Molecular dynamics simulations of atomic-level brittle fracture mechanisms in amorphous silica

2007 ◽  
Vol 42 (12) ◽  
pp. 4159-4169 ◽  
Author(s):  
Krishna Muralidharan ◽  
Ki-Dong Oh ◽  
P. A. Deymier ◽  
K. Runge ◽  
J. H. Simmons
Keyword(s):  
Molecular Dynamics ◽  
Brittle Fracture ◽  
Molecular Dynamics Simulations ◽  
Amorphous Silica ◽  
Atomic Level ◽  
Fracture Mechanisms ◽  
Dynamics Simulations

scholarly journals Exploring Dynamics and Structure of Biomolecules, Cryoprotectants, and Water Using Molecular Dynamics Simulations: Implications for Biostabilization and Biopreservation

2019 ◽  
Vol 21 (1) ◽  
pp. 1-31 ◽  
Author(s):  
Lindong Weng ◽  
Shannon L. Stott ◽  
Mehmet Toner
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Motion ◽  
State Of The Art ◽  
Level Structure ◽  
Cost Effective ◽  
Atomic Level ◽  
Computational Research ◽  
Dynamics Simulations ◽  
Biological Entities

Successful stabilization and preservation of biological materials often utilize low temperatures and dehydration to arrest molecular motion. Cryoprotectants are routinely employed to help the biological entities survive the physicochemical and mechanical stresses induced by cold or dryness. Molecular interactions between biomolecules, cryoprotectants, and water fundamentally determine the outcomes of preservation. The optimization of assays using the empirical approach is often limited in structural and temporal resolution, whereas classical molecular dynamics simulations can provide a cost-effective glimpse into the atomic-level structure and interaction of individual molecules that dictate macroscopic behavior. Computational research on biomolecules, cryoprotectants, and water has provided invaluable insights into the development of new cryoprotectants and the optimization of preservation methods. We describe the rapidly evolving state of the art of molecular simulations of these complex systems, summarize the molecular-scale protective and stabilizing mechanisms, and discuss the challenges that motivate continued innovation in this field.

Multimillion-Atom Simulations of Atomic-Level Surface Stresses and Pressure Distribution on InAs/GaAs Mesas

1999 ◽  
Vol 584 ◽  
Author(s):  
Xiaotao Su ◽  
Rajiv K. Kalia ◽  
Anupam Madhukar ◽  
Aiichiro Nakano ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Chemical Composition ◽  
Pressure Distribution ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Interatomic Potential ◽  
Atomic Level ◽  
Level Surface ◽  
Speed Up ◽  
Dynamics Simulations

AbstractLarge-scale molecular dynamics simulations are performed to investigate the atomiclevel stresses on InAs/GaAs mesas. The simulations are based on an interatomic-potential scheme for InAs/GaAs systems which depends on the local chemical composition. Multiresolution techniques are used to speed up the simulations. InAs/GaAs square mesas with { 101 }-type sidewalls are studied. The atomic-level pressure distribution and surface atomic stresses on the sidewalls with 12, 10, 8 and 6 monolayers of InAs overlayers have been calculated.

scholarly journals Local Structuring of Diketopyrrolopyrrole (DPP)-Based Semiconducting Polymers Using Molecular Dynamics Simulations

2020 ◽  
Author(s):  
Maryam Reisjalali ◽  
Jose Javier Burgos Marmol ◽  
Alessandro Troisi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Electronic Devices ◽  
Atomic Level ◽  
Semiconducting Polymers ◽  
The Other ◽  
Charge Mobility ◽  
High Charge ◽  
High Performing ◽  
Dynamics Simulations

High performing organic semiconducting polymers show great potentials for use in electronic devices which is greatly dependent on the material crystallinity and packing. A series of short oligomers of the diketopyrrolopyrrole (DPP)-based materials that have shown to have high charge mobility are studied to understand the local structuring at atomic level for these materials. The simulations show that the tendency for this material class to form aggregates is driven by the interaction between DPP fragments, but this is modulated by the other conjugated fragments of the materials which afect the rigidity of the polymer and the ability to form aggregates of larger size.<br>

Molecular Dynamics Study of Diffusion Behavior in Amorphous Silica with Hydroxyl Group

2008 ◽  
Vol 368-372 ◽  
pp. 1677-1679
Author(s):  
Fan Wei Zhang ◽  
Qui Ang Zhu ◽  
Yuan Fa Ding ◽  
Yue Zhang ◽  
Da Hai Zhang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amorphous Silica ◽  
Hydroxyl Group ◽  
Theoretical Interpretation ◽  
Hydroxyl Groups ◽  
Diffusion Behavior ◽  
Self Diffusion ◽  
Initial Charge ◽  
Dynamics Simulations

Molecular dynamics simulations are performed to research the diffusion behavior of amorphous silica with hydroxyl group. Muliken analysis is employed for the determination of initial charge status of simulated systems with various hydroxyl contents. Modified BKS potentials for the interactions between introduced hydroxyl groups and other atoms, are adopted in the present molecular dynamics simulations. Short-range atomic arrangement and self diffusion coefficients of hydroxyl-doped amorphous silica systems are calculated and hereafter compared with those of pure amorphous silica. The calculation results suggest that the doped hydroxyl groups play an important role for the mobility of atoms within the system, which can be employed to the theoretical interpretation of the oxidation process of the ceramics such as silicon nitride.

Studies of the Elastic Properties of Amorphous Silica by Molecular Dynamics Simulations

2008 ◽  
Author(s):  
Heikki Ristolainen ◽  
Antti Kuronen ◽  
Kai Nordlund ◽  
Roman Nowak ◽  
Masaki Fujikane
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Elastic Properties ◽  
Amorphous Silica ◽  
Dynamics Simulations

scholarly journals Electrokinetic flow of an aqueous electrolyte in amorphous silica nanotubes

2018 ◽  
Vol 20 (44) ◽  
pp. 27838-27848 ◽  
Author(s):  
Christopher D. Daub ◽  
Natalie M. Cann ◽  
D. Bratko ◽  
Alenka Luzar
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Amorphous Silica ◽  
Aqueous Electrolyte ◽  
Nonequilibrium Molecular Dynamics ◽  
Molecular Models ◽  
Electrokinetic Flow ◽  
Silica Nanotubes ◽  
Dynamics Simulations ◽  
Pressure Driven Flow

We study the pressure-driven flow of aqueous NaCl in amorphous silica nanotubes using nonequilibrium molecular dynamics simulations featuring both polarizable and non-polarizable molecular models.

Mechanisms of constitutive activation of Janus kinase 2-V617F revealed at the atomic level through molecular dynamics simulations

Cancer ◽  
2009 ◽  
Vol 115 (8) ◽  
pp. 1692-1700 ◽  
Author(s):  
Tai-Sung Lee ◽  
Wanlong Ma ◽  
Xi Zhang ◽  
Francis Giles ◽  
Hagop Kantarjian ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Atomic Level ◽  
Janus Kinase ◽  
Janus Kinase 2 ◽  
Constitutive Activation ◽  
Dynamics Simulations
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