A Study of Nanoparticle-Enhanced Heat Transfer

The study of the heat transfer characteristics of nanofluids, i.e. fluids that are suspensions of nanometer size particles, has gained significant attention in the search for new coolants that can effectively service a variety of needs ranging from the increasing heat transfer demands of ever smaller microelectronic devices to mitigating the effects of loss of coolant accidents in nuclear power plants. Experimental data has shown large increases in thermal conductivity and associated increases in the level of critical heat flux in nuclear reactors; however, in some cases the range of the applicability of the experimental results is uncertain and there is a lack of a theory by which this can be resolved. Complicating the theoretical description of heat transfer in nanofluids is the fact that fluids in the vicinity of the nanoparticles are a complex combination of phase transition, interfacial, and transport phenomena. This paper describes a study in which molecular dynamics simulations were used to enhance the understanding of the effect of nanoparticles on heat transfer. The molecular dynamics (MD) simulations presented here model a Lennard-Jones fluid in a channel where the walls are maintained at different temperatures. The heat flux is calculated for a variety of nanoparticle sizes and concentrations. The results are compared to experimental data in order to provide information that will more confidently bound the data and provide information that will guide the development of more comprehensive theories. We also anticipate that this work could contribute to the design of biosensors where suspended molecules are transported through micro- and nano-channels in the presence of heat transfer.

Molecular dynamics simulations and CD spectroscopy reveal hydration-induced unfolding of the intrinsically disordered LEA proteins COR15A and COR15B from Arabidopsis thaliana

Physical Chemistry Chemical Physics ◽

10.1039/c6cp02272c ◽

2016 ◽

Vol 18 (37) ◽

pp. 25806-25816 ◽

Cited By ~ 13

Author(s):

Carlos Navarro-Retamal ◽

Anne Bremer ◽

Jans Alzate-Morales ◽

Julio Caballero ◽

Dirk K. Hincha ◽

...

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Arabidopsis Thaliana ◽

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.

The β-cyclodextrin/benzene complex and its hydrogen bonds – a theoretical study using molecular dynamics, quantum mechanics and COSMO-RS

Beilstein Journal of Organic Chemistry ◽

10.3762/bjoc.9.15 ◽

2013 ◽

Vol 9 ◽

pp. 118-134 ◽

Cited By ~ 19

Author(s):

Jutta Erika Helga Köhler ◽

Nicole Grczelschak-Mick

Keyword(s):

Molecular Dynamics ◽

Quantum Mechanics ◽

Hydrogen Bonds ◽

Md Simulations ◽

Benzene Molecule ◽

Glucose Unit ◽

Hand Orientation ◽

Different Temperatures ◽

Dynamics Simulations ◽

The Right

Four highly ordered hydrogen-bonded models of β-cyclodextrin (β-CD) and its inclusion complex with benzene were investigated by three different theoretical methods: classical quantum mechanics (QM) on AM1 and on the BP/TZVP-DISP3 level of approximation, and thirdly by classical molecular dynamics simulations (MD) at different temperatures (120 K and 273 to 300 K). The hydrogen bonds at the larger O2/O3 rim of empty β-CDs prefer the right-hand orientation, e.g., O3-H…O2-H in the same glucose unit and bifurcated towards …O4 and O3 of the next glucose unit on the right side. On AM1 level the complex energy was −2.75 kcal mol−1 when the benzene molecule was located parallel inside the β-CD cavity and −2.46 kcal mol−1 when it was positioned vertically. The AM1 HOMO/LUMO gap of the empty β-CD with about 12 eV is lowered to about 10 eV in the complex, in agreement with data from the literature. AM1 IR spectra displayed a splitting of the O–H frequencies of cyclodextrin upon complex formation. At the BP/TZVP-DISP3 level the parallel and vertical positions from the starting structures converged to a structure where benzene assumes a more oblique position (−20.16 kcal mol−1 and −20.22 kcal mol−1, resp.) as was reported in the literature. The character of the COSMO-RS σ-surface of β-CD was much more hydrophobic on its O6 rim than on its O2/O3 side when all hydrogen bonds were arranged in a concerted mode. This static QM picture of the β-CD/benzene complex at 0 K was extended by MD simulations. At 120 K benzene was mobile but always stayed inside the cavity of β-CD. The trajectories at 273, 280, 290 and 300 K certainly no longer displayed the highly ordered hydrogen bonds of β-CD and benzene occupied many different positions inside the cavity, before it left the β-CD finally at its O2/O3 side.

Investigating an Efficient and Accurate Protocol for Sampling Structures from Molecular Dynamics Simulations: A Close Look by Different Wavelet Families

10.22541/au.161426744.43901831/v1 ◽

2021 ◽

Author(s):

Mateus Gonçalves ◽

Arismar Junior ◽

Elaine da Cunha ◽

Teodorico Ramalho

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Md Simulations ◽

Quantum Calculations ◽

Sampling Protocol ◽

Molecular Systems ◽

Electronic Parameters ◽

Dynamics Simulations ◽

Over Time ◽

Wavelet Family

Molecular Dynamics (MD) simulations are widely used to predict the behavior of molecular systems over time. However, one of the great challenges of MD simulations is how to treat the thousands of configurations obtained from calculations, since the number of the quantum calculations (QM) required for evaluating electronic parameters is too high and, sometimes, computationally impracticable. Thus, an efficient and accurate sampling protocol is essential for combining classical MD and QM calculations. In this article, based on the OWSCA methodology, 93 wavelet signals were analyzed in order to further refine the methodology and identify the best wavelet family for [Fe(H2O)6]2+ and [Mn(H2O)6]2+ complexes in solution. Our results point out that the bior1.3 was the best wavelet, values closest to the experimental data were obtained for both studied systems.

Molecular dynamics simulations of charged and neutral lipid bilayers: treatment of electrostatic interactions.

Acta Biochimica Polonica ◽

10.18388/abp.2003_3670 ◽

2003 ◽

Vol 50 (3) ◽

pp. 789-798 ◽

Cited By ~ 27

Author(s):

Tomasz Róg ◽

Krzysztof Murzyn ◽

Marta Pasenkiewicz-Gierula

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

Lipid Bilayers ◽

Long Range ◽

Electrostatic Interactions ◽

Md Simulations ◽

Computational Method ◽

Simulation Protocol ◽

Speed Up ◽

Molecular dynamics (MD) simulations complement experimental methods in studies of the structure and dynamics of lipid bilayers. The choice of algorithms employed in this computational method represents a trade-off between the accuracy and real calculation time. The largest portion of the simulation time is devoted to calculation of long-range electrostatic interactions. To speed-up evaluation of these interactions, various approximations have been used. The most common ones are the truncation of long-range interactions with the use of cut-offs, and the particle-mesh Ewald (PME) method. In this study, several multi-nanosecond cut-off and PME simulations were performed to establish the influence of the simulation protocol on the bilayer properties. Two bilayers were used. One consisted of neutral phosphatidylcholine molecules. The other was a mixed lipid bilayer consisting of neutral phosphatidylethanolamine and negatively charged phosphatidylglycerol molecules. The study shows that the cut-off simulation of a bilayer containing charge molecules generates artefacts; in particular the mobility and order of the charged molecules are vastly different from those determined experimentally. In the PME simulation, the bilayer properties are in general agreement with experimental data. The cut-off simulation of bilayers containing only uncharged molecules does not generate artefacts, nevertheless, the PME simulation gives generally better agreement with experimental data.

MOLECULAR DYNAMICS SIMULATIONS OF PHONON HEAT TRANSFER AT THE MICROSCALE

Equipment ◽

10.1615/ihtc13.p14.20 ◽

2006 ◽

Author(s):

P. Heino

Keyword(s):

Heat Transfer ◽

Molecular Dynamics ◽

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

Letters in Drug Design & Discovery ◽

10.2174/1570180815666180604085626 ◽

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). 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. 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. 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.

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

Molecules ◽

10.3390/molecules26061711 ◽

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 ◽

10.1039/d0ce01613f ◽

2021 ◽

Author(s):

Andrey Sarikov ◽

Anna Marzegalli ◽

Luca Barbisan ◽

Massimo Zimbone ◽

Corrado Bongiorno ◽

...

Keyword(s):

Molecular Dynamics ◽

Stacking Faults ◽

Md Simulations ◽

Stacking Fault ◽

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...

Local Structuring of Diketopyrrolopyrrole (DPP)-based Oligomers from Molecular Dynamics Simulations

Physical Chemistry Chemical Physics ◽

10.1039/d1cp03257g ◽

2021 ◽

Author(s):

Maryam Reisjalali ◽

J. Javier Burgos-Marmol ◽

Rex Manurung ◽

Alessandro Troisi

Keyword(s):

Experimental Data ◽

Molecular Dynamics ◽

High Mobility ◽

Semiconducting Polymers ◽

Microscopic Structure ◽

The microscopic structure of high mobility semiconducting polymers is known to be essential for their performance but it cannot be easily deduced from the available experimental data. A series of...

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

Polymers ◽

10.3390/polym13030347 ◽

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 ◽

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.