The interactions of an Aβ protofibril with a cholesterol-enriched membrane and involvement of neuroprotective carbazolium-based substances

2019 ◽  
Vol 21 (21) ◽  
pp. 11066-11078
Author(s):  
Hedayat Karimi ◽  
Maryam Heydari Dokoohaki ◽  
Amin Reza Zolghadr ◽  
Mohammad Hadi Ghatee
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Cholesterol Content ◽  
Strong Interactions ◽  
Membrane Bilayer ◽  
Substantial Role ◽  
Polar Residue ◽  
Large Perturbation ◽  
Simulation Results ◽  
Dynamics Simulations

The molecular dynamics simulations indicate that the cholesterol content of the membrane could not play a substantial role in the emergence of Alzheimer's disease. However, the strong interactions between the polar residue of Aβ and the POPC molecules lead to a large perturbation on the membrane bilayer. The simulation results disclose the neuroprotective property of P7C3-S243 molecule.

Self-Assembly of Graphene Nanoribbons with Unsaturated Edges

2012 ◽  
Vol 1407 ◽  
Author(s):  
Andrew L. J. Pang ◽  
Viacheslav Sorkin ◽  
Yong-Wei Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Self Assembly ◽  
Bond Order ◽  
Graphene Nanoribbons ◽  
The Self ◽  
Graphene Nanoscrolls ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Stable Structures

ABSTRACTWe studied the self-assembly mechanisms of Graphene Nanoribbon (GNR) with unsaturated edges and demonstrated the ability of GNR to self-assemble into novel stable structures. We proposed three mechanisms which dictate the self-assembly evolution of GNR with unsaturated edges. Using the Adaptive Intermolecular Reactive Empirical Bond-Order (AIREBO) potential, we performed molecular dynamics simulations on initially-planar GNRs with unsaturated edges. The simulation results showed that the self-assembly mechanisms and final conformations of the GNRs correlate well with the proposed GNR self-assembly mechanisms. Furthermore, the simulations also showed the ability of a narrow GNR to self-assemble into various nanostructures, such as tapered graphene nano-rings and graphene nanoscrolls with an embedded nanotube.

scholarly journals Lanthanum Influence onEuAlO3Perovskite Structural Properties: Experimental and Molecular Dynamics Studies

2012 ◽  
Vol 2012 ◽  
pp. 1-7 ◽  
Author(s):  
Enrique Lima ◽  
María Elena Villafuerte-Castrejón ◽  
José Saniger ◽  
Victor Lara ◽  
Jorge E. Sánchez-Sánchez ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Structural Properties ◽  
Mas Nmr ◽  
Ftir Spectra ◽  
X Ray Diffraction ◽  
X Ray ◽  
Lanthanum Ions ◽  
Simulation Results ◽  
Dynamics Simulations

X-ray diffraction,27Al MAS NMR, and FTIR spectra along with results of molecular dynamics simulations were used to characterise LaxEu1−xAlO3perovskites forx=0.3,  0.1. Experimental and simulation results show that local changes in the perovskite-like structure can be achieved as lanthanum ions substitute europium ones. The introduction of La3+ions in the EuAlO3parent causes an increase in the mobility of oxygen network.

A Kinetic Formulation of Reacting Molecular Dynamics

2016 ◽  
Author(s):  
Joseph L. Bass ◽  
Eric P. Fahrenthold
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Process Simulation ◽  
Chemical Processes ◽  
Detonation Products ◽  
Kinetic Formulation ◽  
Hamiltonian Methods ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Ab Initio Models

Macroscale, mesoscale, and ab initio models of reacting shock physics are based, in their most general forms, on rate law descriptions of the chemical processes of interest. Reacting molecular dynamics simulations, by contrast, typically employ potential functions to model chemical reactions. An alternative reacting molecular dynamics formulation, employing nonholonomic Hamiltonian methods, models bonding-debonding as a kinetic process. Simulation results using this method are compared with experiment, for energy release and detonation products in HMX. The molecular dynamics simulations may be used to develop a macroscale, adiabatic model of the detonation chemistry.

Molecular Dynamics Simulations of Water, Silica, and Aqueous Mixtures in Bulk and Confinement

2018 ◽  
Vol 232 (7-8) ◽  
pp. 1187-1225 ◽  
Author(s):  
Julian Geske ◽  
Michael Harrach ◽  
Lotta Heckmann ◽  
Robin Horstmann ◽  
Felix Klameth ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Molecular Dynamics Simulations ◽  
Aqueous Mixtures ◽  
Simulation Data ◽  
Hydrogen Bond Networks ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Anomalies Of Water

Abstract Aqueous systems are omnipresent in nature and technology. They show complex behaviors, which often originate in the existence of hydrogen-bond networks. Prominent examples are the anomalies of water and the non-ideal behaviors of aqueous solutions. The phenomenology becomes even richer when aqueous liquids are subject to confinement. To this day, many properties of water and its mixtures, in particular, under confinement, are not understood. In recent years, molecular dynamics simulations developed into a powerful tool to improve our knowledge in this field. Here, our simulation results for water and aqueous mixtures in the bulk and in various confinements are reviewed and some new simulation data are added to improve our knowledge about the role of interfaces. Moreover, findings for water are compared with results for silica, exploiting that both systems form tetrahedral networks.

Unravelling the nature of glyphosate binding to goethite surfaces by ab initio molecular dynamics simulations

2017 ◽  
Author(s):  
Ashour A. Ahmed ◽  
P. Leinweber ◽  
Oliver Kühn
Keyword(s):  
Molecular Dynamics ◽  
Binding Energy ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Effect Of Water ◽  
Simulation Results ◽  
Dynamics Simulations

Simulation results are presented which quantify the binding energy of glyphosate to different goethite surfaces. Further the effect of water and pH is addressed.

Molecular dynamics simulations of sliding friction of Langmuir-Blodgett monolayers

1996 ◽  
Vol 464 ◽  
Author(s):  
Asako Koike ◽  
Makoto Yoneya ◽  
Yutaka Ito
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Frictional Force ◽  
Sliding Friction ◽  
Frictional Coefficient ◽  
Perfluorocarboxylic Acid ◽  
Langmuir Blodgett ◽  
Simulation Results ◽  
Dynamics Simulations ◽  
Frictional Coefficients

AbstractMolecular dynamics simulations have been performed to study friction in Langmuir-Blodgett monolayers of perfluorocarboxylic acid, semifluoro acid and hydrocarboxylic acid on SiO2. The frictional coefficient of perfluorocarboxylic acid is about three times as large as that of hydrocarboxylic acid, while the frictional coefficient of semifluorocarboxylic acid is about two times as large as that of hydrocarboxylic acid. The qualitative aspects of these simulation results are consistent with known experimental results. In order to interpret the difference in the frictional coefficient, a series of simulations have been carried out by changing molecular potential parameters. The simulation results suggest that the 1,4-van der Waals interaction is the main cause of the larger frictional force for perfluorocarboxylic acid than that for hydrocarboxylic acid. Further frictional coefficients of semifluorocarboxylic acid are found to change by the fluorination ratio. The results also show that frictional force is roughly proportional to the excess r.m.s. fluctuation of the potential energy under shear from the equilibrium. The relation between the frictional force and the energy needed for molecular deformation under shear conditions is also discussed.

Effects of Occupation of the Cages on Thermodynamic Stability of SI CO2 Clathrate Hydrate

2011 ◽  
Vol 295-297 ◽  
pp. 1505-1509 ◽  
Author(s):  
Ying Xia Qi ◽  
Hua Zhang ◽  
Sheng Xi Zhao
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Intermolecular Interactions ◽  
Thermodynamic Stability ◽  
Hydration Number ◽  
Large Cage ◽  
Potential Models ◽  
Simulation Results ◽  
The Stability ◽  
Dynamics Simulations

Molecular dynamics simulations are carried out to investigate the effect of the occupation of the cages on the stability of sI CO2 hydrates. Three types of cage occupations are concerned. The TIP4P/EPM2/DUAN potential models are used for the water-water, CO2-CO2, water-CO2 intermolecular interactions. The simulation results show that the occupation of the large cage is preferable compared to the occupation of the small cage. It may be induced that the hydration number of sI CO2 hydrates is mostly to be 9.

Molecular Dynamics Simulations of Uniaxial Compression of Ceria and Gadolinia Doped Ceria

2010 ◽  
Vol 152-153 ◽  
pp. 1180-1183
Author(s):  
Yun Jun Chen ◽  
Yi Sun ◽  
Zhi Wei Cui
Keyword(s):  
Mechanical Properties ◽  
Molecular Dynamics ◽  
Elastic Modulus ◽  
Temperature Dependence ◽  
Molecular Dynamics Simulations ◽  
Uniaxial Compression ◽  
Doped Ceria ◽  
Higher Temperature ◽  
Simulation Results ◽  
Dynamics Simulations

In this paper, we investigate the mechanical properties of ceria and gadolinia doped ceria by molecular dynamics simulations. The doped concentrations and temperature dependence of yield stress and elastic modulus have been evaluated via uniaxial compression. Simulation results reveal that such properties decrease dramatically with higher temperature and doped content. In addition, the attenuated effect of doped content is more significant than that of temperature.

Composition Dependent Ionic Conductivity in ß''-Alumina

1990 ◽  
Vol 210 ◽  
Author(s):  
C. Lane Rohrer ◽  
G. C. Farrington
Keyword(s):  
Molecular Dynamics ◽  
Experimental Study ◽  
Ionic Conductivity ◽  
Impedance Spectroscopy ◽  
Molecular Dynamics Simulations ◽  
Ionic Conductivities ◽  
Experimental Results ◽  
Cation Ordering ◽  
Simulation Results ◽  
Dynamics Simulations

AbstractMolecular dynamics simulations were carried out in an attempt to reproduce and explain the differing composition dependencies of the ionic conductivities of Na(I)-Ba(II)- and Na(I)-Sr(II)- ß' '-alumina. Impedance spectroscopy measurements of Na1.67-2xBaxMg0.67Al10.33O17, where x = 0.0 - 0.835, showed a distinct minimum in the conductivity when x = 0.67, or 80% exchange of Ba(II) for Na(I). Evidence for mobile cation ordering at that composition was seen in the simulation results and the general change in conductivity with Ba(II) content was reproduced rather well. The results of a similar experimental study of Na(I)-Sr(II)-ß' '-alumina did not show a minimum in the conductivity, but our simulations incorrectly predicted the Sr(II) system to behave in the same fashion as the Ba(II) system. Possible reasons for this discrepancy are suggested, including problems with transferring potentials between oxides and the influence of absorbed water on the experimental results.

Sign in / Sign up

Export Citation Format

Share Document