Assessing the Validity of Quantum Corrections to Molecular Dynamics Simulations of Bulk Silicon

2011 ◽  
Vol 483 ◽  
pp. 653-657
Author(s):  
Qi Ming Zhou ◽  
Ke Dong Bi ◽  
Yun Fei Chen
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Calculations ◽  
Md Simulations ◽  
Quantum Systems ◽  
Heat Fluxes ◽  
Quantum Corrections ◽  
Bulk Silicon ◽  
Theoretical Predictions ◽  
Dynamics Simulations ◽  
Thermal Conductivities

Thermal conductivities of bulk silicon are calculated by equilibrium molecular dynamics (MD) simulations. Applying common used quantum corrections to the MD results, does not bring them into better agreement with the theoretical predictions or experimental data, while the uncorrected values are closer to the theoretical predictions and experiments below 400K. By assessing the validity of quantum corrections according to theoretical calculations and MD simulations, we demonstrate that the hypothesis of equating the heat fluxes is not reliable. In addition, we explore that the rations of thermal conductivities of MD simulations and quantum calculations are approximate to 1. Then a modified quantum correction for mapping MD simulations to quantum systems is proposed.

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.

scholarly journals Thermal Conductivity of Polybutadiene Rubber from Molecular Dynamics Simulations and Measurements by the Heat Flow Meter Method

Materials ◽  
2021 ◽  
Vol 14 (24) ◽  
pp. 7737
Author(s):  
Aleksandr Vasilev ◽  
Tommy Lorenz ◽  
Vikram G Kamble ◽  
Sven Wießner ◽  
Cornelia Breitkopf
Keyword(s):  
Molecular Dynamics ◽  
Heat Flow ◽  
Md Simulations ◽  
Flow Meter ◽  
Polybutadiene Rubber ◽  
Polymeric Chains ◽  
Dynamics Simulations ◽  
Heat Flow Meter ◽  
Good Agreement ◽  
Thermal Conductivities

Thermal conductivities of polybutadiene rubbers crosslinked by 2.4 and 2.8 phr of sulfur have been found to be functions of temperature via molecular dynamics (MD) simulations using the Green–Kubo method. From an analysis of the heat flux autocorrelation functions, it has been revealed that the dominant means of heat transport in rubbers is governed by deformations of polymeric chains. Thermal conductivities of rubber samples vulcanized by 2.4 and 2.8 phr of sulfur have been measured by the heat flow meter method between 0 ∘C and 60 ∘C at atmospheric pressure. The temperature dependencies of the thermal conductivities of rubbers and their glass transition temperatures derived from MD simulations are in good agreement with the literature and experimental data. Details are discussed in the paper.

scholarly journals Thermal Conductivity of Polyisoprene and Polybutadiene from Molecular Dynamics Simulations and Transient Measurements

Polymers ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 1081 ◽  
Author(s):  
Aleksandr Vasilev ◽  
Tommy Lorenz ◽  
Cornelia Breitkopf
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Weight ◽  
Atmospheric Pressure ◽  
Md Simulations ◽  
Wire Method ◽  
Dynamics Simulations ◽  
Transient Measurements ◽  
Good Agreement ◽  
Thermal Conductivities

The thermal conductivities of untreated polyisoprene and polybutadiene were calculated by molecular dynamics (MD) simulations using a Green-Kubo approach between −10 °C and 50 °C at atmospheric pressure. For comparison, the thermal conductivities of untreated polyisoprene with a molecular weight of 54,000 g/mol and untreated polybutadiene with a molecular weight of 45,000 g/mol were measured by the transient hot wire method in similar conditions. The simulation results of both polymers are in good agreement with the experimental data. We observed that the MD simulations slightly overestimate the thermal conductivity due to the chosen force field description. Details are discussed in the paper.

scholarly journals Thermal Conductivities of Crosslinked Polyisoprene and Polybutadiene from Molecular Dynamics Simulations

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 315
Author(s):  
Aleksandr Vasilev ◽  
Tommy Lorenz ◽  
Cornelia Breitkopf
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Temperature Dependence ◽  
Molecular Dynamics Simulations ◽  
Md Simulations ◽  
Dynamics Simulations ◽  
First Time ◽  
Soft Rubber ◽  
Good Agreement ◽  
Thermal Conductivities

For the first time, the thermal conductivities of vulcanized polybutadiene and polyisoprene have been investigated according to their degree of crosslinking. The C-C and C-S-S-C crosslink bridges, which can be obtained via vulcanization processes using peroxides and sulfur, respectively, are considered. The temperature dependence of the thermal conductivity of soft rubber derived from molecular dynamics (MD) simulations is in very good agreement with the experimental results. The contributions of bonded and non-bonded interactions in the MD simulations and their influence on the thermal conductivities of polyisoprene and polybutadiene are presented. The details are discussed in this paper.

Assessing the Antimalarial Potentials of Phytochemicals: Virtual Screening, Molecular Dynamics and In-Vitro Investigations

2019 ◽  
Vol 16 (3) ◽  
pp. 291-300
Author(s):  
Saumya K. Patel ◽  
Mohd Athar ◽  
Prakash C. Jha ◽  
Vijay M. Khedkar ◽  
Yogesh Jasrai ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Structural Integrity ◽  
Md Simulations ◽  
Tylophora Indica ◽  
Multidrug Resistance Protein 1 ◽  
Receptor Complexes ◽  
Resistance Protein ◽  
Dynamics Simulations ◽  
Stable Trajectory

Background: Combined in-silico and in-vitro approaches were adopted to investigate the antiplasmodial activity of Catharanthus roseus and Tylophora indica plant extracts as well as their isolated components (vinblastine, vincristine and tylophorine). </P><P> Methods: We employed molecular docking to prioritize phytochemicals from a library of 26 compounds against Plasmodium falciparum multidrug-resistance protein 1 (PfMDR1). Furthermore, Molecular Dynamics (MD) simulations were performed for a duration of 10 ns to estimate the dynamical structural integrity of ligand-receptor complexes. </P><P> Results: The retrieved bioactive compounds viz. tylophorine, vinblastin and vincristine were found to exhibit significant interacting behaviour; as validated by in-vitro studies on chloroquine sensitive (3D7) as well as chloroquine resistant (RKL9) strain. Moreover, they also displayed stable trajectory (RMSD, RMSF) and molecular properties with consistent interaction profile in molecular dynamics simulations. </P><P> Conclusion: We anticipate that the retrieved phytochemicals can serve as the potential hits and presented findings would be helpful for the designing of malarial therapeutics.

scholarly journals Unveiling Carbon Dioxide and Ethanol Diffusion in Carbonated Water-Ethanol Mixtures by Molecular Dynamics Simulations

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1711
Author(s):  
Mohamed Ahmed Khaireh ◽  
Marie Angot ◽  
Clara Cilindre ◽  
Gérard Liger-Belair ◽  
David A. Bonhommeau
Keyword(s):  
Carbon Dioxide ◽  
Molecular Dynamics ◽  
Diffusion Coefficients ◽  
Hydrodynamic Radius ◽  
Md Simulations ◽  
Molecular Models ◽  
Experimental Values ◽  
Carbon Dioxide Co2 ◽  
Dynamics Simulations ◽  
Apparent Disagreement

The diffusion of carbon dioxide (CO2) and ethanol (EtOH) is a fundamental transport process behind the formation and growth of CO2 bubbles in sparkling beverages and the release of organoleptic compounds at the liquid free surface. In the present study, CO2 and EtOH diffusion coefficients are computed from molecular dynamics (MD) simulations and compared with experimental values derived from the Stokes-Einstein (SE) relation on the basis of viscometry experiments and hydrodynamic radii deduced from former nuclear magnetic resonance (NMR) measurements. These diffusion coefficients steadily increase with temperature and decrease as the concentration of ethanol rises. The agreement between theory and experiment is suitable for CO2. Theoretical EtOH diffusion coefficients tend to overestimate slightly experimental values, although the agreement can be improved by changing the hydrodynamic radius used to evaluate experimental diffusion coefficients. This apparent disagreement should not rely on limitations of the MD simulations nor on the approximations made to evaluate theoretical diffusion coefficients. Improvement of the molecular models, as well as additional NMR measurements on sparkling beverages at several temperatures and ethanol concentrations, would help solve this issue.

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...

Impact of vibronic coupling effects on light-driven charge transfer in pyrene-functionalized middle and large-sized Metalloid Gold Nanoclusters from Ehrenfest dynamics.

2021 ◽  
Author(s):  
Adrian Dominguez-Castro ◽  
Thomas Frauenheim
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Gold Nanoclusters ◽  
Tight Binding ◽  
Time Dependent ◽  
Effective Strategy ◽  
Dynamics Simulations ◽  
Dependent Density

Theoretical calculations are an effective strategy to comple- ment and understand experimental results in atomistic detail. Ehrenfest molecular dynamics simulations based on the real-time time-dependent density functional tight-binding (RT-TDDFTB) approach...

scholarly journals Molecular Dynamics Simulations of Crystal Nucleation near Interfaces in Incompatible Polymer Blends

Polymers ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 347
Author(s):  
Wenlin Zhang ◽  
Lingyi Zou
Keyword(s):  
Molecular Dynamics ◽  
Polymer Blends ◽  
Md Simulations ◽  
Nucleation And Growth ◽  
Crystal Nucleation ◽  
Crystalline Order ◽  
Mobile Species ◽  
Deep Supercooling ◽  
Crystallizable Polymer ◽  
Dynamics Simulations

We apply molecular dynamics (MD) simulations to investigate crystal nucleation in incompatible polymer blends under deep supercooling conditions. Simulations of isothermal nucleation are performed for phase-separated blends with different degrees of incompatibility. In weakly segregated blends, slow and incompatible chains in crystallizable polymer domains can significantly hinder the crystal nucleation and growth. When a crystallizable polymer is blended with a more mobile species in interfacial regions, enhanced molecular mobility leads to the fast growth of crystalline order. However, the incubation time remains the same as that in pure samples. By inducing anisotropic alignment near the interfaces of strongly segregated blends, phase separation also promotes crystalline order to grow near interfaces between different polymer domains.

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