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Journal articles on the topic 'Molecular simulation'

To see the other types of publications on this topic, follow the link: Molecular simulation.

Author: Grafiati

Published: 4 June 2021

Last updated: 7 July 2024

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1

Okumura, Hisashi, Satoru G. Itoh, and Yuko Okamoto. "1P585 Explicit Symplectic Molecular Dynamics Simulation for Rigid-Body Molecules in the Canonical Ensemble(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S293. http://dx.doi.org/10.2142/biophys.46.s293_1.

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2

Osborne, I. S. "Molecular simulation." Science 349, no. 6254 (September 17, 2015): 1297–98. http://dx.doi.org/10.1126/science.349.6254.1297-e.

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3

Potoff, Jeffrey, and Ioannis Economou. "Molecular simulation." Fluid Phase Equilibria 498 (October 2019): 160. http://dx.doi.org/10.1016/j.fluid.2019.05.027.

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4

Liu, Zhimin, Zhigang Xu, Dan Wang, Yuming Yang, Yunli Duan, Liping Ma, Tao Lin, and Hongcheng Liu. "A Review on Molecularly Imprinted Polymers Preparation by Computational Simulation-Aided Methods." Polymers 13, no. 16 (August 10, 2021): 2657. http://dx.doi.org/10.3390/polym13162657.

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Molecularly imprinted polymers (MIPs) are obtained by initiating the polymerization of functional monomers surrounding a template molecule in the presence of crosslinkers and porogens. The best adsorption performance can be achieved by optimizing the polymerization conditions, but this process is time consuming and labor-intensive. Theoretical calculation based on calculation simulations and intermolecular forces is an effective method to solve this problem because it is convenient, versatile, environmentally friendly, and inexpensive. In this article, computational simulation modeling methods are introduced, and the theoretical optimization methods of various molecular simulation calculation software for preparing molecularly imprinted polymers are proposed. The progress in research on and application of molecularly imprinted polymers prepared by computational simulations and computational software in the past two decades are reviewed. Computer molecular simulation methods, including molecular mechanics, molecular dynamics and quantum mechanics, are universally applicable for the MIP-based materials. Furthermore, the new role of computational simulation in the future development of molecular imprinting technology is explored.

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5

Katkar, Ashwini, and Vinitkumar Jayaprakash Dongre. "Assessing Molecular Throughput and Efficiency through Simulation in Diffusion-Based Molecular Communication." Indian Journal Of Science And Technology 17, no. 6 (February 12, 2024): 524–32. http://dx.doi.org/10.17485/ijst/v17i6.2814.

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Objectives: This study investigates the correlation of critical factors influencing throughput and efficiency in diffusion-based molecular communication systems. Method: The study presents a simulation model for 3-D diffusion-based molecular communication, incorporating essential parameters such as molecule size, transmission rate, diffusion rate, and transmitter-receiver distance. Findings: Through comprehensive simulations, the study reveals the effects of different parameters on throughput and efficiency in diffusion-based molecular communication. It highlights the critical trade-offs associated with system design and optimization. The study reveals the key factors influencing the transmission capabilities, the receiver congestion, and the overall efficiency of the communication system. Novelty: In this study, we give a study overview of the latest work of performance metrics in the field of molecular communication. A novel algorithm is proposed to find the throughput and efficiency of molecular communication. The proposed framework analyzes the intricate relationship between system parameters and performance metrics, emphasizing the potential for system optimization. Our simulation work demonstrates how the model parameters influence the performance of the molecular communication system, providing insights for enhancing the system's performance in applications such as targeted drug delivery in the future. Keywords: Molecular Communication, Diffusion, Transmission Rate, Throughput, Efficiency

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6

Chen, Xueye. "Molecular dynamics simulation of nanofluidics." Reviews in Chemical Engineering 34, no. 6 (November 27, 2018): 875–85. http://dx.doi.org/10.1515/revce-2016-0060.

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Abstract This review reports the progress on the recent development of molecular dynamics simulation of nanofluidics. Molecular dynamics simulations of nanofluidics in nanochannel structure, surface roughness of nanochannel, carbon nanotubes, electrically charged, thermal transport in nanochannels and gases in nanochannels are illustrated and discussed. This paper will provide an expedient and valuable reference to designers who intend to research molecular dynamics simulation of nanofluidic devices.

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7

Rakkapao, Natthida. "Molecular Dynamics Simulation of Gas Transport in Polyisoprene Matrix." Advanced Materials Research 844 (November 2013): 209–13. http://dx.doi.org/10.4028/www.scientific.net/amr.844.209.

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Molecular Dynamics (MD) simulation was employed to study the diffusivity of biogas in a PI matrix with the aim to verify simulations as a useful tool to predict PI membrane properties for biogas treatment. The simulation model of PI numerical was reliable and accurate in predicting both the material properties and the diffusivity of gases in PI matrix. The diffusion coefficients (D) of the major components in biogas, namely CH4, CO2, H2O, O2, and N2, were computed by simulating trajectories of each gas in PI matrix at 300 K. The simulations gave DCO2 that was 6 times larger than DCH4, and this agrees well with permeabilities reported in the literature. This suggests that PI membranes could be used to treat biogas by separating CO2 and CH4. However, the diffusivities of N2, H2O, and CH4 are closely similar, so PI membranes are not capable of separating these. The potential application of PI membrane to CO2/CH4 separation seems worth further exploration.

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8

MAHAJAN, DHIRAJ K., and SUMIT BASU. "ON THE SIMULATION OF UNIAXIAL, COMPRESSIVE BEHAVIOR OF AMORPHOUS, GLASSY POLYMERS WITH MOLECULAR DYNAMICS." International Journal of Applied Mechanics 02, no. 03 (September 2010): 515–41. http://dx.doi.org/10.1142/s1758825110000639.

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Molecular dynamics (MD) simulations offer an interesting route to simulating deformation and fracture behavior of amorphous glassy polymers. However, MD simulations are performed at extremely high rates and on very small samples (though periodic boundary conditions are routinely used) containing at most hundreds of chains which are much shorter than in real life. In this work, we try to assess the extent to which MD simulations produce physically realistic stress–strain responses and identify aspects of the simulation procedure that can be controlled closely in order to avoid numerical artifacts. We show that, when an appropriate protocol for sample generation and simulation of deformation is followed, in spite of the obvious constraints imposed by the simulation technique, MD simulations have the capability to generate realistic stress–strain curves and reproduce many experimental trends pertaining to them.

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9

SHINTO, Hiroyuki. "Molecular Dynamics Simulation." Journal of the Japan Society of Colour Material 86, no. 10 (2013): 380–85. http://dx.doi.org/10.4011/shikizai.86.380.

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10

Frenkel, Daan, Berend Smit, Jan Tobochnik, Susan R. McKay, and Wolfgang Christian. "Understanding Molecular Simulation." Computers in Physics 11, no. 4 (1997): 351. http://dx.doi.org/10.1063/1.4822570.

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11

Krienke, Hartmut. "Molecular dynamics simulation." Journal of Molecular Liquids 75, no. 3 (March 1998): 271–72. http://dx.doi.org/10.1016/s0167-7322(97)00106-2.

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12

Rapaport, D. C. "Molecular dynamics simulation." Computing in Science & Engineering 1, no. 1 (1999): 70–71. http://dx.doi.org/10.1109/5992.743625.

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13

Fogolari, Federico, Alessandra Corazza, Stefano Toppo, Silvio C. E. Tosatto, Paolo Viglino, Fulvio Ursini, and Gennaro Esposito. "Studying Interactions by Molecular Dynamics Simulations at High Concentration." Journal of Biomedicine and Biotechnology 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/303190.

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Molecular dynamics simulations have been used to study molecular encounters and recognition. In recent works, simulations using high concentration of interacting molecules have been performed. In this paper, we consider the practical problems for setting up the simulation and to analyse the results of the simulation. The simulation of beta 2-microglobulin association and the simulation of the binding of hydrogen peroxide by glutathione peroxidase are provided as examples.

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14

Yana, Janchai, Piyarat Nimmanpipug, and Vannajan Sanghiran Lee. "J-9 DRY AND WET MOLECULAR DYNAMICS SIMULATIONS OF NAFION(R) POLYMER ELECTROLYTE FUEL CELL MEMBRANE(Session: Simulation)." Proceedings of the Asian Symposium on Materials and Processing 2006 (2006): 165. http://dx.doi.org/10.1299/jsmeasmp.2006.165.

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15

Mao, B. "Molecular-dynamics investigation of molecular flexibility in ligand binding." Biochemical Journal 288, no. 1 (November 15, 1992): 109–16. http://dx.doi.org/10.1042/bj2880109.

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The molecular flexibility of an inhibitor in ligand-binding process has been investigated by the mass-weighted molecular-dynamics simulation, a computational method adopted from the standard molecular-dynamics simulation and one by which the conformational space of a biomolecular system over potential energy barriers can be sampled effectively. The bimolecular complex of the aspartyl proteinase from Rhizopus chinensis, rhizopuspepsin, and an octapeptide inhibitor was previously studied in a mass-weighted molecular-dynamics simulation; the study has been extended for investigating the molecular flexibility in ligand binding. A series of mass-weighted molecular-dynamics simulations was carried out in which libration of the inhibitor dihedral angles was parametrically controlled, and threshold values of dihedral angle libration amplitudes were observed from monitoring the sampling of the enzyme binding pocket by the inhibitor in the simulations. The computational results are consistent with the general notion of molecular-flexibility requirement for ligand binding; the freedom of dihedral rotations of side-chain groups was found to be particularly important for ligand binding. Thus the critical degree of molecular flexibility which would contribute to effective enzyme inhibition can be obtained precisely from the modified molecular-dynamics simulations; the procedure described herein represents a first step toward providing quantitative measures of such a molecular-flexibility index for inhibitor molecules that have been otherwise targeted for optimal protein-ligand interactions.

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16

YONEDA, Tomoyuki, Moritaka HIDA, and Akira SAKAKIBARA. "Molecular Dynamics Simulations. Molecular Dynamics Simulation of Ni Crystals under Uniaxial Deformation." Journal of the Society of Materials Science, Japan 46, no. 3 (1997): 228–31. http://dx.doi.org/10.2472/jsms.46.228.

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17

NAKATANI, Keiko, Akihiro NAKATANI, Hiroshi KITAGAWA, and Yoshihiko SUGIYAMA. "Molecular Dynamics Simulations. Molecular Dynamics Simulation on Crack Growth in Amorphous Metal." Journal of the Society of Materials Science, Japan 49, no. 3 (2000): 275–81. http://dx.doi.org/10.2472/jsms.49.275.

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18

Hannon, L., G. C. Lie, and E. Clementi. "Molecular dynamics simulation simulation of channel flow." Physics Letters A 119, no. 4 (December 1986): 174–77. http://dx.doi.org/10.1016/0375-9601(86)90440-8.

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19

Noé, Frank, Alexandre Tkatchenko, Klaus-Robert Müller, and Cecilia Clementi. "Machine Learning for Molecular Simulation." Annual Review of Physical Chemistry 71, no. 1 (April 20, 2020): 361–90. http://dx.doi.org/10.1146/annurev-physchem-042018-052331.

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Machine learning (ML) is transforming all areas of science. The complex and time-consuming calculations in molecular simulations are particularly suitable for an ML revolution and have already been profoundly affected by the application of existing ML methods. Here we review recent ML methods for molecular simulation, with particular focus on (deep) neural networks for the prediction of quantum-mechanical energies and forces, on coarse-grained molecular dynamics, on the extraction of free energy surfaces and kinetics, and on generative network approaches to sample molecular equilibrium structures and compute thermodynamics. To explain these methods and illustrate open methodological problems, we review some important principles of molecular physics and describe how they can be incorporated into ML structures. Finally, we identify and describe a list of open challenges for the interface between ML and molecular simulation.

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20

LÜ, Shouqin, and Mian LONG. "Molecular Dynamics Simulation and Molecular Biomechanics." ACTA BIOPHYSICA SINICA 28, no. 1 (2012): 6. http://dx.doi.org/10.3724/sp.j.1260.2012.10150.

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21

PEI, Q. X., C. LU, F. Z. FANG, and H. WU. "MOLECULAR DYNAMICS SIMULATION OF NANOMETRIC CUTTING PROCESS." International Journal of Nanoscience 05, no. 04n05 (August 2006): 633–38. http://dx.doi.org/10.1142/s0219581x06004905.

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Nanoscale machining involves changes in only a few atomic layers at the surface. Molecular dynamics (MD) simulation can play a significant role in addressing a number of machining problems at the atomic scale. In this paper, we employed MD simulations to study the nanometric cutting process of single crystal copper. Instead of the widely used Morse potential, we used the Embedded Atom Method (EAM) potential for this study. The simulations were carried out for various tool geometries at different cutting speeds. Attention was paid to the cutting chip formation, the cutting surface morphology and the cutting force. The MD simulation results show that both the tool geometry and the cutting speed have great influence on the chip formation, the smoothness of machined surface and the cutting force.

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22

Yu, Shi, Ruizhi Chu, Xiao Li, Guoguang Wu, and Xianliang Meng. "Nonequilibrium Molecular Dynamics Simulations of Coal Ash." Energies 14, no. 1 (December 22, 2020): 11. http://dx.doi.org/10.3390/en14010011.

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Both molecular dynamics (MD) and nonequilibrium molecular dynamics (NEMD) simulations were performed to simulate coal ashes using the Guillot-Sator model in this work. The structural and transport properties of coal ashes at high temperatures have been obtained. Superheating of coal ash system with anorthite crystal structure initial configuration has been observed for MD simulation which explains the discrepancy between previous MD simulation results and FactSage thermochemical calculations. The fluxing effects of both calcium oxide and sodium oxide have been investigated systematically through MD and NEMD simulations. Moreover, the viscosities of coal ash systems have been computed by two methods: (1) Stokes-Einstein equation; (2) NEMD simulations. Estimations of viscosities for various coal ash systems based on Stokes-Einstein equation exhibit a strong temperature dependence of viscosity, which agrees with previous experimental results. On the other hand, NEMD simulation results that showed a strong shear-thinning feature, failed to reproduce this strong temperature dependence of viscosity, possibly due to the short simulation time. Nevertheless, NEMD simulations not only provide us detailed information about atoms dynamics under shear, but also allow us to model the coal ash system far from equilibrium which cannot be accessed by thermodynamics calculation using software like FactSage.

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23

Terada, Tohru, and Kentaro Shimizu. "1P581 Improving efficiency of conformation sampling in multicanonical molecular dynamics simulation(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S292. http://dx.doi.org/10.2142/biophys.46.s292_1.

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24

Sinha, Siddharth, Benjamin Tam, and San Ming Wang. "Applications of Molecular Dynamics Simulation in Protein Study." Membranes 12, no. 9 (August 29, 2022): 844. http://dx.doi.org/10.3390/membranes12090844.

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Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study protein function, protein stability, protein–protein interaction, enzymatic reactions and drug–protein interactions, and membrane proteins. In this review, we provide a brief review for the history of MD Simulations application and the current status of MD Simulations applications in protein studies.

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25

Larsen, Andreas Haahr. "Molecular Dynamics Simulations of Curved Lipid Membranes." International Journal of Molecular Sciences 23, no. 15 (July 22, 2022): 8098. http://dx.doi.org/10.3390/ijms23158098.

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Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and thereby be trafficked to specific locations. The description of curvature sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow researcher to closely match the conditions of experimental studies of membrane curvatures.

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26

Zhang, Fan, Rui Yang, and Diannan Lu. "Investigation of Polymer Aging Mechanisms Using Molecular Simulations: A Review." Polymers 15, no. 8 (April 18, 2023): 1928. http://dx.doi.org/10.3390/polym15081928.

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Aging has a serious impact on the properties of functional polymers. Therefore, it is necessary to study the aging mechanism to prolong the service and storage life of polymer-based devices and materials. Due to the limitations of traditional experimental methods, more and more studies have adopted molecular simulations to analyze the intrinsic mechanisms of aging. In this paper, recent advances in molecular simulations of the aging of polymers and their composites are reviewed. The characteristics and applications of commonly used simulation methods in the study of the aging mechanisms (traditional molecular dynamics simulation, quantum mechanics, and reactive molecular dynamics simulation) are outlined. The current simulation research progress of physical aging, aging under mechanical stress, thermal aging, hydrothermal aging, thermo-oxidative aging, electric aging, aging under high-energy particle impact, and radiation aging is introduced in detail. Finally, the current research status of the aging simulations of polymers and their composites is summarized, and the future development trend has been prospected.

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27

Esparza, C. H., and H. Kronmüller. "Canonical molecular dynamics simulation." Molecular Physics 68, no. 6 (December 20, 1989): 1341–52. http://dx.doi.org/10.1080/00268978900102951.

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28

., Guruprasad P. Yennikoppa. "NANO TECHNOLOGY: MOLECULAR SIMULATION." International Journal of Research in Engineering and Technology 04, no. 24 (October 25, 2015): 7–15. http://dx.doi.org/10.15623/ijret.2015.0424002.

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29

Case, Fiona. "Nanotechnology and molecular simulation." Molecular Simulation 37, no. 8 (July 2011): 647. http://dx.doi.org/10.1080/08927022.2011.593318.

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30

Gubbins, Keith E. "Applications of molecular simulation." Fluid Phase Equilibria 83 (February 1993): 1–14. http://dx.doi.org/10.1016/0378-3812(93)87001-h.

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31

Zhang, Min, Guo Fang Zhang, and Yu Xi Jia. "Molecular Dynamic and Mesoscopic Dynamic Simulations for Polymer Blends." Advanced Materials Research 1033-1034 (October 2014): 496–500. http://dx.doi.org/10.4028/www.scientific.net/amr.1033-1034.496.

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The compatibilities of polymer blends, Polypropylene (PP) and Polyamide12(PA12) with the quantity ratio 10/90, was simulated by Molecular Dynamics (MD) and Mesoscopic Dynamic simulation (MesoDyn) simulations. Cohesive energy density (CED) and solubility parameters (δ) of pure substances and PP/PA12 blends were got by MD simulations. Flory-Huggins parameter was calculated based on CED values. The mesoscale simulation was related to the molecular simulation through Flory-Huggins parameter. Free energy density and the density profiles were got through MesoDyn simulation. Results showed that solubility parameter difference (Δδ) of PP/PA12 is 4.092 and free energy density value is 0.17 in the equivalent system. And phase separation behavior was observed in the density profiles. All these indicates that PP and PA12 is not miscible which is the same as the experiment results.

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32

Fuchigami, Sotaro, Mitsunori Ikeguchi, and Akinori Kidera. "1P564 All-Atom Molecular Dynamics Simulation of Conformational Changes in Adenylate Kinase(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S287. http://dx.doi.org/10.2142/biophys.46.s287_4.

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33

Schreiner, Wolfgang, Rudolf Karch, Bernhard Knapp, and Nevena Ilieva. "Relaxation Estimation of RMSD in Molecular Dynamics Immunosimulations." Computational and Mathematical Methods in Medicine 2012 (2012): 1–9. http://dx.doi.org/10.1155/2012/173521.

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Molecular dynamics simulations have to be sufficiently long to draw reliable conclusions. However, no method exists to prove that a simulation has converged. We suggest the method of “lagged RMSD-analysis” as a tool to judge if an MD simulation has not yet run long enough. The analysis is based on RMSD values between pairs of configurations separated by variable time intervals Δt. Unless RMSD(Δt) has reached a stationary shape, the simulation has not yet converged.

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34

Bisson, Mauro, Massimo Bernaschi, and Simone Melchionna. "Parallel Molecular Dynamics with Irregular Domain Decomposition." Communications in Computational Physics 10, no. 4 (October 2011): 1071–88. http://dx.doi.org/10.4208/cicp.140810.021210a.

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AbstractThe spatial domain of Molecular Dynamics simulations is usually a regular box that can be easily divided in subdomains for parallel processing. Recent efforts aimed at simulating complex biological systems, like the blood flow inside arteries, require the execution of Parallel Molecular Dynamics (PMD) in vessels that have, by nature, an irregular shape. In those cases, the geometry of the domain becomes an additional input parameter that directly influences the outcome of the simulation. In this paper we discuss the problems due to the parallelization of MD in complex geometries and show an efficient and general method to perform MD in irregular domains.

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35

Yu, Kuan, and Bo Zhu. "Recent Development of Molecular Simulation Based on GPU in Material Science." Advanced Materials Research 79-82 (August 2009): 1309–12. http://dx.doi.org/10.4028/www.scientific.net/amr.79-82.1309.

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Molecular simulation can provide mechanism insights into how material behaviour related to molecular properties and microscopic details of the arrangement of many molecules. With the development of Graphics Processing Unit (GPU), scientists have realized general purpose molecular simulations on GPU and the Common Unified Device Architecture (CUDA) environment. In this paper, we provided a brief overview of molecular simulation and CUDA, introduced the recent achievements in molecular simulation based on GPU in material science, mainly about Monte Carlo method and Molecular Dynamics. The recent research achievements have shown that GPUs can provide unprecedented computational power for scientific applications. With optimized algorithms and program codes, a single GPU can provide a performance equivalent to that of a distributed computer cluster. So, study of molecular simulations based on GPU will accelerate the development of material science in the future.

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36

Khairudin, Nurul Bahiyah Ahmad, and Fatahiya Mohamed Tap. "Molecular Dynamics Folding Simulation of Amyloid A4 Peptide in Implicit Solvent." International Journal of Bioscience, Biochemistry and Bioinformatics 4, no. 5 (2014): 351–54. http://dx.doi.org/10.7763/ijbbb.2014.v4.369.

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37

Alper, Pahsa. "MOLECULAR DYNAMIC SIMULATION OF PLASMA MATERIAL INTERACTION TOCALCULATE THEORETICAL SPUTTERING YIELD." Eurasian Physical Technical Journal 20, no. 2 (44) (June 21, 2023): 127–37. http://dx.doi.org/10.31489/2023no2/127-137.

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In a fusion reaction two light nuclei, Deuterium and Tritium merge to form a single heavier nucleus Helium. However, two positive nuclei repel each other. In order to merge two nuclei they need to have very high velocities. High speed means, high temperature. For the reaction it is significant for a nuclei to keep at 100 million °C temperature. At this temperature D and T atoms form a plasma. In order the reaction to take place, the plasma temperature must be conserved or plasma should not be cooled. Tokamak reactors are designed to confine the plasma in a magnetic field. Thus, the cooling of the plasma is prevented by hitting the reactor walls. Plasma density and temperature must be at a certain level in order to initiate the reaction and to ensure continuity. During the reaction process, positive and negative ions escaping from the magnetic field environment interact with Tokamak walls and cause deformation. This causes the plasma wall to deteriorate over time and the release of neutrons to the environment. Plasma-Wall interaction is one of the most important problems that cause interruption of fusion in Tokamak rectors. The materials which most resistant to ion corrosion in the plasma wall are graphite, beryllium, aluminium and tungsten. In this work, plasma-material interaction is studied theoretically physical and chemical erosion caused by the plasma interactions of different wall material samples (graphite, aluminium and Tungsten) used in the fusion reactor and investigated with the Monte Carlo method with molecular dynamics.

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38

Lee, Jeongwoo, and Yung C. Shin. "Molecular Dynamics Study of Bulk Properties of Polycrystalline NiTi." Metals 11, no. 8 (August 4, 2021): 1237. http://dx.doi.org/10.3390/met11081237.

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Molecular dynamics (MD) simulations were carried out to study the bulk polycrystalline properties of NiTi. Thermally driven phase transitions of NiTi between martensite and austenitewere simulated using single crystalline simulation domains. With external stress boundary conditions, MD simulation successfully predicted experimentally observed phase transformation temperatures of bulk polycrystalline. Elastic characteristics of NiTi martensite were simulated using polycrystalline simulation domains that consist of realistic disorientations and grain boundary structures. The existence of grain disorientation and grain boundary lowered the potential energy of the simulation domain, which led to more realistic elastic modulus prediction. Analysis of simulation domains that predicted realistic bulk polycrystalline properties showed that the major difference between single crystalline and polycrystalline structures is atomic stress distribution.

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39

Li, Dong Jie, Li Zhang, and Jian Song. "Molecular Dynamics Simulation of ZnO Nanowire Manipulation." Key Engineering Materials 609-610 (April 2014): 400–405. http://dx.doi.org/10.4028/www.scientific.net/kem.609-610.400.

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In order to achieve a better manipulation performance of ZnO nanowire, the ZnO nanowire forces are analysed, and molecular dynamics simulations are conducted. Force model of ZnO nanowire is established to interprete the drifting, bending and fracturing conditions in ZnO nanowire transfer experiment. As ZnO nanowire force is too complex to build a precise mathematical model, molecular dynamics is proposed to simulate the process. Based on the analysis of ZnO nanostructure, the probe-nanowire-substrate model is established. Through changing the operation path of the probe and operation area between the probe and nanowire, simulation results are got. By the Analysis and comparison of simulation results, the optimal operation path and operation area are obtained.

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40

Mahboub, Radia. "Studies of Trans- and Cis-Xylomollin Molecular Structures Using Molecular Dynamics Simulations." International Letters of Chemistry, Physics and Astronomy 5 (September 2013): 46–58. http://dx.doi.org/10.18052/www.scipress.com/ilcpa.5.46.

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The present work describes the comparative study of the trans- and the cis-xylomollin structures. We have determined the two bridgehead H5 and H9 configurations using simulation calculations for both trans- and cis- distereoisomers. Molecular Dynamic (MD) simulations of the trans- and cis- xylomollin were performed with an efficient program. The geometries, interaction energies, bonds, angles, and the Van der Waals (VDW) interactions were carried out in solution and gas phases. This comparative study shows that the trans-xylomollin acquires the high configuration energy under the AMBER field using MD method. This molecule reaches its high stable configuration state in solution environment. Our MD simulation results are goods and in agreement with those of literature.

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41

Mahboub, Radia. "Studies of Trans- and Cis-Xylomollin Molecular Structures Using Molecular Dynamics Simulations." International Letters of Chemistry, Physics and Astronomy 5 (December 19, 2012): 46–58. http://dx.doi.org/10.56431/p-n74vg3.

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The present work describes the comparative study of the trans- and the cis-xylomollin structures. We have determined the two bridgehead H5 and H9 configurations using simulation calculations for both trans- and cis- distereoisomers. Molecular Dynamic (MD) simulations of the trans- and cis- xylomollin were performed with an efficient program. The geometries, interaction energies, bonds, angles, and the Van der Waals (VDW) interactions were carried out in solution and gas phases. This comparative study shows that the trans-xylomollin acquires the high configuration energy under the AMBER field using MD method. This molecule reaches its high stable configuration state in solution environment. Our MD simulation results are goods and in agreement with those of literature.

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Miyagawa, Hiroh, and Kunihiro Kitamura. "1P565 Molecular dynamics simulations of association and docking between an inhibitor and an enzyme.(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_1.

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Hirano, Yoshinori, Noriaki Okimoto, Atsushi Suenaga, Makoto Taiji, Naoko Imamoto, Masato Yasui, and Toshikazu Ebisuzaki. "1P590 Investigation of The Structure-Function Relationship of Importin-β by Molecular Dynamics Simulations(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S294. http://dx.doi.org/10.2142/biophys.46.s294_2.

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Sheng, Chunyang, Kenichi Nomura, Pankaj Rajak, Aiichiro Nakano, Rajiv K. Kalia, and Priya Vashishta. "Quantum Molecular Dynamics Validation of Nanocarbon Synthesis by High-Temperature Oxidation of Nanoparticles." MRS Advances 1, no. 24 (2016): 1811–16. http://dx.doi.org/10.1557/adv.2016.413.

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ABSTRACTThis study uses ab initio quantum molecular dynamics (QMD) simulations to validate multimillion-atom reactive molecular dynamics (RMD) simulations, and predicts unexpected condensation of carbon atoms during high-temperature oxidation of silicon-carbide nanoparticles (nSiC). For the validation process, a small nSiC in oxygen environment is chosen to perform QMD simulation. The QMD results provide the number of Si-O and C-O bonds as a function of time. RMD simulation is then performed under the identical condition. The time evolutions of different bonds are compared between the QMD and RMD simulations. We observe the condensation of large number of C-cluster nuclei into larger C clusters in both simulations, thereby validating RMD. Furthermore, we use the QMD simulation results as an input to a multi-objective genetic algorithm to train the RMD force-field parameters. The resulting force field far better reproduces the ground-truth QMD simulation results.

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Kadupitiya, JCS, Geoffrey C. Fox, and Vikram Jadhao. "Machine learning for parameter auto-tuning in molecular dynamics simulations: Efficient dynamics of ions near polarizable nanoparticles." International Journal of High Performance Computing Applications 34, no. 3 (January 14, 2020): 357–74. http://dx.doi.org/10.1177/1094342019899457.

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Simulating the dynamics of ions near polarizable nanoparticles (NPs) using coarse-grained models is extremely challenging due to the need to solve the Poisson equation at every simulation timestep. Recently, a molecular dynamics (MD) method based on a dynamical optimization framework bypassed this obstacle by representing the polarization charge density as virtual dynamic variables and evolving them in parallel with the physical dynamics of ions. We highlight the computational gains accessible with the integration of machine learning (ML) methods for parameter prediction in MD simulations by demonstrating how they were realized in MD simulations of ions near polarizable NPs. An artificial neural network–based regression model was integrated with MD simulation and predicted the optimal simulation timestep and optimization parameters characterizing the virtual system with 94.3% success. The ML-enabled auto-tuning of parameters generated accurate dynamics of ions for ≈ 10 million steps while improving the stability of the simulation by over an order of magnitude. The integration of ML-enhanced framework with hybrid Open Multi-Processing / Message Passing Interface (OpenMP/MPI) parallelization techniques reduced the computational time of simulating systems with thousands of ions and induced charges from thousands of hours to tens of hours, yielding a maximum speedup of ≈ 3 from ML-only acceleration and a maximum speedup of ≈ 600 from the combination of ML and parallel computing methods. Extraction of ionic structure in concentrated electrolytes near oil–water emulsions demonstrates the success of the method. The approach can be generalized to select optimal parameters in other MD applications and energy minimization problems.

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Zhang, Hedong, Yasunaga Mitsuya, and Maiko Yamada. "Spreading Characteristics of Molecularly Thin Lubricant on Surfaces With Groove-Shaped Textures: Effects of Molecular Weight and End-Group Functionality." Journal of Tribology 125, no. 2 (March 19, 2003): 350–57. http://dx.doi.org/10.1115/1.1509771.

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Effects of molecular weight and end-group functionality on spreading of molecularly thin perfluoropolyether (PFPE) film over solid surfaces with groove-shaped textures have been studied by experiments and Monte Carlo simulations. In the experiments, lubricant spreading on a surface with groove-shaped textures was measured by making use of the phenomenon in which diffracted light weakens in the lubricant-covered region. It is found that grooves serve to accelerate spreading and this effect increases for deeper grooves, and also the accelerating rate becomes larger for a lubricant having a larger molecular weight or functional end-groups. In the simulations, the Monte Carlo method based on the Ising model was extended to enable us to evaluate the effect of molecular weight on the spreading of non-functional lubricant inside a groove. The validity of the newly developed simulation method was well confirmed from the agreement between the simulation and experimental results.

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Stadler, J., R. Mikulla, and H. R. Trebin. "IMD: A Software Package for Molecular Dynamics Studies on Parallel Computers." International Journal of Modern Physics C 08, no. 05 (October 1997): 1131–40. http://dx.doi.org/10.1142/s0129183197000990.

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We report on implementation and performance of the program IMD, designed for short range molecular dynamics simulations on massively parallel computers. After a short explanation of the cell-based algorithm, its extension to parallel computers as well as two variants of the communication scheme are discussed. We provide performance numbers for simulations of different sizes and compare them with values found in the literature. Finally we describe two applications, namely a very large scale simulation with more than 1.23×109 atoms, to our knowledge the largest published MD simulation up to this day and a simulation of a crack propagating in a two-dimensional quasicrystal.

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Higuchi, Mariko, and Miroslav Pinak. "1P566 Molecular dynamics simulation of clustered DNA damage site with DNA repair enzyme MutM(27. Molecular dynamics simulation,Poster Session,Abstract,Meeting Program of EABS & BSJ 2006)." Seibutsu Butsuri 46, supplement2 (2006): S288. http://dx.doi.org/10.2142/biophys.46.s288_2.

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Al-Sayegh, Rajab, and Charalampos Makatsoris. "Vision-Augmented Molecular Dynamics Simulation of Nanoindentation." Journal of Nanomaterials 2015 (2015): 1–11. http://dx.doi.org/10.1155/2015/857574.

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We present a user-friendly vision-augmented technique to carry out atomic simulation using hand gestures. The system is novel in its concept as it enables the user to directly manipulate the atomic structures on the screen, in 3D space using hand gestures, allowing the exploration and visualisation of molecular interactions at different relative conformations. The hand gestures are used to pick and place atoms on the screen allowing thereby the ease of carrying out molecular dynamics simulation in a more efficient way. The end result is that users with limited expertise in developing molecular structures can now do so easily and intuitively by the use of body gestures to interact with the simulator to study the system in question. The proposed system was tested by simulating the crystal anisotropy of crystalline silicon during nanoindentation. A long-range (Screened bond order) Tersoff potential energy function was used during the simulation which revealed the value of hardness and elastic modulus being similar to what has been found previously from the experiments. We anticipate that our proposed system will open up new horizons to the current methods on how an MD simulation is designed and executed.

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Zhang, Z. Q., D. K. Ward, Y. Xue, H. W. Zhang, and M. F. Horstemeyer. "Interfacial Characteristics of Carbon Nanotube-Polyethylene Composites Using Molecular Dynamics Simulations." ISRN Materials Science 2011 (September 25, 2011): 1–10. http://dx.doi.org/10.5402/2011/145042.

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The rate-dependent interfacial behavior between a carbon nanotube (CNT) and a polyethylene (PE) matrix is investigated using molecular dynamics (MD) simulations. Various MD simulations were set up to determine the “size” effects on the interfacial properties, such as the molecular weight, or the length of the polymer, the diameter of the CNT, and the simulation model size. The interfacial rate-dependency was probed by applying various relative sliding velocities between the CNT and the polymer. Two quantities, directly obtained from the MD simulations, described the interfacial properties: the critical interfacial shear stress (CISS) and the steady interfacial shear stress (SISS). The simulations show that the SISS was not sensitive to the simulation size. In addition, the CISS was dependent upon the combined factors of the variation in PE stiffness, induced by simulation size changes and the effect of the fixed boundaries of the simulation models. The CISS increases almost linearly with the relative sliding velocity of CNTs. Also, a linear relationship between the SISS and the CNT-sliding velocity is observed when the SISS drops below a critical value. A clear size scaling is observed as the CISS and SISS decrease with increasing CNT radius and increase with the increasing polymer chain length.

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