scholarly journals Anomalous dynamics of water at the octopeptide lanreotide surface

RSC Advances ◽  
2020 ◽  
Vol 10 (56) ◽  
pp. 33903-33910
Author(s):  
Florian Pinzan ◽  
Franck Artzner ◽  
Aziz Ghoufi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Dynamics ◽  
Atomistic Simulations ◽  
Hydration State ◽  
Dynamics Simulations ◽  
Anomalous Dynamics ◽  
Cyclic Octapeptide

Molecular dynamics simulations of a hydrated mutated lanreotide, a cyclic octapeptide, were carried out to characterize its hydration state. We studied the water dynamics close to the peptide using atomistic simulations.

Tunable Gigahertz Oscillators of Gliding Incommensurate Bilayer Graphene Sheets

2013 ◽  
Vol 80 (4) ◽  
Author(s):  
Ming Luo ◽  
Zhuhua Zhang ◽  
Boris I. Yakobson
Keyword(s):  
Molecular Dynamics ◽  
Surface Energy ◽  
Molecular Dynamics Simulations ◽  
Friction Force ◽  
Function Theory ◽  
Bilayer Graphene ◽  
Atomistic Simulations ◽  
Graphene Sheets ◽  
Dynamics Simulations ◽  
Oscillation Frequencies

Oscillators composed of incommensurate graphene sheets have been investigated by molecular dynamics simulations. The oscillation frequencies can reach tens of gigahertz range and depend on the surface energy of the bilayer graphene and the oscillatory amplitude. We demonstrate the tunability of such an oscillator in terms of frequency and friction by its varying geometric parameters. Exploration of the damping mechanism by combining the autocorrelation function theory and the direct atomistic simulations reveals that the friction force is proportional to the velocity of oscillatory motion. The results should help optimize the design of graphene-based nanoelectromechanical devices.

Atomistic simulations of TeO2-based glasses: interatomic potentials and molecular dynamics

2014 ◽  
Vol 16 (27) ◽  
pp. 14150-14160 ◽  
Author(s):  
Anastasia Gulenko ◽  
Olivier Masson ◽  
Abid Berghout ◽  
David Hamani ◽  
Philippe Thomas
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Interatomic Potential ◽  
Atomistic Simulations ◽  
Interatomic Potentials ◽  
First Results ◽  
Dynamics Simulations

This article derives the interatomic potential for the TeO2 system and presents the first results of molecular dynamics simulations of the pure TeO2 structure.

scholarly journals Thermodynamics of the self-assembly of non-ionic chromonic molecules using atomistic simulations. The case of TP6EO2M in aqueous solution

Soft Matter ◽  
2015 ◽  
Vol 11 (4) ◽  
pp. 680-691 ◽  
Author(s):  
Anna Akinshina ◽  
Martin Walker ◽  
Mark R. Wilson ◽  
Gordon J. T. Tiddy ◽  
Andrew J. Masters ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Liquid Crystal ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
The Self ◽  
Atomistic Simulations ◽  
Aggregation Behaviour ◽  
Dynamics Simulations

Molecular dynamics simulations of non-ionic triphenylene-based chromonic liquid crystal molecules demonstrate self-assembly of the molecules into stacks and “quasi-isodesmic” aggregation behaviour.

On the Formation of Carbon Nanotube Serpentines: Insights from Multi-Million Atom Molecular Dynamics Simulation

2011 ◽  
Vol 1284 ◽  
Author(s):  
Leonardo D. Machado ◽  
Sergio B. Legoas ◽  
Jaqueline S. Soares ◽  
Nitzan Shadmi ◽  
Ado Jorio ◽  
...  
Keyword(s):  
Carbon Nanotubes ◽  
Molecular Dynamics ◽  
Carbon Nanotube ◽  
Molecular Dynamics Simulations ◽  
Classical Mechanics ◽  
Dynamics Simulation ◽  
Atomistic Simulations ◽  
Molecular Force ◽  
Short Period ◽  
Dynamics Simulations

ABSTRACTIn this work we present preliminary results from molecular dynamics simulations for carbon nanotubes serpentine dynamics formation. These S-like nanostructures consist of a series of parallel and straight nanotube segments connected by alternating U-turn shaped curves. Nanotube serpentines were experimentally synthesized and reported in recent years, but up to now no atomistic simulations have been carried out to address the dynamics of formation of these structures. We have carried out fully atomistic molecular dynamics simulations in the framework of classical mechanics with a standard molecular force field. Multi-million atoms structures formed by stepped substrates with a carbon nanotube (about 1 micron in length) placed on top of them have been considered in our simulations. A force is applied to the upper part of the tube during a short period of time and then turned off and the system set free to evolve in time. Our results showed that these conditions are sufficient to form robust serpentines and validate the general features of the ‘falling spaghetti mechanism’ previously proposed to explain their formation.

scholarly journals Hydration water mobility is enhanced around tau amyloid fibers

2015 ◽  
Vol 112 (20) ◽  
pp. 6365-6370 ◽  
Author(s):  
Yann Fichou ◽  
Giorgio Schirò ◽  
François-Xavier Gallat ◽  
Cedric Laguri ◽  
Martine Moulin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Fiber Formation ◽  
Human Protein ◽  
Water Dynamics ◽  
Hydration Water ◽  
Water Mobility ◽  
Intrinsically Disordered ◽  
Dynamics Simulations

The paired helical filaments (PHF) formed by the intrinsically disordered human protein tau are one of the pathological hallmarks of Alzheimer disease. PHF are fibers of amyloid nature that are composed of a rigid core and an unstructured fuzzy coat. The mechanisms of fiber formation, in particular the role that hydration water might play, remain poorly understood. We combined protein deuteration, neutron scattering, and all-atom molecular dynamics simulations to study the dynamics of hydration water at the surface of fibers formed by the full-length human protein htau40. In comparison with monomeric tau, hydration water on the surface of tau fibers is more mobile, as evidenced by an increased fraction of translationally diffusing water molecules, a higher diffusion coefficient, and increased mean-squared displacements in neutron scattering experiments. Fibers formed by the hexapeptide 306VQIVYK311 were taken as a model for the tau fiber core and studied by molecular dynamics simulations, revealing that hydration water dynamics around the core domain is significantly reduced after fiber formation. Thus, an increase in water dynamics around the fuzzy coat is proposed to be at the origin of the experimentally observed increase in hydration water dynamics around the entire tau fiber. The observed increase in hydration water dynamics is suggested to promote fiber formation through entropic effects. Detection of the enhanced hydration water mobility around tau fibers is conjectured to potentially contribute to the early diagnosis of Alzheimer patients by diffusion MRI.

The usefulness of molecular-dynamics simulations in clarifying the activation enthalpy of oxygen-vacancy migration in the perovskite oxide BaTiO3

2020 ◽  
Vol 22 (10) ◽  
pp. 5413-5417 ◽  
Author(s):  
Johannes Kaub ◽  
Joe Kler ◽  
Stephen C. Parker ◽  
Roger A. De Souza
Keyword(s):  
Molecular Dynamics ◽  
Oxygen Vacancy ◽  
Molecular Dynamics Simulations ◽  
Activation Enthalpy ◽  
Perovskite Oxide ◽  
Atomistic Simulations ◽  
Vacancy Migration ◽  
Dynamics Simulations

Activation enthalpies of oxygen-vacancy migration in BaTiO3 reported in the literature from experiment and from static atomistic simulations.

Water Dynamics:  Vibrational Echo Correlation Spectroscopy and Comparison to Molecular Dynamics Simulations

2004 ◽  
Vol 108 (7) ◽  
pp. 1107-1119 ◽  
Author(s):  
John B. Asbury ◽  
Tobias Steinel ◽  
C. Stromberg ◽  
S. A. Corcelli ◽  
C. P. Lawrence ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Correlation Spectroscopy ◽  
Water Dynamics ◽  
Dynamics Simulations ◽  
Vibrational Echo

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.

Priming effects in the crystallization of the phase change compound GeTe from atomistic simulations

2019 ◽  
Vol 213 ◽  
pp. 287-301 ◽  
Author(s):  
Silvia Gabardi ◽  
Gabriele G. Sosso ◽  
Joerg Behler ◽  
Marco Bernasconi
Keyword(s):  
Molecular Dynamics ◽  
Phase Change ◽  
Molecular Dynamics Simulations ◽  
Atomistic Simulations ◽  
Priming Effects ◽  
Dynamics Simulations

Molecular dynamics simulations provide insights into the priming effects in the crystallization of the phase change compound GeTe.

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