首页 > 最新文献

Molecular Simulation最新文献

英文 中文
Effects of lattice orientation and defect degree on Si/Al solid interfacial structure and thermal resistance 晶格取向和缺陷程度对Si/Al固体界面结构和热阻的影响
IF 2.1 4区 化学 Q2 Mathematics Pub Date : 2023-11-16 DOI: 10.1080/08927022.2023.2281982
Liying Wang, Jiansheng Wang, Xueling Liu, Xinli Lu
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...
本文采用非平衡分子动力学方法探讨了Si/Al界面结构的变化对热性能的影响,采用了两种不同的方法。
{"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":null,"pages":null},"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}
引用次数: 0
Computational and in vitro targeting of HUVECs by ARA-Linker-TGFαL3 through VEGFR2 ara - linker - tgf - l3通过VEGFR2对huvec进行计算和体外靶向
IF 2.1 4区 化学 Q2 Mathematics Pub Date : 2023-11-15 DOI: 10.1080/08927022.2023.2281980
Abdolamir Ghadaksaz, Abbas Ali Imani Fooladi, Hamideh Mahmoodzadeh Hosseini, Mohsen Amin, Fatemeh Adami Ghamsari
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) ...
血管生成阻断是一种抑制肿瘤生长及其进展和转移的治疗策略。靶向血管内皮生长因子受体2 (VEGFR2)…
{"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":null,"pages":null},"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}
引用次数: 0
A molecular dynamic simulation-based study on nanoscale friction stir welding between copper and aluminium 基于分子动力学模拟的纳米级铜铝搅拌摩擦焊接研究
4区 化学 Q2 Mathematics Pub Date : 2023-11-14 DOI: 10.1080/08927022.2023.2279135
Roshan Kumar Jha, K. Vijay Reddy, Snehanshu Pal
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).
摘要本研究的主要目的是在原子水平上提高我们对搅拌摩擦焊接(FSW)的认识。为了实现这一目标,我们利用分子动力学模拟来研究不同金属(即铝和铜)的纳米级熔焊,通过FSW方法。我们特别关注的是工具的转速如何影响纳米级FSW过程中的结构变化和缺陷演变。我们的研究结果表明,在FSW运行过程中,由于广泛的塑性变形,受摩擦搅拌的区域发生了相变。值得注意的是,当刀具旋转并进入搅拌摩擦区时,在前进侧主要观察到堆积缺陷和类似缺陷。此外,对原子剪切应变快照的研究表明,较高的转速导致摩擦搅拌区更宽、更分散,与较慢的转速相比,需要更长的恢复时间。此外,还利用位移矢量、浓度分布和扩散系数等参数研究了FSW过程中原子浓度的变化。我们还进行了基于模拟的拉伸和剪切变形测试,结果表明,更高的刀具转速可以增强材料联锁,从而提高FSW接头的机械强度。关键词:异种材料搅拌摩擦焊分子动力学模拟纳米焊接利益冲突作者声明,他们没有已知的竞争经济利益或个人关系,可能会影响本文所报道的工作。作者贡献声明所有作者都积极参与了概念化;数据管理;正式的分析;调查;方法;资源;软件;监督;验证;可视化;写作-原稿初稿;写作-审查和编辑。数据可用性再现这些发现所需的原始/处理数据目前不能共享,因为它是正在进行的研究的一部分。披露声明作者未报告潜在的利益冲突。
{"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":null,"pages":null},"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}
引用次数: 0
Hydrogen embrittlement of iron nanowires: investigating size and orientation dependence on loading behaviour 铁纳米线的氢脆:研究尺寸和取向对加载行为的依赖
4区 化学 Q2 Mathematics Pub Date : 2023-11-14 DOI: 10.1080/08927022.2023.2279136
Liam S. Morrissey
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.
摘要随着纳米线的使用和应用的不断增加,了解环境相互作用如何改变纳米线独特的机械性能和负载行为变得前所未有的迫切。虽然实验研究表明,原子氢通过氢脆降低机械性能,但结果是有限的,通常没有直接量化氢浓度或考虑小直径纳米线。在本研究中,我们利用分子动力学模拟研究了原子氢对不同取向和直径的铁纳米线的影响。结果表明,与考虑的所有直径和方向的无氢情况相比,随着氢浓度的增加,弹性模量和屈服应力明显降低。此外,这种机械性能的降低似乎与尺寸有关,在横截面直径较大的纳米线中发现了更大的降低。我们认为,较小直径的纳米线,具有较高的表面原子与体原子的比例,受自由表面原子的影响比氢原子的晶格畸变更大。随着表面原子与体积原子的比例降低,直径较大的纳米线受自由表面的影响较小,更容易受到氢原子的影响。关键词:纳米线氢脆弹性模量Morrissey要感谢加拿大国家科学与工程研究委员会通过发现基金对这项研究的支持。披露声明作者未报告潜在的利益冲突。本研究得到了加拿大自然科学与工程研究委员会的支持。
{"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":null,"pages":null},"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}
引用次数: 0
Simulations of the thermodynamic properties of the helium fluid from the state-of-the-art ab initio potentials and their uncertainty estimation 从最先进的从头算势及其不确定度估计的氦流体热力学性质的模拟
4区 化学 Q2 Mathematics Pub Date : 2023-11-10 DOI: 10.1080/08927022.2023.2276871
Pan Xu, Qing-Yao Luo, Bo Dong, Bo Song
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]
摘要基于最先进的从头算势,采用分子动力学模拟方法研究了氦的内能、压强、等时热容和声速。模拟覆盖了(20-2000)K和(0.0005-70)molL−1的温度和密度范围。从势的不确定性和仿真方法的不确定性两个方面对仿真数据的不确定性进行了评价。在低于300 K的温度下,引入了量子Feynman-Hibbs修正势和Wigner-Kirkwood修正势,结果与原始从头算势基本一致。修正势不能合理地描述氦流体在低温下的量子效应,在200 K以下变得明显。将二体从头算势与三体从头算势相结合,评价了高密度下多体相互作用的影响。当密度低于45 mol / l−1时,三体项对模拟数据的贡献不显著。因此,我们在计算中省略了三体势,以提高整体的计算效率。在温度高于200 K,密度低于45 molL−1时,本工作的热力学性质数据与文献中的实验数据以及NIST Refprop 10.0数据一致。关键词:氦流体热力学性质,初始计算,潜在分子动力学,不确定性披露声明作者未报告潜在的利益冲突。基金资助:国家自然科学基金项目[批准号:51936009]和陕西省自然科学基础研究计划项目[批准号:2022JQ-393]
{"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":null,"pages":null},"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}
引用次数: 0
Molecular dynamics study on friction of polymer material polyamide 6 (PA 6) 高分子材料聚酰胺6 (pa6)摩擦的分子动力学研究
4区 化学 Q2 Mathematics Pub Date : 2023-11-06 DOI: 10.1080/08927022.2023.2276290
Xinmin Li, Zhengjie Qiu, Yonglong Wu, Feilong Li, Runzhi Zhang
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).
摘要树脂材料PA6因其优异的力学性能在工程上有着广泛的应用。本文采用分子动力学模拟方法研究了pa6的摩擦行为。研究了温度、滑动速度和磨损深度对PA6摩擦性能的影响,并分析了PA6模型的表面微观形貌。主要结论如下:在本实验选择的温度范围内,温度对PA6的摩擦和表面微观形貌没有显著影响。随着摩擦速度的减小,摩擦力略有减小。随着摩擦速度的增加,摩擦系数略有增加。磨损深度越大,PA6表面的犁耕和碎屑堆积越明显。随着磨损深度的增加,摩擦系数略有增加,但不显著。磨损深度越大,摩擦波动越大。关键词:分子动力学模拟pa6摩擦滑动温度披露声明作者未报告潜在利益冲突。
{"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":null,"pages":null},"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}
引用次数: 0
Assessing the structural dynamics of the glucose-6-phosphate dehydrogenase dimer interface using molecular dynamics simulation and ligand screening using computer aided drug discovery 利用分子动力学模拟和计算机辅助药物发现的配体筛选评估葡萄糖-6-磷酸脱氢酶二聚体界面的结构动力学
4区 化学 Q2 Mathematics Pub Date : 2023-11-01 DOI: 10.1080/08927022.2023.2274871
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
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.
葡萄糖-6-磷酸脱氢酶缺乏症是最常见的酶病。目前针对G6PD缺乏症的治疗方法无法治疗广泛的致病变异。在这项研究中,我们使用分子动力学模拟来评估6种G6PD变异的结构动力学,以关联它们的基因型和表型属性。G6PD的聚合受到其配体G6P和NADP的高度影响,前者破坏二聚体的形成,后者促进四聚体的形成。我们的模拟结果表明,WT和相对稳定的变体(G131V)被发现具有更大的NADP结合占用率和每个单体亚基βN片之间的氢键,从而增加了二聚体界面的稳定性。在二聚体界面处具有高结构完整性的G6PD蛋白结构紧凑,具有低旋转半径值的特点,并且在四聚体盐桥残基处增加表面积或高溶剂可及表面积。利用突变聚类方法,在βK -βL环上发现了一个关键的G6PD区域,可能是治疗的潜在靶点。我们进一步扩展了这项研究,利用计算机辅助药物发现来识别诱导蛋白质调节作用的化合物,这需要进一步的研究和未来的测试。关键词:葡萄糖-6-磷酸脱氢酶缺陷蛋白多聚分子动力学模拟计算机辅助药物发现分子对接披露声明作者未报告潜在利益冲突。本研究得到马来西亚高等教育部(MoHE)基础研究资助计划(FRGS)的支持,资助号为FRGS/1/2019/SKK08/UTM/02/1,授予Syazwani Itri Amran博士。这项工作还得到了校内研究基金的支持,赠款编号为4B363,由沙特阿拉伯王国卫生部授予muawia Ahmed Hamza博士。我们也感谢马来西亚科技大学(UTM)的资助,资助号为15J90。我们感谢吴建茂博士通过对项目的理智讨论提供的帮助。
{"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":null,"pages":null},"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}
引用次数: 0
DFT Study of adsorption and diffusion of CO 2 on bimetallic surfaces 二氧化碳在双金属表面吸附和扩散的DFT研究
4区 化学 Q2 Mathematics Pub Date : 2023-11-01 DOI: 10.1080/08927022.2023.2274880
Hamideh Khodabandeh, Ali Nakhaei Pour, Ali Mohammadi
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].
摘要本文研究了CO2在Cu(111)表面和钨(W)和铂(Pt)改性Cu(111)表面的吸附和扩散,并利用密度泛函理论(DFT)模拟研究了它们的电子性能。为了确定最有利的吸附位点,计算了CO2在不同表面位点上的吸附能和吸附距离,包括顶部、六方密装(HCP)和桥。采用晶体轨道重叠居群分析方法研究了其化学键的性质和特点。计算不同催化剂表面CO2分子的Bader原子电荷表明,Cu-W合金表面比其他表面具有更高的净电荷转移。结果表明,Cu-W合金表面对CO2的吸附比其他表面更强。结果表明,CO2在表面的吸附顺序为Cu- w合金> Cu- pt合金> Cu。合金表面的扩散速度比Cu表面快,证实了吸附能的存在。本文作者感谢伊朗马什哈德Ferdowsi大学马什哈德研究委员会(Grant No. 3/58558)的资助。披露声明作者未报告潜在的利益冲突。本研究由马什哈德Ferdowsi大学资助:[资助号3/58558]。
{"title":"DFT Study of adsorption and diffusion of CO <sub>2</sub> 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":null,"pages":null},"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}
引用次数: 0
Proposed modification to a muscle-like acid-base switchable [2](2)rotaxane for improved force delivery 提出了一种类似肌肉的酸碱可切换[2](2)轮烷的修改,以改善力的传递
4区 化学 Q2 Mathematics Pub Date : 2023-10-27 DOI: 10.1080/08927022.2023.2272635
Tina T. Dinh, Gloria Bazargan, Karl Sohlberg
{"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":null,"pages":null},"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}
引用次数: 0
Effect of methanol on the pyrolysis behaviour of kerogen by ReaxFF molecular dynamics simulations ReaxFF分子动力学模拟甲醇对干酪根热解行为的影响
4区 化学 Q2 Mathematics Pub Date : 2023-10-26 DOI: 10.1080/08927022.2023.2271080
Mingyue Yu, Jin-Hui Zhan, Xiang Li, Wen He, Xiaoxing Liu
{"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":null,"pages":null},"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}
引用次数: 0
期刊
Molecular Simulation
全部 Acc. Chem. Res. ACS Applied Bio Materials ACS Appl. Electron. Mater. ACS Appl. Energy Mater. ACS Appl. Mater. Interfaces ACS Appl. Nano Mater. ACS Appl. Polym. Mater. ACS BIOMATER-SCI ENG ACS Catal. ACS Cent. Sci. ACS Chem. Biol. ACS Chemical Health & Safety ACS Chem. Neurosci. ACS Comb. Sci. ACS Earth Space Chem. ACS Energy Lett. ACS Infect. Dis. ACS Macro Lett. ACS Mater. Lett. ACS Med. Chem. Lett. ACS Nano ACS Omega ACS Photonics ACS Sens. ACS Sustainable Chem. Eng. ACS Synth. Biol. Anal. Chem. BIOCHEMISTRY-US Bioconjugate Chem. BIOMACROMOLECULES Chem. Res. Toxicol. Chem. Rev. Chem. Mater. CRYST GROWTH DES ENERG FUEL Environ. Sci. Technol. Environ. Sci. Technol. Lett. Eur. J. Inorg. Chem. IND ENG CHEM RES Inorg. Chem. J. Agric. Food. Chem. J. Chem. Eng. Data J. Chem. Educ. J. Chem. Inf. Model. J. Chem. Theory Comput. J. Med. Chem. J. Nat. Prod. J PROTEOME RES J. Am. Chem. Soc. LANGMUIR MACROMOLECULES Mol. Pharmaceutics Nano Lett. Org. Lett. ORG PROCESS RES DEV ORGANOMETALLICS J. Org. Chem. J. Phys. Chem. J. Phys. Chem. A J. Phys. Chem. B J. Phys. Chem. C J. Phys. Chem. Lett. Analyst Anal. Methods Biomater. Sci. Catal. Sci. Technol. Chem. Commun. Chem. Soc. Rev. CHEM EDUC RES PRACT CRYSTENGCOMM Dalton Trans. Energy Environ. Sci. ENVIRON SCI-NANO ENVIRON SCI-PROC IMP ENVIRON SCI-WAT RES Faraday Discuss. Food Funct. Green Chem. Inorg. Chem. Front. Integr. Biol. J. Anal. At. Spectrom. J. Mater. Chem. A J. Mater. Chem. B J. Mater. Chem. C Lab Chip Mater. Chem. Front. Mater. Horiz. MEDCHEMCOMM Metallomics Mol. Biosyst. Mol. Syst. Des. Eng. Nanoscale Nanoscale Horiz. Nat. Prod. Rep. New J. Chem. Org. Biomol. Chem. Org. Chem. Front. PHOTOCH PHOTOBIO SCI PCCP Polym. Chem.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1