scholarly journals An atomistic model for the thermal resistance of a liquid–solid interface

2022 ◽  
Vol 934 ◽  
Author(s):  
N.G. Hadjiconstantinou ◽  
M.M. Swisher
Keyword(s):  
Molecular Dynamics ◽  
Thermal Resistance ◽  
Heat Transport ◽  
Partial Evaluation ◽  
Quantitative Model ◽  
Point Of View ◽  
Atomistic Model ◽  
Level System ◽  
System Parameters ◽  
Dynamics Simulations

The thermal resistance associated with the interface between a solid and a liquid is analysed from an atomistic point of view. Partial evaluation of the associated Green–Kubo integral elucidates the various factors governing heat transport across the interface and leads to a quantitative model for the thermal resistance in terms of atomistic-level system parameters. The model is validated using molecular dynamics simulations.

Design of Inhibitors for Glyceraldehyde-3-phosphate Dehydrogenase (GAPDH) Enzyme of Leishmania mexicana

2020 ◽  
Vol 16 (6) ◽  
pp. 784-795
Author(s):  
Krisnna M.A. Alves ◽  
Fábio José Bonfim Cardoso ◽  
Kathia M. Honorio ◽  
Fábio A. de Molfetta
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Binding Site ◽  
Point Of View ◽  
New Drugs ◽  
Leishmania Mexicana ◽  
Receptor Complexes ◽  
Starting Point ◽  
Dynamics Simulations ◽  
Selection Of

Background:: Leishmaniosis is a neglected tropical disease and glyceraldehyde 3- phosphate dehydrogenase (GAPDH) is a key enzyme in the design of new drugs to fight this disease. Objective:: The present study aimed to evaluate potential inhibitors of GAPDH enzyme found in Leishmania mexicana (L. mexicana). Methods: A search for novel antileishmanial molecules was carried out based on similarities from the pharmacophoric point of view related to the binding site of the crystallographic enzyme using the ZINCPharmer server. The molecules selected in this screening were subjected to molecular docking and molecular dynamics simulations. Results:: Consensual analysis of the docking energy values was performed, resulting in the selection of ten compounds. These ligand-receptor complexes were visually inspected in order to analyze the main interactions and subjected to toxicophoric evaluation, culminating in the selection of three compounds, which were subsequently submitted to molecular dynamics simulations. The docking results showed that the selected compounds interacted with GAPDH from L. mexicana, especially by hydrogen bonds with Cys166, Arg249, His194, Thr167, and Thr226. From the results obtained from molecular dynamics, it was observed that one of the loop regions, corresponding to the residues 195-222, can be related to the fitting of the substrate at the binding site, assisting in the positioning and the molecular recognition via residues responsible for the catalytic activity. Conclusion:: he use of molecular modeling techniques enabled the identification of promising compounds as inhibitors of the GAPDH enzyme from L. mexicana, and the results obtained here can serve as a starting point to design new and more effective compounds than those currently available.

Molecular Dynamics Simulations of Interfacial Heat and Mass Transfer at Nanostructured Surface

2007 ◽  
Author(s):  
Gyoko Nagayama ◽  
Masako Kawagoe ◽  
Takaharu Tsuruta
Keyword(s):  
Heat Transfer ◽  
Molecular Dynamics ◽  
Boundary Condition ◽  
Thermal Resistance ◽  
Hydrodynamic Resistance ◽  
Hydrophilic Surface ◽  
Dynamics Simulations ◽  
Solid Liquid Interface ◽  
Solid Liquid ◽  
The Continuum

The nanoscale heat and mass transport phenomena play important roles on the applications of nanotechnologies with great attention to its differences from the continuum mechanics. In this paper, the breakdown of the continuum assumption for nanoscale flows has been verified based on the molecular dynamics simulations and the heat transfer mechanism at the nanostructured solid-liquid interface in the nanochannels is studied from the microscopic point of view. Simple Lennard-Jones (LJ) fluids are simulated for thermal energy transfer in a nanochannel using nonequilibrium molecular dynamics techniques. Multi-layers of platinum atoms are utilized to simulate the solid walls with arranged nanostructures and argon atoms are employed as the LJ fluid. The results show that the interface structure (i.e. the solid-like structure formed by the adsorption layers of liquid molecules) between solid and liquid are affected by the nanostructures. It is found that the hydrodynamic resistance and thermal resistance dependents on the surface wettability and for the nanoscale heat and fluid flows, the interface resistance cannot be neglected but can be reduced by the nanostructures. For the hydrodynamic boundary condition at the solid-liquid interface, the no-slip boundary condition holds good at the super-hydrophilic surface with large hydrodynamic resistance. However, apparent slip is observed at the low hydrodynamic resistance surface when the driving force overcomes the interfacial resistance. For the thermal boundary condition, it is found that the thermal resistance at the interface depends on the interface wettability and the hydrophilic surface has lower thermal resistance than that of the hydrophobic surfaces. The interface thermal resistance decreases at the nanostructed surface and significant heat transfer enhancement has been achieved at the hydrophilic nanostructured surfaces. Although the surface with nanostrutures has larger surface area than the flat surface, the rate of heat flux increase caused by the nanostructures is remarkable.

Thermal conductivity and interfacial Thermal Resistance Behavior for the Polyaniline (C3N)– boron carbide (BC3) Heterostructure

2021 ◽  
Author(s):  
Arian Mayelifartash ◽  
Mohammad Ali Abdol ◽  
Sadegh Sadeghzadeh
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Thermal Resistance ◽  
Boron Carbide ◽  
Molecular Dynamics Simulations ◽  
Thermal Conductance ◽  
Interfacial Thermal Resistance ◽  
Non Equilibrium Molecular Dynamics ◽  
Dynamics Simulations ◽  
Non Equilibrium

In this paper, by employing non-equilibrium molecular dynamics simulations (NEMD), the thermal conductance of hybrid formed by polyaniline (C3N) and boron carbide (BC3) in both armchair and zigzag configurations has...

Heat controlling in the mass-graded harmonic lattices with double-well on-site potential

2018 ◽  
Vol 32 (20) ◽  
pp. 1850217
Author(s):  
Peng Kong ◽  
Zhengzheng Wei ◽  
Tao Hu ◽  
Yi Tang
Keyword(s):  
Molecular Dynamics ◽  
Heat Flux ◽  
Power Spectrum ◽  
Molecular Dynamics Simulations ◽  
Heat Transport ◽  
Nonequilibrium Molecular Dynamics ◽  
Thermal Rectification ◽  
Average Temperature ◽  
New Type ◽  
Dynamics Simulations

Using nonequilibrium molecular dynamics simulations, we investigate thermal rectification in mass-graded lattices with a new type on-site potential which has a physical picture of the double-well. By adjusting the ratio of harmonic on-site potential and anharmonic on-site potential, we could obtain the optimal heat transport and the best thermal rectification. In addition, we observe the reversal thermal rectification by changing the ratio of on-site potential and analyzes the mechanism of thermal rectification through the power spectrum. At last, we also study the heat flux and thermal rectification in a different case of average temperature and mass gradient.

Molecular Dynamics Study of Interfacial Thermal Resistance of Mercapto-Alkanol Self-Assembled Monolayer and Water

2009 ◽  
Author(s):  
Touru Kawaguchi ◽  
Gota Kikugawa ◽  
Ikuya Kinefuchi ◽  
Taku Ohara ◽  
Shinichi Yatuzuka ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Thermal Resistance ◽  
Chem Phys ◽  
Nonequilibrium Molecular Dynamics ◽  
Interfacial Thermal Resistance ◽  
Water Molecules ◽  
Self Assembled Monolayer ◽  
Self Assembled ◽  
Dynamics Simulations

The interfacial thermal resistance of 11-mercaptoundecanol (-S(CH2)11OH) self-assembled monolayer (SAM) adsorbed on Au(111) substrate and water was investigated using nonequilibrium molecular dynamics simulations. The interfacial thermal resistance was found to be a half of that in the system which consists of 1-dodecanthiol (-S(CH2)11CH3) SAM adsorbed on Au(111) and toluene [Kikugawa G. et al., J. Chem. Phys. (2009)]. The effective thermal energy transfer originates from hydrogen-bond structure between the SAM and water molecules in spite of weak structurization of water molecules near the SAM surface.

A Molecular Dynamics Study on the Effects of Nanostructural Clearances on Thermal Resistance at a Liquid-Solid Interface

2009 ◽  
Author(s):  
Masahiko Shibahara ◽  
Kiyoshi Takeuchi
Keyword(s):  
Molecular Dynamics ◽  
Thermal Resistance ◽  
Surface Area ◽  
Solid Wall ◽  
Potential Parameter ◽  
Liquid Region ◽  
Solid Interface ◽  
Dynamics Simulations ◽  
Geometric Surface ◽  
Geometric Surface Area

The effects of the surface structures and the surface structural clearances at the nanometer scale on the thermal resistance at a liquid water-solid interface, as well as the dynamic behaviors of liquid molecules, were investigated directly by the classical molecular dynamics simulations. The thermal resistance between the solid wall and the liquid region was calculated by the temperature discontinuity at a liquid-solid interface and the energy flux that was added or subtracted by the Langevin method per unit area so as to maintain a constant solid wall temperature. When the potential parameter between liquid molecules and nanostructure atoms is equal to that between liquid molecules and solid wall atoms, the geometric surface area change depending on the nanostructures as well as their clearances and the dynamic behaviour change of the fluid molecules at the interface depending on the nanostructural clearances cause the thermal resistance reduction depending on the nanostructures at the liquid-solid interface. When the potential parameter between liquid molecules and nanostructure atoms is different from that between liquid molecules and solid wall atoms, the thermal resistance at the interface is dependent on the potential parameter between liquid molecules and nanostructure atoms rather than the geometric surface area in a molecular scale depending on the nanostructures as well as their clearances.

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