ) fluids (A, B) was revealed by performing a large-scale molecular dynamics (MD) simulation with a sufficient interfacial area and cutting distance. A unique phenomenon was observed in symmetric binary LJ fluids, where two surfaces of tension existed on both sides of an equimolar dividing surface. The range of interaction εAB between the different liquids and the temperature in which the two LJ fluids partially mixed was clarified, and the Tolman length exceeded 3 σ when εAB was strong at higher temperatures. The results show that as the temperature or εAB increases, the Tolman length increases and the interfacial tension decreases. This very long Tolman length indicates that one should be very careful when applying the concept of the liquid–liquid interface in the usual continuum approximation to nanoscale droplets and capillary phase separation in nanopores.

Molecular dynamics simulation of interhalogen compounds using two potential models 2. Liquid bromine trifluoride (BrF3) — structure and thermodynamics

1993 ◽  
Vol 71 (12) ◽  
pp. 2189-2193 ◽  
Author(s):  
Vivek Saxena
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Pair Potential ◽  
Dynamics Simulation ◽  
Gaseous State ◽  
Self Diffusion ◽  
Lennard Jones ◽  
Interaction Terms ◽  
Liquid Bromine ◽  
Bromine Trifluoride

This paper reports on the molecular dynamics simulation results of liquid bromine trifluoride (BrF3) at 299, 315, and 363 K. We have assumed that the molecules interact via Lennard–Jones 12–6 site–site pair potential and Lennard–Jones site–site + fractional charges over atomic sites. Lennard–Jones potential parameters of Singer et al. (Mol. Phys. 33, 1757 (1977)) have been used for Br–Br, and F–F interactions and cross interaction terms are calculated using Lorentz–Berthelot mixing rules. Fractional charges are assigned to reproduce the experimentally determined gaseous-state molecular dipole moment. Various structural and thermodynamic properties for liquid state are reported and compared in detail with results from diffraction studies (Mittkin et al. J. Struct. Chem. 28, 60 (1987)). Some mechanical properties such as mean-square force and torque, self-diffusion coefficient have also been calculated. The repulsive part of the proposed atom–atom pair potential is a good approximation since both molecular configurations are in good agreement with experimental results.

The dynamical complexity of work-hardening: a large-scale molecular dynamics simulation

2005 ◽  
Vol 21 (2) ◽  
pp. 103-111 ◽  
Author(s):  
Markus J. Buehler ◽  
Alexander Hartmaier ◽  
Huajian Gao ◽  
Mark A. Duchaineau ◽  
Farid F. Abraham
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Work Hardening ◽  
Large Scale ◽  
Dynamics Simulation ◽  
Dynamical Complexity

scholarly journals TRILLION-ATOM MOLECULAR DYNAMICS BECOMES A REALITY

2008 ◽  
Vol 19 (09) ◽  
pp. 1315-1319 ◽  
Author(s):  
TIMOTHY C. GERMANN ◽  
KAI KADAU
Keyword(s):  
Molecular Dynamics ◽  
Large Scale ◽  
Shear Instability ◽  
Dynamics Simulation ◽  
Massively Parallel ◽  
Lennard Jones ◽  
Simple Cubic ◽  
Simple Cubic Lattice ◽  
Future Potential ◽  
Large Scale Simulations

By utilizing the molecular dynamics code SPaSM on Livermore's BlueGene/L architecture, consisting of 212 992 IBM PowerPC440 700 MHz processors, a molecular dynamics simulation was run with one trillion atoms. To demonstrate the practicality and future potential of such ultra large-scale simulations, the onset of the mechanical shear instability occurring in a system of Lennard-Jones particles arranged in a simple cubic lattice was simulated. The evolution of the instability was analyzed on-the-fly using the in-house developed massively parallel graphical object-rendering code MD_render.

Investigation of Argon Flow Induced by Temperature Difference Using the Molecular Dynamics Simulation

2011 ◽  
Author(s):  
Payam Radmehr ◽  
Reza Kamali
Keyword(s):  
Molecular Dynamics ◽  
Pair Potential ◽  
Potential Interaction ◽  
Dynamics Simulation ◽  
Square Cavity ◽  
3 Dimensional ◽  
Lennard Jones ◽  
Molecular Potential ◽  
Argon Flow ◽  
Simulated System

In the present work, Molecular Dynamics technique is performed to study free convection in the square cavity. Simulated system is a 3-dimensional box containing fluid atoms. The walls of box are solid and formed in FCC. Fluid and solid atoms are chosen as argon and platinum respectively. The pair potential between fluid-fluid and fluid-wall atoms is governed by truncated Lennard-Jones (6–12) potential as these molecules have well-established molecular potential interaction. The periodic boundary condition (PBC) is applied in only one direction being perpendicular to the simulation surface. It helps ignore the effects of wall in this dimension. Half of the box is remained in a constant temperature (T1) and the temperature of opposite half is set to different value (T2). The velocity field is obtained and its dependency to the temperature ratio (T1/T2) is investigated. Also, we are eager to obtain the effect of gravity force on the velocity fields.

Combustion Driven by Fragment-based Ab Initio Molecular Dynamics Simulation

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.

scholarly journals Modeling and Molecular Dynamics of the 3D Structure of the HPV16 E7 Protein and Its Variants

2021 ◽  
Vol 22 (3) ◽  
pp. 1400
Author(s):  
Ciresthel Bello-Rios ◽  
Sarita Montaño ◽  
Olga Lilia Garibay-Cerdenares ◽  
Lilian Esmeralda Araujo-Arcos ◽  
Marco Antonio Leyva-Vázquez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
3D Structure ◽  
Epidemiological Studies ◽  
Dynamics Simulation ◽  
Structural Refinement ◽  
Oncogenic Potential ◽  
Structural Differences ◽  
Reference Protein ◽  
E6 And E7 ◽  
First Time

The oncogenic potential of high-risk human papillomavirus (HPV) is predicated on the production of the E6 and E7 oncoproteins, which are responsible for disrupting the control of the cell cycle. Epidemiological studies have proposed that the presence of the N29S and H51N variants of the HPV16 E7 protein is significantly associated with cervical cancer. It has been suggested that changes in the amino acid sequence of E7 variants may affect the oncoprotein 3D structure; however, this remains uncertain. An analysis of the structural differences of the HPV16 E7 protein and its variants (N29S and H51N) was performed through homology modeling and structural refinement by molecular dynamics simulation. We propose, for the first time, a 3D structure of the E7 reference protein and two of Its variants (N29S and H51N), and conclude that the mutations induced by the variants in N29S and H51N have a significant influence on the 3D structure of the E7 protein of HPV16, which could be related to the oncogenic capacity of this protein.

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