scholarly journals All-atom molecular dynamics simulations of spin labelled double and single-strand DNA for EPR studies

2018 ◽  
Vol 20 (19) ◽  
pp. 13461-13472 ◽  
Author(s):  
C. Prior ◽  
L. Danilāne ◽  
V. S. Oganesyan
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Single Strand ◽  
Epr Spectra ◽  
Dna Structures ◽  
Dynamics Simulations

Prediction of motional EPR spectra of spin labelled DNA structures from fully atomistic MD simulations.

Mechanism of stacking fault annihilation in 3C-SiC epitaxially grown on Si(001) by molecular dynamics simulations

CrystEngComm ◽  
2021 ◽  
Author(s):  
Andrey Sarikov ◽  
Anna Marzegalli ◽  
Luca Barbisan ◽  
Massimo Zimbone ◽  
Corrado Bongiorno ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Stacking Faults ◽  
Md Simulations ◽  
Stacking Fault ◽  
Dynamics Simulations

In this work, annihilation mechanism of stacking faults (SFs) in epitaxial 3C-SiC layers grown on Si(001) substrates is studied by molecular dynamics (MD) simulations. The evolution of SFs located in...

scholarly journals Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

2016 ◽  
Vol 18 (37) ◽  
pp. 25806-25816 ◽  
Author(s):  
Carlos Navarro-Retamal ◽  
Anne Bremer ◽  
Jans Alzate-Morales ◽  
Julio Caballero ◽  
Dirk K. Hincha ◽  
...  
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Arabidopsis Thaliana ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Cd Spectroscopy ◽  
Lea Proteins ◽  
Intrinsically Disordered ◽  
Dynamics Simulations ◽  
Crowded Environment

Unfolding of intrinsically unstructured full-length LEA proteins in a differentially crowded environment can be modeled by 30 ns MD simulations in accordance with experimental data.

Structural stability of CmTin microclusters and nanoparticles: Molecular–dynamics simulations

2005 ◽  
Vol 1 (4) ◽  
pp. 204-209
Author(s):  
O.B. Malcıoğlu ◽  
Ş. Erkoç
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binary Systems ◽  
Minimum Energy ◽  
Potential Energy Function ◽  
Md Simulations ◽  
Atomic Interactions ◽  
Dynamics Simulations ◽  
Three Body ◽  
Initial Geometry

The minimum energy structures of CmTin microclusters and nanoparticles have been investigated theoretically by performing molecular–dynamics (MD) simulations. Selected crystalline and completely random initial geometries are considered. The potential energy function (PEF) used in the calculations includes two– and three–body atomic interactions for C-Ti binary systems. Molecular–dynamics simulations have been performed at 1 K and 300 K. It has been found that initial geometry has a very strong influence on relaxed geometry

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

scholarly journals Evaluation of the effect of nickel clusters on the formation of incipient soot particles from polycyclic aromatic hydrocarbons via ReaxFF molecular dynamics simulations

2019 ◽  
Vol 21 (19) ◽  
pp. 9865-9875 ◽  
Author(s):  
Sharmin Shabnam ◽  
Qian Mao ◽  
Adri C. T. van Duin ◽  
K. H. Luo
Keyword(s):  
Molecular Dynamics ◽  
Polycyclic Aromatic Hydrocarbons ◽  
Molecular Dynamics Simulations ◽  
Aromatic Hydrocarbons ◽  
Md Simulations ◽  
Soot Particles ◽  
Nickel Clusters ◽  
Polycyclic Aromatic ◽  
Dynamics Simulations

Effect of nickel clusters on the formation of incipient soot from PAH precursors via ReaxFF-MD simulations.

scholarly journals Molecular dynamics simulations of the self-organization of side-chain decorated polyaromatic conjugation molecules: phase separated lamellar and columnar structures and dispersion behaviors in toluene solvent

RSC Advances ◽  
2018 ◽  
Vol 8 (20) ◽  
pp. 11134-11144 ◽  
Author(s):  
Lanyan He ◽  
Pingmei Wang ◽  
Lipeng He ◽  
Zhou Qu ◽  
Jianhui Luo ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Dynamic ◽  
Md Simulations ◽  
The Self ◽  
Self Organization ◽  
Side Chain ◽  
Dynamics Simulations

The self-organization of five model side-chain decorated polyaromatic asphaltene molecules with or without toluene solvent was investigated by means of molecular dynamic (MD) simulations.

Surface structure of organoclays as examined by X-ray photoelectron spectroscopy and molecular dynamics simulations

Clay Minerals ◽  
2015 ◽  
Vol 50 (3) ◽  
pp. 353-367 ◽  
Author(s):  
B. Schampera ◽  
R. Solc ◽  
S.K. Woche ◽  
R. Mikutta ◽  
S. Dultz ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Photoelectron Spectroscopy ◽  
Md Simulations ◽  
Organic Cations ◽  
Conformational Structure ◽  
Xps Spectra ◽  
X Ray ◽  
Dynamics Simulations ◽  
External Interface

AbstractOrganoclays are sorbent materials prepared from clays by exchanging inorganic with organic cations. Their properties depend on the loading and conformational structure of the organic cations, but little information is available about the surface structures of organoclays. In this work, X-ray photoelectron spectroscopy (XPS) and classical molecular dynamics (MD) simulations are combined to characterize the external interface of an organoclay prepared from hexadecylpyridinium (HDPy+) and bentonite. The XPS survey spectra show well the varying elemental composition of the surface with increasing amount of surfactant, showing a decreasing contribution of clay-derived elements with increasing organic coverage. The high-resolution C 1s XPS spectra depict sensitively the surface arrangement of the surfactant. In combination with MD simulations, the results implied a monolayer coating for low surfactant coverage and a disordered bilayer arrangement at high surfactant uptakes. Molecular dynamics simulations showed that for very high cation uptake a quasi-paraffin-like configuration is also possible. The combination of experimental and modelling methods yielded congruent information on the molecular-scale arrangement of organic cations at the organoclay surfaces and the controlling mechanisms.

Normal and abnormal heme biosynthesis Part 4: Molecular dynamics simulations of coproporphyrinogen-III and related di- and tricarboxylic acids

2005 ◽  
Vol 09 (03) ◽  
pp. 170-185 ◽  
Author(s):  
Jingyuan He ◽  
Todd A. Kaprak ◽  
Marjorie A. Jones ◽  
Timothy D. Lash
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Biosynthetic Pathway ◽  
Local Environment ◽  
Md Simulations ◽  
Structural Requirement ◽  
Coproporphyrinogen Oxidase ◽  
Flat Structures ◽  
Dynamics Simulations ◽  
Intramolecular Hydrogen

The first cyclic tetrapyrrolic intermediates in the heme biosynthetic pathway are generated as porphyrinogens (hexahydroporphyrins), but unlike the aromatic porphyrin nucleus these structures must take on highly distorted conformations. Although this structural requirement is self-evident, these intermediates are often represented as flat structures. In order to gain a better understanding of the enzyme coproporphyrinogen oxidase, which is responsible for the conversion of coproporphyrinogen-III to protoporphyrinogen-IX, conformational studies were performed using molecular dynamics simulations. These studies were carried out on the natural substrate and six synthetic analogues using a Silicon Graphics workstation and the BIOGRAF 3.1 program (Molecular Simulations Inc.). The dynamics were run for 50 ps using the Verlet algorithm and Dreiding force field for each porphyrinogen with 500 quenching steps at 300 and 500 K. The five lowest energy conformations were then used as starting structures for simulations of 200 ps. The data show that the propionic acid side chains critically affect the conformations by hydrogen bonding interactions, and the chair and saddle forms are the most stable conformations. In many cases the B ring propionate moiety, which is known to be crucial for substrate recognition for coproporphyrinogen oxidase, is found to be free of intramolecular hydrogen bonds. However, simulations in the presence of water molecules gave chaise longe conformations and intermolecular interactions overwhelmed other effects for solvated porphyrinogens. Although the local environment will influence the preferred conformations, these MD simulations provide insights into how natural porphyrinogens can behave under physiological conditions.

scholarly journals Parallelization of Molecular-Dynamics Simulations Using Tasks

2015 ◽  
Vol 1753 ◽  
Author(s):  
Ralf Meyer ◽  
Chris M. Mangiardi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Shared Memory ◽  
Md Simulations ◽  
Xeon Phi ◽  
Intel Xeon Phi ◽  
Novel Algorithms ◽  
Dynamics Simulations ◽  
Many Core ◽  
Intel Xeon

ABSTRACTThis article discusses novel algorithms for molecular-dynamics (MD) simulations with short-ranged forces on modern multi- and many-core processors like the Intel Xeon Phi. A task-based approach to the parallelization of MD on shared-memory computers and a tiling scheme to facilitate the SIMD vectorization of the force calculations is described. The algorithms have been tested with three different potentials and the resulting speed-ups on Intel Xeon Phi coprocessors are shown.

Temperature profiles and heat fluxes observed in molecular dynamics simulations of force-driven liquid flows

2017 ◽  
Vol 19 (16) ◽  
pp. 10317-10325 ◽  
Author(s):  
Jafar Ghorbanian ◽  
Ali Beskok
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Heat Fluxes ◽  
Temperature Profiles ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Liquid Flows ◽  
Non Equilibrium

This paper concentrates on the unconventional temperature profiles and heat fluxes observed in non-equilibrium molecular dynamics (MD) simulations of force-driven liquid flows in nano-channels.

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