Dynamical matrix propagator scheme for large-scale proton dynamics simulations

2020 ◽  
Vol 152 (11) ◽  
pp. 114114 ◽  
Author(s):  
Christian Dreßler ◽  
Gabriel Kabbe ◽  
Martin Brehm ◽  
Daniel Sebastiani
Keyword(s):  
Large Scale ◽  
Dynamical Matrix ◽  
Proton Dynamics ◽  
Dynamics Simulations

scholarly journals Elucidating the Onset of Plasticity in Sliding Contacts Using Differential Computational Orientation Tomography

2021 ◽  
Vol 69 (3) ◽  
Author(s):  
S. J. Eder ◽  
P. G. Grützmacher ◽  
M. Rodríguez Ripoll ◽  
J. F. Belak
Keyword(s):  
Grain Boundary ◽  
Large Scale ◽  
Surface Deformation ◽  
Boundary Migration ◽  
Material Design ◽  
Lattice Rotation ◽  
Time Resolved ◽  
Near Surface ◽  
Color Saturation ◽  
Dynamics Simulations

Abstract Depending on the mechanical and thermal energy introduced to a dry sliding interface, the near-surface regions of the mated bodies may undergo plastic deformation. In this work, we use large-scale molecular dynamics simulations to generate “differential computational orientation tomographs” (dCOT) and thus highlight changes to the microstructure near tribological FCC alloy surfaces, allowing us to detect subtle differences in lattice orientation and small distances in grain boundary migration. The analysis approach compares computationally generated orientation tomographs with their undeformed counterparts via a simple image analysis filter. We use our visualization method to discuss the acting microstructural mechanisms in a load- and time-resolved fashion, focusing on sliding conditions that lead to twinning, partial lattice rotation, and grain boundary-dominated processes. Extracting and laterally averaging the color saturation value of the generated tomographs allows us to produce quantitative time- and depth-resolved maps that give a good overview of the progress and severity of near-surface deformation. Corresponding maps of the lateral standard deviation in the color saturation show evidence of homogenization processes occurring in the tribologically loaded microstructure, frequently leading to the formation of a well-defined separation between deformed and undeformed regions. When integrated into a computational materials engineering framework, our approach could help optimize material design for tribological and other deformation problems. Graphic Abstract .

scholarly journals Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

2016 ◽  
Vol 34 (4) ◽  
pp. 041509 ◽  
Author(s):  
Daniel Edström ◽  
Davide G. Sangiovanni ◽  
Lars Hultman ◽  
Ivan Petrov ◽  
J. E. Greene ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Epitaxial Film ◽  
Film Growth ◽  
Dynamics Simulations ◽  
Epitaxial Film Growth

scholarly journals Bimodal Grain-Size Scaling of Thermal Transport in Polycrystalline Graphene from Large-Scale Molecular Dynamics Simulations

Nano Letters ◽  
2017 ◽  
Vol 17 (10) ◽  
pp. 5919-5924 ◽  
Author(s):  
Zheyong Fan ◽  
Petri Hirvonen ◽  
Luiz Felipe C. Pereira ◽  
Mikko M. Ervasti ◽  
Ken R. Elder ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Grain Size ◽  
Molecular Dynamics Simulations ◽  
Thermal Transport ◽  
Large Scale ◽  
Size Scaling ◽  
Dynamics Simulations ◽  
Bimodal Grain Size

Large-scale molecular dynamics simulations of nanomachining

2017 ◽  
pp. 141-177 ◽  
Author(s):  
Stefan J. Eder ◽  
Ulrike Cihak-Bayr ◽  
Davide Bianchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Dynamics Simulations

scholarly journals Making Soup: Preparing and Validating Molecular Simulations of the Bacterial Cytoplasm

2019 ◽  
Author(s):  
Leandro Oliveira Bortot ◽  
Zahedeh Bashardanesh ◽  
David van der Spoel
Keyword(s):  
Large Scale ◽  
Biological Properties ◽  
Computational Power ◽  
E Coli ◽  
Solvent Models ◽  
Explicit Solvent ◽  
Computational Modeling And Simulation ◽  
Dynamics Simulations ◽  
The Individual ◽  
Bacterial Cytoplasm

Biomolecular crowding affects the biophysical and biochemical behavior of macro- molecules when compared to the dilute environment present in experiments made with isolated proteins. Computational modeling and simulation are useful tools to study how crowding affects the structural dynamics and biological properties of macromolecules. As computational power increased, modeling and simulating large scale all-atom explicit solvent models of the prokaryote cytoplasm become possible. In this work, we build an atomistic model of the cytoplasm of Escherichia coli composed of 1.5 million atoms and submit it to a total of 3 μs of molecular dynamics simulations. The properties of biomolecules under crowding conditions are compared to those from simulations of the individual compounds under dilute conditions. The simulation model is found to be consistent with experimental data about the diffusion coefficient and stability of macromolecules under crowded conditions. In order to stimulate further work we provide a Python script and a set of files that enables other researchers to build their own E. coli cytoplasm models to address questions related to crowding.<br>

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