scholarly journals Molecular Dynamics Simulations of the Host Defense Peptide Temporin L and Its Q3K Derivative: An Atomic Level View from Aggregation in Water to Bilayer Perturbation

Molecules ◽  
2017 ◽  
Vol 22 (7) ◽  
pp. 1235 ◽  
Author(s):  
Andrea Farrotti ◽  
Paolo Conflitti ◽  
Saurabh Srivastava ◽  
Jimut Ghosh ◽  
Antonio Palleschi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Host Defense ◽  
Atomic Level ◽  
Host Defense Peptide ◽  
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.

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

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>

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

scholarly journals Direct observation of realistic-temperature fuel combustion mechanisms in atomistic simulations

2016 ◽  
Vol 7 (8) ◽  
pp. 5280-5286 ◽  
Author(s):  
Kristof M. Bal ◽  
Erik C. Neyts
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Direct Observation ◽  
Fuel Combustion ◽  
Atomic Level ◽  
Atomistic Simulations ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations

Advanced accelerated molecular dynamics simulations provide a detailed atomic-level picture of combustion at realistic temperatures and pressures.

How calcium ion binding induces the conformational transition of the calmodulin N-terminal domain—an atomic level characterization

2019 ◽  
Vol 21 (36) ◽  
pp. 19795-19804 ◽  
Author(s):  
Likun Zhao ◽  
Luhua Lai ◽  
Zhuqing Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Calcium Ion ◽  
Conformational Transition ◽  
Atomic Level ◽  
Ion Binding ◽  
Terminal Domain ◽  
Calcium Ion Binding ◽  
Dynamics Simulations ◽  
Conformation Transition

The Ca2+ binding and triggering conformation transition of nCaM were detected in unbiased molecular dynamics simulations.

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