Ab Initio Molecular Dynamics Study of Nanoscale Thermal Energy Transport

2008 ◽  
Vol 130 (12) ◽  
Author(s):  
Tengfei Luo ◽  
John R. Lloyd
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Thermal Energy ◽  
Density Functional ◽  
Energy Transport ◽  
Power Spectra ◽  
Ab Initio Molecular Dynamics ◽  
Nanoscale Structures ◽  
Different Temperatures ◽  
Thermal Energy Transport

Ab initio molecular dynamics, which employs density functional theory, is used to study thermal energy transport phenomena in nanoscale structures. Thermal equilibration in multiple thin layer structures with thicknesses less than 1 nm per layer is simulated. Different types of layer combinations are investigated. Periodic boundary conditions in all directions are used in all cases. Two neighboring layers are first set to different temperatures using Nosé–Hoover thermostats, and then the process of energy equilibration is simulated with a “free run” (without any thermostat controlling the temperatures). The temperature evolutions in the two neighboring layers are computed. The atomic vibration power spectra are calculated and used to explain the phenomena observed in the simulation.

Ab-Initio Molecular Dynamics Study of Nano-Scale Thermal Energy Transport

2007 ◽  
Author(s):  
Tengfei Luo ◽  
John R. Lloyd
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Thermal Energy ◽  
Density Functional ◽  
Energy Transport ◽  
Power Spectra ◽  
Ab Initio Molecular Dynamics ◽  
Nano Scale ◽  
Different Temperatures ◽  
Thermal Energy Transport

Ab-initio molecular dynamics (MD) which employs density functional theory (DFT) is used to study thermal energy transport phenomena in nano-scale structures. Thermal equilibration in multiple thin layer structures with thicknesses less than 1 nanometer per layer is simulated. Different types of layer combinations are investigated. Periodic boundary conditions in all directions are used in all cases. Two neighboring layers are first set to different temperatures using Nose-Hoover thermostats, and then the process of energy equilibration is simulated with a “free run” (without any thermostat controlling the temperatures). The temperature evolutions in the two neighboring layers are computed. The atomic vibration power spectra are calculated and used to explain the phenomena observed in the simulation.

scholarly journals Ab initio molecular dynamics of hydrogen on tungsten surfaces

2021 ◽  
Author(s):  
Alberto Rodríguez-Fernández ◽  
Laurent Bonnet ◽  
Pascal Larrégaray ◽  
Ricardo Díez Muiño
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Dissociation Process ◽  
Functional Theory ◽  
Classical Molecular Dynamics ◽  
Hydrogen Molecules

The dissociation process of hydrogen molecules on W(110) was studied using density functional theory and classical molecular dynamics.

scholarly journals Computational Methods for Ab Initio Molecular Dynamics

2018 ◽  
Vol 2018 ◽  
pp. 1-14 ◽  
Author(s):  
Eric Paquet ◽  
Herna L. Viktor
Keyword(s):  
Molecular Dynamics ◽  
Quantum Mechanics ◽  
Ab Initio ◽  
First Principles ◽  
Density Functional ◽  
Path Integrals ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Systems ◽  
Hartree Fock ◽  
Computational Perspective

Ab initio molecular dynamics is an irreplaceable technique for the realistic simulation of complex molecular systems and processes from first principles. This paper proposes a comprehensive and self-contained review of ab initio molecular dynamics from a computational perspective and from first principles. Quantum mechanics is presented from a molecular dynamics perspective. Various approximations and formulations are proposed, including the Ehrenfest, Born–Oppenheimer, and Hartree–Fock molecular dynamics. Subsequently, the Kohn–Sham formulation of molecular dynamics is introduced as well as the afferent concept of density functional. As a result, Car–Parrinello molecular dynamics is discussed, together with its extension to isothermal and isobaric processes. Car–Parrinello molecular dynamics is then reformulated in terms of path integrals. Finally, some implementation issues are analysed, namely, the pseudopotential, the orbital functional basis, and hybrid molecular dynamics.

scholarly journals Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

Polymers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 3434
Author(s):  
Khagendra Baral ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Molecular Dynamics ◽  
Body Temperature ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Rgd Peptide ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Aqueous Environment ◽  
Structure And Properties

The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

scholarly journals Unexpectedly Large Couplings Between Orthogonal Units in Anthraquinone Polymers

2019 ◽  
Author(s):  
Rocco Peter Fornari ◽  
Piotr de Silva
Keyword(s):  
Molecular Dynamics ◽  
Density Functional Theory ◽  
Ab Initio ◽  
Density Functional ◽  
Lone Pair ◽  
Localized States ◽  
Ab Initio Molecular Dynamics ◽  
Coupling Mechanism ◽  
Functional Theory ◽  
Pi Interactions

Directly linked polyanthraquinones have relatively large electronic couplings between charge-localized states despite near-orthogonality of the monomer units. By using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations, we investigate this unusual coupling mechanism and show that this is due to strong lone pair-pi interactions, which are maximized around orthogonal conformations. We find that such materials are largely resilient to dynamic disorder and are promising for organic electronics applications.

Ti and Zr Transition Metals Effect in the D03 Fe3Al by Ab Initio Study Approach

2014 ◽  
Vol 783-786 ◽  
pp. 1640-1645
Author(s):  
Jean Marc Raulot ◽  
S. Chentouf ◽  
T. Grosdidier ◽  
Hafid Aourag
Keyword(s):  
Molecular Dynamics ◽  
Transition Metals ◽  
Ab Initio ◽  
Density Functional ◽  
Ab Initio Molecular Dynamics ◽  
Effect Of Temperature ◽  
Site Preference ◽  
Functional Theory ◽  
Study Approach

The effect of the Ti and Zr transition metals on the D03-Fe3Al intermetallic compounds has been investigated by means of ab initio Pseudo Potentials numerical simulations based on Density Functional Theory. Two main issues will be addressed the understanding of the role of these two transition metals in terms of stability of the bulk at the light of their site preference in the D03-Fe3Al structure the behaviour of Ti and Zr transition metals in the sigma 5 (310) [001] grain boundary and their effect on the structural stability of this interface. An important issue when studying these aspects is to take into accounts the effect of temperature. This requires a molecular dynamics treatment of the atoms in the supercell. The technique known as ab initio molecular dynamics (AIMD) solves these problems by combining ‘on the fly’ electronic structure calculations with finite temperature dynamics. Thus, our study was conducted both using the conventional static ab initio calculations (0K) as well as by taking into account the effect of temperature (Ab Initio Molecular Dynamics).

scholarly journals Molecular dynamics simulation of thermal energy transport in polydimethylsiloxane

2011 ◽  
Vol 109 (7) ◽  
pp. 074321 ◽  
Author(s):  
Tengfei Luo ◽  
Keivan Esfarjani ◽  
Junichiro Shiomi ◽  
Asegun Henry ◽  
Gang Chen
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Thermal Energy ◽  
Energy Transport ◽  
Dynamics Simulation ◽  
Thermal Energy Transport

scholarly journals Equilibrium Molecular Dynamics Study of Lattice Thermal Conductivity/Conductance of Au-SAM-Au Junctions

2009 ◽  
Vol 132 (3) ◽  
Author(s):  
Tengfei Luo ◽  
John R. Lloyd
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Energy ◽  
Energy Transport ◽  
Thermal Conductance ◽  
Finite Size ◽  
Thickness Effect ◽  
Finite Size Effect ◽  
Substrate Thickness ◽  
Thermal Energy Transport

In this paper, equilibrium molecular dynamics simulations were performed on Au-SAM (self-assembly monolayer)-Au junctions. The SAM consisted of alkanedithiol (–S–(CH2)n–S–) molecules. The out-of-plane (z-direction) thermal conductance and in-plane (x- and y-direction) thermal conductivities were calculated. The simulation finite size effect, gold substrate thickness effect, temperature effect, normal pressure effect, molecule chain length effect, and molecule coverage effect on thermal conductivity/conductance were studied. Vibration power spectra of gold atoms in the substrate and sulfur atoms in the SAM were calculated, and vibration coupling of these two parts was analyzed. The calculated thermal conductance values of Au-SAM-Au junctions are in the range of experimental data on metal-nonmetal junctions. The temperature dependence of thermal conductance has a similar trend to experimental observations. It is concluded that the Au-SAM interface resistance dominates thermal energy transport across the junction, while the substrate is the dominant media in which in-plane thermal energy transport happens.

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