Molecular Simulation最新文献

{"title":"Statement of Retraction: Ir-decorated gallium nitride nanotubes as a chemical sensor for recognition of mesalamine drug: a DFT study","authors":"","doi":"10.1080/08927022.2023.2267407","DOIUrl":"https://doi.org/10.1080/08927022.2023.2267407","url":null,"abstract":"Published in Molecular Simulation (Ahead of Print, 2023)","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"37 12","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138507078","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"pH-Dependent conformational stability of SpeB from Thermus thermophilus HB8: insights from molecular dynamics simulation","authors":"Malaisamy Veerapandian, Nagarajan Hemavathy, Alagesan Karthika, Jayaraman Manikandan, Umashankar Vetrivel, Jeyaraman Jeyakanthan","doi":"10.1080/08927022.2023.2281987","DOIUrl":"https://doi.org/10.1080/08927022.2023.2281987","url":null,"abstract":"N(1)-aminopropyl agmatine ureohydrolase (SpeB) is considered an essential enzyme for the growth and survival of thermophiles, it is involved in the biosynthesis of polyamines. The present study inv...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"228 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138507108","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Effects of lattice orientation and defect degree on Si/Al solid interfacial structure and thermal resistance","authors":"Liying Wang, Jiansheng Wang, Xueling Liu, Xinli Lu","doi":"10.1080/08927022.2023.2281982","DOIUrl":"https://doi.org/10.1080/08927022.2023.2281982","url":null,"abstract":"The effect of variation in the Si/Al interface structure on the thermal properties is explored with non-equilibrium molecular dynamics method in present work, and two distinct approaches are employ...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"36 10","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-11-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138507080","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Computational and in vitro targeting of HUVECs by ARA-Linker-TGFαL3 through VEGFR2","authors":"Abdolamir Ghadaksaz, Abbas Ali Imani Fooladi, Hamideh Mahmoodzadeh Hosseini, Mohsen Amin, Fatemeh Adami Ghamsari","doi":"10.1080/08927022.2023.2281980","DOIUrl":"https://doi.org/10.1080/08927022.2023.2281980","url":null,"abstract":"Angiogenesis blockade represents a therapeutic strategy to inhibit the growth of the tumour and its progression and metastasis. Targeting the vascular endothelial growth factor receptor 2 (VEGFR2) ...","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"226 ","pages":""},"PeriodicalIF":2.1,"publicationDate":"2023-11-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"138507109","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A molecular dynamic simulation-based study on nanoscale friction stir welding between copper and aluminium","authors":"Roshan Kumar Jha, K. Vijay Reddy, Snehanshu Pal","doi":"10.1080/08927022.2023.2279135","DOIUrl":"https://doi.org/10.1080/08927022.2023.2279135","url":null,"abstract":"ABSTRACTThe primary aim of this study is to enhance our understanding of friction stir welding (FSW) at the atomic level. To accomplish this, we utilised molecular dynamics simulations to examine the nanoscale fusion welding of dissimilar metals, i.e. aluminium and copper, through the FSW method. Our particular focus was on how the rotation speed of the tool affects structural changes and defect evolution during the nanoscale FSW process. Our research findings revealed that the region subjected to frictional stirring undergoes a phase change as a result of extensive plastic deformation during the FSW operation. Notably, stacking faults and similar defects were predominantly observed on the advancing side as the tool rotated and moved into the friction stir zone. Further, investigation of atomic shear strain snapshots indicated that higher rotational speeds resulted in a broader and more scattered friction stir zone, requiring a longer recovery time compared to slower rotational speeds. Additionally, the changes in atomic concentration during FSW have been studied using displacement vectors, concentration profiles and diffusion coefficient parameters. We also conducted simulation-based tensile and shear deformation tests, which revealed that higher tool rotational speeds led to enhanced material interlocking, consequently improving the mechanical strength of the FSW joints.KEYWORDS: Dissimilar materialfriction stir weldingmolecular dynamic simulationnano welding Conflicts of interestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.Authors contribution statementAll the authors are actively involved in Conceptualisation; Data curation; Formal analysis; Investigation; Methodology; Resources; Software; Supervision; Validation; Visualisation; Writing – original manuscript draft; Writing – review & editing.Data availabilityThe raw/processed data required to reproduce these findings cannot be shared at this time because it is a part of an ongoing study.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"76 8","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134901571","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Hydrogen embrittlement of iron nanowires: investigating size and orientation dependence on loading behaviour","authors":"Liam S. Morrissey","doi":"10.1080/08927022.2023.2279136","DOIUrl":"https://doi.org/10.1080/08927022.2023.2279136","url":null,"abstract":"ABSTRACTWith the ever-increasing use and applications of nanowires it has never been more imperative to understand how environmental interactions modify their unique mechanical properties and loading behaviour. While experimental research has shown that atomic hydrogen degrades mechanical properties through hydrogen embrittlement, results are limited and often do not directly quantify the hydrogen concentration or consider small diameter nanowires. In this study, we have used molecular dynamics simulations to the study the effect of atomic hydrogen on iron nanowires with various orientations and diameters. Results demonstrate that with increasing hydrogen concentration there is a clear reduction in the elastic modulus and yield stress as compared to the hydrogen free case for all diameters and orientations considered. In addition, this reduction in mechanical properties appears to exhibit a size dependence, with larger reductions being found in nanowires with larger cross-sectional diameters. We suggest that smaller diameter nanowires, with a higher ratio of surface to bulk atoms, are more influenced by free surface atoms than lattice distortions from atomic hydrogen. As this ratio of surface to bulk atoms is decreased, the larger diameter nanowires become less affected by free surfaces and more susceptible to the effect of atomic hydrogen.KEYWORDS: Nanowireshydrogen embrittlementelastic modulus AcknowledgementsDr. Morrissey would like to acknowledge the National Sciences and Engineering Research Council of Canada for their support of the research via the Discovery Grant.Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by Natural Sciences and Engineering Research Council of Canada.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"54 47","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134902794","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Simulations of the thermodynamic properties of the helium fluid from the state-of-the-art <i>ab initio</i> potentials and their uncertainty estimation","authors":"Pan Xu, Qing-Yao Luo, Bo Dong, Bo Song","doi":"10.1080/08927022.2023.2276871","DOIUrl":"https://doi.org/10.1080/08927022.2023.2276871","url":null,"abstract":"ABSTRACTThe molecular dynamics simulation method is used to study the internal energy, pressure, isochoric heat capacity, and sound speed of helium based on the state-of-the-art ab initio potentials. The simulations cover a wide temperature and density range of (20–2000) K and (0.0005–70) molL−1. The uncertainty of simulation data are evaluated based on the uncertainty of the potential and the uncertainty of the simulation method. At temperatures below 300 K, the quantum Feynman-Hibbs modified potential and the Wigner-Kirkwood modified potential are introduced and the results are almost the same as those by the original ab initio potential. The modified potentials can not reasonably describe the quantum effects for the helium fluid at low temperatures, which become obvious below 200 K. The two-body ab initio potential is combined with the three-body ab initio potential to evaluate the influence of multi-body interactions at high densities. When the density is lower than 45 molL−1, the contribution of the three-body term to our simulation data is not significant. As a result, the three-body potential is omitted in our calculations to improve the overall computational efficiency. The thermodynamic property data of this work show agreement with the experimental data in the literature as well as the NIST Refprop 10.0 data at temperatures above 200 K and densities below 45 molL−1.KEYWORDS: Helium fluidthermodynamic propertyab initio potentialmolecular dynamicsuncertainty Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by the National Natural Science Foundation of China [grant number 51936009] and the Natural Science Basic Research Program of Shaanxi [grant number 2022JQ-393]","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"70 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135093457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Molecular dynamics study on friction of polymer material polyamide 6 (PA 6)","authors":"Xinmin Li, Zhengjie Qiu, Yonglong Wu, Feilong Li, Runzhi Zhang","doi":"10.1080/08927022.2023.2276290","DOIUrl":"https://doi.org/10.1080/08927022.2023.2276290","url":null,"abstract":"ABSTRACTThe resin material PA6 has a wide range of application in engineering due to its excellent mechanical properties. The friction behaviour of PA 6 was studied using molecular dynamics simulation method in this study. The effects of temperature, sliding speed and wear depth on the friction performance of PA6 were studied, and the surface micromorphology of PA 6 model also was analysed. The main conclusions are as follows: Within the temperature range selected in this experiment, the temperature has no significant influence on friction and surface micromorphology of PA6. As the friction speed decreases, the friction decreases slightly. The coefficient of friction increases slightly with the increase of friction speed. The greater the wear depth is, the more pronounced the ploughing and debris accumulation on the surface of PA6 is. The friction coefficient increases slightly with the increase of wear depth, but not significantly. The greater the wear depth is, the larger the friction fluctuation is.KEYWORDS: Molecular dynamics simulationPA6frictionslidingtemperature Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"118 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135679745","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Assessing the structural dynamics of the glucose-6-phosphate dehydrogenase dimer interface using molecular dynamics simulation and ligand screening using computer aided drug discovery","authors":"Naveen Eugene Louis, Muaawia Ahmed Hamza, Puteri Nur Sarah Diana Engku Baharuddin, Shamini Chandran, Nurriza Ab Latif, Mona Awad Alonazi, Joazaizulfazli Jamalis, Arjumand Warsy, Syazwani Itri Amran","doi":"10.1080/08927022.2023.2274871","DOIUrl":"https://doi.org/10.1080/08927022.2023.2274871","url":null,"abstract":"ABSTRACTGlucose-6-phosphate-dehydrogenase deficiency is the most common enzymopathy. Current therapies for G6PD deficiency are unable to treat a broad range of pathogenic variants. In this study, we assess the structural dynamics of six G6PD variants using molecular dynamics simulation to correlate their genotypic and phenotypic attributes. G6PD multimerisation is highly influenced by its ligands G6P and NADP, where the former disrupts dimer formation, and the latter facilitates tetramerisation. Results of our simulation demonstrate that the WT and a relatively stable variant (G131V), were found to have greater NADP binding occupancy and hydrogen bonds between βN sheet of each monomeric subunit, thereby increasing the stability of the dimer interface. G6PD protein structures with high structural integrity at the dimer interface were found to be compact, characterised by low radius of gyration values, and increased surface area or high solvent-accessible surface area at the tetramer salt bridge residues. Using mutational clustering methods, a critical G6PD region at the βK–βL loop was identified and may serve as a potential target for treatment. We further extend this study to identify chemical compounds that induce modulatory effects on the protein using computer aided drug discovery which warrant further studies and future testing.KEYWORDS: Glucose-6-phosphate-dehydrogenase deficiencyprotein multimerisationmolecular dynamics simulationcomputer aided drug discoverymolecular docking Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by the Fundamental Research Grant Scheme (FRGS) from the Malaysian Ministry of Higher Education (MoHE) under grant number FRGS/1/2019/SKK08/UTM/02/1 awarded to Dr Syazwani Itri Amran. This work was also supported by the Intramural Research Fund under grant number 4B363 from the Ministry of Health, Kingdom of Saudi Arabia awarded to Dr Muaawia Ahmed Hamza. We also acknowledge support from University of Technology Malaysia (UTM) under grant number 15J90. We thank Dr Goh Kian Mau for assistance through intellectual discussions about the project.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"42 3","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135325750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"DFT Study of adsorption and diffusion of CO ₂ on bimetallic surfaces","authors":"Hamideh Khodabandeh, Ali Nakhaei Pour, Ali Mohammadi","doi":"10.1080/08927022.2023.2274880","DOIUrl":"https://doi.org/10.1080/08927022.2023.2274880","url":null,"abstract":"ABSTRACTIn this work, adsorption and diffusion of CO2 on the Cu (111) surface, and Cu (111) surface modified by tungsten (W) and platinum (Pt) were studied and their electronic properties were examined using Density-functional theory (DFT) simulations. To specify the most favourable adsorption sites, the adsorption energies and distances of CO2 on various surface sites including on top, hexagonal close-packed (HCP), and bridge were calculated. The crystal orbital overlap population analysis was employed to investigate the properties and characteristics of chemical bonding. The computed Bader atomic charges of CO2 molecules on different catalyst surfaces indicated that the Cu-W alloy surface had a higher net charge transfer than other surfaces. This result suggests that the adsorption of CO2 on the Cu-W alloy surface is more powerful than on other surfaces. The outcomes indicated that the CO2 adsorption on the surfaces follows the order of Cu-W alloy > Cu-Pt alloy > Cu. Also, the diffusion on the alloy surfaces was faster than on the Cu surface, which confirms the adsorption energy.KEYWORDS: Adsorptionbimetallic surfacescopperplatinumtungsten AcknowledgmentThe authors of this work appreciate the financial support of the Ferdowsi University of Mashhad Research Council, Mashhad, Iran (Grant No. 3/58558).Disclosure statementNo potential conflict of interest was reported by the author(s).Additional informationFundingThis work was supported by Ferdowsi University of Mashhad: [grant number 3/58558].","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"33 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135325516","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}