Molecular Simulation最新文献

{"title":"Proposed modification to a muscle-like acid-base switchable [2](2)rotaxane for improved force delivery","authors":"Tina T. Dinh, Gloria Bazargan, Karl Sohlberg","doi":"10.1080/08927022.2023.2272635","DOIUrl":"https://doi.org/10.1080/08927022.2023.2272635","url":null,"abstract":"","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"47 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136317358","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":"Effect of methanol on the pyrolysis behaviour of kerogen by ReaxFF molecular dynamics simulations","authors":"Mingyue Yu, Jin-Hui Zhan, Xiang Li, Wen He, Xiaoxing Liu","doi":"10.1080/08927022.2023.2271080","DOIUrl":"https://doi.org/10.1080/08927022.2023.2271080","url":null,"abstract":"","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"71 2","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134907517","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 attractive inter-particle interaction on cross-transport coefficient between mass and heat in binary fluids","authors":"Tatsuma Oishi, Yuya Doi, Yuichi Masubuchi, Takashi Uneyama","doi":"10.1080/08927022.2023.2268730","DOIUrl":"https://doi.org/10.1080/08927022.2023.2268730","url":null,"abstract":"ABSTRACTIn some binary fluids, mass transport is observed under a temperature gradient. This phenomenon is called the Soret effect. In this study, we discuss the influence of inter-particle interaction. We considered equimolar binary Lennard–Jones fluids with a mass contrast, whereas the interaction was common for all the particle pairs with various cut-off lengths. We performed molecular dynamics simulations of such fluids under equilibrium to obtain the cross-transport coefficients L1q between the fluxes of mass and heat. The simulation revealed that this quantity strongly depends on the cut-off length. Further, we decomposed the heat flux into kinetic and potential contributions and calculated the cross-correlations between decomposed fluxes and the mass flux. The result indicates that the potential contribution dominates L1q, implying that the Soret coefficient is altered by the inter-particle interaction.KEYWORDS: Soret effecttransport coefficientlinear response theorybinary fluidscut-off length AcknowledgmentsThe authors thank Prof. Sasa (Kyoto University) for informing the authors of his work on the derivation of hydrodynamic equations from the Hamiltonian dynamics.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"14 7","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135265712","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 investigation of the interaction between volatile organic compounds and deep eutectic solvents","authors":"Deepak Kumar Panda, B. L. Bhargava","doi":"10.1080/08927022.2023.2268729","DOIUrl":"https://doi.org/10.1080/08927022.2023.2268729","url":null,"abstract":"ABSTRACTMixtures of tetrabutylammonium-chloride-based deep eutectic solvent (DES) and three volatile organic compounds (VOCs) – butanal, ethanol, and toluene – have been investigated using classical molecular dynamics simulations. Various structural analyses like radial and spatial distribution functions reveal the presence of specific interactions between DES components and VOCs. The interaction between the VOC and DES components depends on the nature of the former. Both ethanol and butanal have an H-bond interaction with chloride and ethylene glycol. Tetrabutylammonium cations are present above and below the ring of toluene due to the presence of π electron cloud, and toluene also forms π hydrogen bonds with ethylene glycol. The structure of DES is not significantly affected by the absorption of VOCs, which is reflected in their radial distribution functions. Components of DES become more mobile with the addition of VOCs. The interfacial region was found to be the most favourable location for the presence of VOCs.KEYWORDS: Molecular dynamicsvolatile organic compoundsdeep eutectic solventsradial distribution functionssurface composition AcknowledgmentsThe authors gratefully acknowledge NISER – Bhubaneswar for providing the computational resources.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"8 9","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"135567645","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 and integral equation study of the structure and dynamics of solid and liquid magnesium phosphide","authors":"Yenal Aydın, Seçkin D. Günay, Ünsal Akdere, Çetin Taşseven","doi":"10.1080/08927022.2023.2267681","DOIUrl":"https://doi.org/10.1080/08927022.2023.2267681","url":null,"abstract":"ABSTRACTThe static structure and self-ionic transport in solid and molten magnesium phosphide (Mg3P2) are investigated by means of the molecular dynamics simulation and the hypernetted-chain theory of liquids using a newly developed semiempirical pairwise potential. Parameters of the potential were fitted to the lattice constant and bulk modulus, and then it was tested in NVE ensemble simulation at 300 K at which X-ray powder diffraction pattern was correctly reproduced. The static structure and the dynamics of self-ion transport were investigated in NPT simulations between 300 and 1500 K. The temperature evolution of the radial distribution functions, coordination numbers, mean square displacements, self-diffusion coefficients and solid–liquid transition were established at solid and liquid phases that will be informative for the thermoelectronic, optoelectronic and energy storage applications of the magnesium phosphide.KEYWORDS: Magnesium phosphidemodel potentialstatic and dynamic propertiesmolecular dynamics simulationhypernetted-chain theory AcknowledgmentsThe authors would like to acknowledge that this paper is submitted in partial fulfilment of the requirements for PhD degree at Yildiz Technical University.Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"278 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136037945","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":"Rapid screening of gas solubility in ionic liquids using biased particle insertions with pre-sampled liquid trajectories","authors":"Ryan W. Smith, Edward J. Maginn","doi":"10.1080/08927022.2023.2268752","DOIUrl":"https://doi.org/10.1080/08927022.2023.2268752","url":null,"abstract":"ABSTRACTWe present an efficient, general-purpose variant of the Widom test particle insertion method for computing chemical potentials of gaseous solutes in fluids or porous solids. The method is implemented in the Monte Carlo molecular simulation engine Cassandra, but receiving phase configurations are independent of this process and may be pre-sampled by other molecular simulation engines such as molecular dynamics codes. Efficiency enhancements present in this method include configurational biasing and accelerated atomic overlap detection. When applied to the estimation of Henry's law constants of atomistic difluoromethane and pentafluoroethane in ionic liquids, the accelerated overlap detection results in a speedup of more than an order of magnitude compared to conventional methods without sacrificing accuracy. We found good agreement between this method and Hamiltonian replica exchange (HREX) for Henry's law constant and absorption isotherm estimation. This embarrassingly parallel method is especially well suited for screening Henry's law constants of many small gases in the same solvents, since a liquid trajectory can be reused for as many solutes as desired.KEYWORDS: Free energycell listionic liquidsWidom insertionshydrofluorocarbons AcknowledgmentsComputing resources were provided by the Center for Research Computing (CRC) at the University of Notre Dame. We thank Dr. Ryan DeFever for providing us with HREX results.Disclosure statementNo potential conflict of interest was reported by the author(s).Associated contentExample input files for LAMMPS and Cassandra simulations like those performed for this work are provided at https://github.com/MaginnGroup/widom_IL_examples.The repository for Cassandra can be found at https://github.com/MaginnGroup/Cassandra.Additional informationFundingThe authors are thankful for the financial support from the National Science Foundation via grant EFRI DChem: Next-generation Low Global Warming Refrigerants, Award No. 2029354.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"56 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136032516","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":"Modulation of ion transport through nanopores in water desalination: a molecular dynamics study","authors":"Lanlan Qin, Haiou Huang, Jian Zhou","doi":"10.1080/08927022.2023.2268205","DOIUrl":"https://doi.org/10.1080/08927022.2023.2268205","url":null,"abstract":"ABSTRACTA good understanding of ion transport mechanisms through nanopores is an important issue for the development of advanced water desalination technologies. We use the molecular dynamics simulation method to systematically investigate the translation dynamics of ions through nanopores in the water desalination process by designing four kinds of nano-membranes based on carbon nanomaterials. Results indicate that circular-shaped pore exhibits better water permeability, nevertheless, the slit pore has a lower resistance due to the larger pore area; nanochannel membranes increase the residence time of ions. Fluorination induces more ordered ionic hydration structures, and enhances Na + -Cl- ion pair association. -OH groups replace partial ionic hydration water molecules and facilitate ions transport into membranes. The -NH3+, -COO- groups can strongly adsorb the oppositely charged ions, and substantially slow down ion dynamics. Functionalisation within nanochannel interior can further enhance interfacial friction and transport resistance, even causing pore blocking by charged groups. The fluorinated nanochannel membrane demonstrates complete rejection of ions with a water permeability coefficient of 1.88 × 104 L·m−2·h−1·bar−1, breaking the permeability-selectivity trade-off. This study indicates that ion transport in nanopores could be finely modulated to obtain enhanced performance in water desalination.KEYWORDS: Ion transportnanoporemolecular dynamics simulationwater desalinationnano-membrane AcknowledgementsLanlan Qin: Methodology, software, validation, formal analysis, investigation, data curation, writing – original draft, visualization and funding acquisition. Haiou Huang: Resources and writing – review and editing. Jian Zhou: Conceptualization, resources, writing – review and editing, supervision, project administration and funding acquisition.Disclosure statementNo potential conflict of interest was reported by the authors.Data availability statementThe data that support the findings of this study are available from the corresponding author upon reasonable request.Additional informationFundingThis work was supported by the Guangzhou Basic and Applied Basic Research Foundation (2023A04J1363), the GuangDong Basic and Applied Basic Research Foundation (2022A1515010876) and the National Natural Science Foundation of China (No. 22378134).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136032830","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":"Effect of sliding velocity on the nanoscale friction behaviour of articular cartilage contact interface: insights from all-atom molecular dynamics investigation","authors":"Abhinava Chatterjee, Sujeet K. Sinha, Devendra K. Dubey","doi":"10.1080/08927022.2023.2252101","DOIUrl":"https://doi.org/10.1080/08927022.2023.2252101","url":null,"abstract":"ABSTRACTThis study employs molecular dynamics simulations to explore nanoscale friction behaviour as a function of varying loading and sliding speeds on a developed top-layer articular cartilage contact interface atomistic model. To investigate nanotribological behaviour, sliding speed variations on the normal force, friction force, non-bonded interaction energy and interface temperature is obtained at the inter-cartilage interface. Analysis conducted at high velocity in a simplified tissue-like hydrated environment revealed ice-like dynamic smooth sliding behaviour of protein chains when cartilage interfaces are even 3.8 Å apart. With an increase in velocity, the coefficient of friction (COF) increases significantly in a hydrated environment. Additionally, at lower loads, the effect of sliding velocity is more pronounced than at higher loads. However, results show that articular cartilage adapts to higher load and speed sliding conditions exhibiting lower friction (COF-0.03–1.17) by means of interfacial water rearrangements and protein side-chain non-bonded interactions reducing heavy shear deformation. This is attributed to an alteration in the load-bearing and friction mechanism owing to water rearrangement and adsorption at nanoconfined biointerfaces. This study provides mechanistic insights into friction mechanisms at the cartilage interface which could lead to wear-like conditions under physiological sliding contact conditions, thereby facilitating the design of better implants.KEYWORDS: Articular cartilagenanomechanicsbiotribologysliding velocity dependenceatomistic simulations Disclosure statementNo potential conflict of interest was reported by the author(s).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"49 43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136033290","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":"Probing the mechanical and deformation behaviour of CNT-reinforced AlCoCrFeNi high-entropy alloy – a molecular dynamics approach","authors":"Subrata Barman, Sudip Dey","doi":"10.1080/08927022.2023.2268184","DOIUrl":"https://doi.org/10.1080/08927022.2023.2268184","url":null,"abstract":"ABSTRACTThis present study investigates the mechanical and deformation behaviour of pristine and carbon nanotube (CNT)-reinforced AlCoCrFeNi high-entropy alloys (HEAs) using molecular dynamics (MD) simulations. The results reveal that an increase in the atomic fraction of Al in pristine AlCoCrFeNi HEAs leads to reduced mechanical behaviour. The mechanical behaviour of the pristine AlCoCrFeNi HEAs notably improves following CNT reinforcement, particularly when using CNT with higher chirality. As the chirality of the CNT increases from (6,6) to (15,15), Young's modulus, yield stress, and toughness of the (15,15) CNT-Al20CoCrFeNi HEA enhance by 17.34%, 29.44%, and 44.44% compared to the (6,6) CNT – Al20CoCrFeNi HEA. HEAs with lower Al fractions experience more substantial stress drops due to rapid structural changes. CNT reinforcement, particularly with higher chirality, decelerates this structural transformation, enhancing yield strength greatly. The analysis of the dislocation evolution revealed that the CNT-reinforced HEA exhibits higher dislocation density compared to the pristine HEA, indicating strain hardening from CNT reinforcement. Furthermore, examination of atomic shear strain reveals confined deformation along shear bands in CNT-reinforced HEAs, leading to the deformation and eventual fracture of CNTs. This study provides valuable insights for enhancing the mechanical behaviour of CNT-reinforced AlCoCrFeNi HEAs, aiding in their design and development.KEYWORDS: AlCoCrFeNihigh-entropy alloyscarbon nanotube (CNT)molecular dynamics (MD)uniaxial tensile loading Disclosure statementNo potential conflict of interest was reported by the author(s).Data availability statementData will be made available from the corresponding author, upon reasonable request.Additional informationFundingThis work was supported by Ministry of Education, India.","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"22 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"136013800","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":"Effect of twin boundary spacing on the mechanical properties of nano-columnar crystalline Cu-Ni alloy","authors":"Xuefeng Lu, Xu Yang, Wei Zhang, Xin Guo, Junqiang Ren, Hongtao Xue, Junchen Li, Fu Ling Tang","doi":"10.1080/08927022.2023.2264941","DOIUrl":"https://doi.org/10.1080/08927022.2023.2264941","url":null,"abstract":"ABSTRACTNanotwinned exist in crystals as coherent interfaces with low interfacial energy, which can not only improve the strength of metal materials, but also increase the ductility. In this manuscript, we have performed molecular dynamics simulations of the mechanical properties of a nano-columnar crystalline Cu-Ni alloy with different twin boundary spacing. It is found that the model without twin has a stacking fault tetrahedron composed of stair-rod dislocations, which results in a small change in dislocation density at the later stage of deformation, and the average stress after yielding is lower than that of the model with twin. During the deformation process, with the increase of Other atoms, the dislocation slip barrier is enhanced, the tensile strength is increased, and the yield phenomenon is delayed, which is more obvious with the decrease of twin boundary spacing. The dislocation density decreases with the decrease of the spacing of the twin boundary, and the dislocation segments become shorter. When the twin boundary spacing is 0.625 nm, the tensile strength is increased by about 71% compared with the model without twin structure.KEYWORDS: Nanotwinnedmechanical propertiesmolecular dynamicsCu-Ni alloy Disclosure statementThe 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.Additional informationFundingThe work was supported by Local Science and Technology Development Fund Projects Guided by the Central Government of China (grant number 23ZYQB300), the National Key R&D Program of China (grant numbers 2017YFA0700701, 2017YFA0700703), National Natural Science Foundation of China (grant number 52061025), Key Research Program of Education Department of Gansu Province (grant number GSSYLXM-03).","PeriodicalId":18863,"journal":{"name":"Molecular Simulation","volume":"105 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2023-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134973677","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}