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Lennard-Jones Potential (Lennard-Jone + potential)
Selected AbstractsMolecular dynamics simulation of self-diffusion coefficient and its relation with temperature using simple Lennard-Jones potentialHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 2 2008Li Wei-Zhong Abstract The diffusion coefficient is indispensable to chemical engineering design and research. In practical engineering and research, there is still a great lack of available data. Therefore, methods need to be developed to solve this problem. In this paper, a molecular dynamics simulation method is used to predict the self-diffusion coefficient for a simple fluid by using the Green, Kubo relation (VACF) and the Einstein relation (MSD). The simulation results are in good agreement with experimental findings except for an error of about 10%. The algorithm average of the two methods (AV) reduces the error to 7%. The relationship of the diffusion coefficient with temperature has also been simulated. According to the simulation data, whose correlation is all above 0.99, the diffusion coefficient agrees well with temperature following the Arrenhius relationship. Activation energy for self-diffusion has been calculated and the result were 1258(VACF), 1272(MSD), and 1265(AV) J/mol separately. © 2008 Wiley Periodicals, Inc. Heat Trans Asian Res, 37(2): 86,93, 2008; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20191 [source] Molecular dynamics of the generation process of double-walled carbon nanotubes from peapodsHEAT TRANSFER - ASIAN RESEARCH (FORMERLY HEAT TRANSFER-JAPANESE RESEARCH), Issue 4 2006Yasushi Shibuta Abstract The generation process of a double-walled carbon nanotube (DWNT) from a "peapod" was studied by classical molecular dynamics simulation. Starting from a peapod structure, defined by five C60 molecules inside a (10,10) single-walled carbon nanotube (SWNT), polymerized fullerenes, a peanut-like structure and an almost nanotube-like structure were obtained under suitable conditions of temperature control. The mean distance between the two layers of the DWNT agreed with an experimental report that it is larger than the interlayer spacing found in multi-walled carbon nanotubes (MWNTs). In addition, the chirality dependence of the potential energy of a DWNT on the relative chirality of its constituent tubes was examined using a 6-12 Lennard-Jones potential. It was found that the potential energy depends only on the distance between the two layers, not on the relative chiralities. © 2006 Wiley Periodicals, Inc. Heat Trans Asian Res, 35(4): 254,264, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/htj.20115 [source] Simulations of Xe@C60 collisions with graphitic filmsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 15 2008Victor V. Albert Abstract Collisions between Xe@C60 and sheets of graphite of various dimensions were simulated. A Tersoff many-body potential modeled the interactions between carbon atoms and a Lennard-Jones potential simulated the xenon-carbon interactions. The simulations were compared to experiment and with simulations which implemented other potentials. The results indicate that a relatively small graphite film can be an accurate approximation for a nearly infinite sheet of graphite. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Quantitative prediction of protein,protein binding affinity with a potential of mean force considering volume correctionPROTEIN SCIENCE, Issue 12 2009Yu Su Abstract Quantitative prediction of protein,protein binding affinity is essential for understanding protein,protein interactions. In this article, an atomic level potential of mean force (PMF) considering volume correction is presented for the prediction of protein,protein binding affinity. The potential is obtained by statistically analyzing X-ray structures of protein,protein complexes in the Protein Data Bank. This approach circumvents the complicated steps of the volume correction process and is very easy to implement in practice. It can obtain more reasonable pair potential compared with traditional PMF and shows a classic picture of nonbonded atom pair interaction as Lennard-Jones potential. To evaluate the prediction ability for protein,protein binding affinity, six test sets are examined. Sets 1,5 were used as test set in five published studies, respectively, and set 6 was the union set of sets 1,5, with a total of 86 protein,protein complexes. The correlation coefficient (R) and standard deviation (SD) of fitting predicted affinity to experimental data were calculated to compare the performance of ours with that in literature. Our predictions on sets 1,5 were as good as the best prediction reported in the published studies, and for union set 6, R = 0.76, SD = 2.24 kcal/mol. Furthermore, we found that the volume correction can significantly improve the prediction ability. This approach can also promote the research on docking and protein structure prediction. [source] The SAAP force field: Development of the single amino acid potentials for 20 proteinogenic amino acids and Monte Carlo molecular simulation for short peptides,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 13 2009Michio Iwaoka Abstract Molecular simulation by using force field parameters has been widely applied in the fields of peptide and protein research for various purposes. We recently proposed a new all-atom protein force field, called the SAAP force field, which utilizes single amino acid potentials (SAAPs) as the fundamental elements. In this article, whole sets of the SAAP force field parameters in vacuo, in ether, and in water have been developed by ab initio calculation for all 20 proteinogenic amino acids and applied to Monte Carlo molecular simulation for two short peptides. The side-chain separation approximation method was employed to obtain the SAAP parameters for the amino acids with a long side chain. Monte Carlo simulation for Met-enkephalin (CHO-Tyr-Gly-Gly-Phe-Met-NH2) by using the SAAP force field revealed that the conformation in vacuo is mainly controlled by strong electrostatic interactions between the amino acid residues, while the SAAPs and the interamino acid Lennard-Jones potentials are predominant in water. In ether, the conformation would be determined by the combination of the three components. On the other hand, the SAAP simulation for chignolin (H-Gly-Tyr-Asp-Pro-Glu-Thr-Gly-Thr-Trp-Gly-OH) reasonably reproduced a native-like ,-hairpin structure in water although the C-terminal and side-chain conformations were different from the native ones. It was suggested that the SAAP force field is a useful tool for analyzing conformations of polypeptides in terms of intrinsic conformational propensities of the single amino acid units. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] | ||||||||||