Analysis of Heat Conduction in Silicon Using Molecular Dynamics Simulations

2006 ◽  
Author(s):  
Asegun S. Henry ◽  
Gang Chen
Keyword(s):  
Molecular Dynamics ◽  
Lattice Dynamics ◽  
Crystalline Silicon ◽  
Relaxation Times ◽  
Normal Modes ◽  
Md Simulations ◽  
Dynamics Simulations ◽  
Technological Significance ◽  
Fitting Parameters ◽  
Phonon Properties

Silicon's material properties, have been studied extensively because of its technological significance in a variety of industries, including microelectronics. Yet, questions surrounding the phonon relaxation times in silicon continue to linger.1,2 Previous theoretical works3-5 have generated qualitative expressions for phonon relaxation times, however these approaches require fitting parameters that cannot be determined reliably. This paper first discusses implementation issues associated with using the Green-Kubo method in molecular dynamics (MD) simulations. We compare various techniques used in similar works and discusses several implementation issues that have arisen in the literature. We then describe an alternative procedure for analyzing the normal modes of a crystal to extract phonon relaxation times. As an example material we study bulk crystalline silicon using equilibrium MD simulations and lattice dynamics. The environment dependent interatomic potential6 is used to model the interactions and frequency dependent phonon properties are extracted from the MD simulations.

Predicting Phonon Properties From Molecular Dynamics Simulations Using the Spectral Energy Density

2011 ◽  
Author(s):  
Joseph E. Turney ◽  
John A. Thomas ◽  
Alan J. H. McGaughey ◽  
Cristina H. Amon
Keyword(s):  
Molecular Dynamics ◽  
Energy Density ◽  
Molecular Dynamics Simulations ◽  
Lattice Dynamics ◽  
Relaxation Times ◽  
Mode Analysis ◽  
Spectral Energy ◽  
Spectral Energy Density ◽  
Dynamics Simulations ◽  
Phonon Properties

Using lattice dynamics theory, we derive the spectral energy density and the relation between the spectral energy density and the phonon frequencies and relaxation times. We then calculate the spectral energy density and phonon frequencies and relaxation times for a test system of Lennard-Jones argon using velocities obtained from molecular dynamics simulations. The phonon properties, which can be used to calculate thermal conductivity, are compared to predictions made using (i) anharmonic lattice dynamics calculations and (ii) a technique that performs normal mode analysis on the positions and velocities obtained from molecular dynamics simulations.

Thermal Conductivity of Crystalline Nanoporous Silicon Using Molecular Dynamics Simulations

2011 ◽  
Author(s):  
Jin Fang ◽  
Laurent Pilon
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Effective Thermal Conductivity ◽  
Crystalline Silicon ◽  
Interfacial Area ◽  
Md Simulations ◽  
Nanoporous Silicon ◽  
Vacancy Defects ◽  
Interfacial Area Concentration ◽  
Dynamics Simulations

This study establishes that the effective thermal conductivity keff of crystalline nanoporous silicon is strongly affected not only by the porosity fv and the system’s length Lz but also by the pore interfacial area concentration Ai. The thermal conductivity of crystalline nanoporous silicon was predicted using non-equilibrium molecular dynamics (NEMD) simulations. The Stillinger-Weber potential for silicon was used to simulate the interatomic interactions. Spherical pores organized in a simple cubic lattice were introduced in a crystalline silicon matrix by removing atoms within selected regions of the simulation cell. Effects of the (i) system length ranging from 13 to 130 nm, (ii) pore diameter varying between 1.74 and 5.86 nm, and (iii) porosity ranging from 8% to 38%, on thermal conductivity were investigated. A physics-based model was also developed by combining kinetic theory and the coherent potential approximation. The effective thermal conductivity was proportional to (1–1.5fv) and inversely proportional to the sum (Ai/4+1/Lz). This model was in excellent agreement with the thermal conductivity of nanoporous silicon predicted by MD simulations for spherical pores (present study) as well as for cylindrical pores and vacancy defects reported in the literature. These results will be useful in designing nanostructured materials with desired thermal conductivity by tuning their morphology.

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...

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.

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.

scholarly journals Tight-Binding Molecular Dynamics Simulations on Point Defects Diffusion and Interactions in Crystalline Silicon

1995 ◽  
Vol 396 ◽  
Author(s):  
M. tang ◽  
L. colombo ◽  
T. Diaz De La Rubia
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Point Defects ◽  
Crystalline Silicon ◽  
Tight Binding ◽  
Diffusion Path ◽  
Binding Energies ◽  
Defect Clusters ◽  
Dynamics Simulations

AbstractTight-binding molecular dynamics (TBMD) simulations are performed (i) to evaluate the formation and binding energies of point defects and defect clusters, (ii) to compute the diffusivity of self-interstitial and vacancy in crystalline silicon, and (iii) to characterize the diffusion path and mechanism at the atomistic level. In addition, the interaction between individual defects and their clustering is investigated.

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