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Atomistic understanding of interfacial processing mechanism of silicon in water environment: A ReaxFF moleculardynamics simulation

《机械工程前沿（英文）》 2021年 第16卷 第3期   页码 570-579 doi: 10.1007/s11465-021-0642-6

摘要： The interfacial wear between silicon and amorphous silica in water environment is critical in numerous applications. However, the understanding regarding the micro dynamic process is still unclear due to the limitations of apparatus. Herein, reactive force field simulations are utilized to study the interfacial process between silicon and amorphous silica in water environment, exploring the removal and damage mechanism caused by pressure, velocity, and humidity. Moreover, the reasons for high removal rate under high pressure and high velocity are elucidated from an atomic perspective. Simulation results show that the substrate is highly passivated under high humidity, and the passivation layer could alleviate the contact between the abrasive and the substrate, thus reducing the damage and wear. In addition to more Si-O-Si bridge bonds formed between the abrasive and the substrate, new removal pathways such as multibridge bonds and chain removal appear under high pressure, which cause higher removal rate and severer damage. At a higher velocity, the abrasive can induce extended tribochemical reactions and form more interfacial Si-O-Si bridge bonds, hence increasing removal rate. These results reveal the internal cause of the discrepancy in damage and removal rate under different conditions from an atomic level.

关键词： silicon     ReaxFF     molecular dynamics     friction     damage    

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Molecular dynamics simulation of diffusivity

LIU Juanfang, ZENG Danling, LI Qin, GAO Hong

《能源前沿（英文）》 2008年 第2卷 第3期   页码 359-362 doi: 10.1007/s11708-008-0039-9

摘要： Equilibrium molecular dynamics simulation was performed on water to calculate its diffusivity by adopting different potential models. The results show that the potential models have great influence on the simulated results. In addit

关键词： diffusivity     Equilibrium molecular     influence     potential    

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Effect of ligand chain length on hydrophobic charge induction chromatography revealed by molecular dynamics

Lin ZHANG, Yan SUN

《化学科学与工程前沿（英文）》 2013年 第7卷 第4期   页码 456-463 doi: 10.1007/s11705-013-1357-y

摘要： Hydrophobic charge induction chromatography (HCIC) is a mixed-mode chromatography which is advantageous for high adsorption capacity and facile elution. The effect of the ligand chain length on protein behavior in HCIC was studied. A coarse-grain adsorbent pore model established in an earlier work was modified to construct adsorbents with different chain lengths, including one with shorter ligands (CL2) and one with longer ligands (CL4). The adsorption, desorption, and conformational transition of the proteins with CL2 and CL4 were examined using molecular dynamics simulations. The ligand chain length has a significant effect on both the probability and the irreversibility of the adsorption/desorption. Longer ligands reduced the energy barrier of adsorption, leading to stronger and more irreversible adsorption, as well as a little more unfolding of the protein. The simulation results elucidated the effect of the ligand chain length, which is beneficial for the rational design of adsorbents and parameter optimization for high-performance HCIC.

关键词： adsorption     desorption     irreversibility     protein conformational transition     molecular dynamics simulation    

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Molecular dynamics simulation on DNA translocating through MoS

Daohui Zhao, Huang Chen, Yuqing Wang, Bei Li, Chongxiong Duan, Zhixian Li, Libo Li

《化学科学与工程前沿（英文）》 2021年 第15卷 第4期   页码 922-934 doi: 10.1007/s11705-020-2004-z

摘要： The emergence of MoS nanopores has provided a new avenue for high performance DNA sequencing, which is critical for modern chemical/biological research and applications. Herein, molecular dynamics simulations were performed to design a conceptual device to sequence DNA with MoS nanopores of different structures (e.g., pore rim contained Mo atoms only, S atoms only, or both Mo and S atoms), where various unfolded single-stranded DNAs (ssDNAs) translocated through the nanopores driven by transmembrane bias; the sequence content was identified by the associating ionic current. All ssDNAs adsorbed onto the MoS surface and translocated through the nanopores by transmembrane electric field in a stepwise manner, where the pause between two permeation events was long enough for the DNA fragments in the nanopore to produce well-defined ionic blockage current to deduce the DNA’s base sequence. The transmembrane bias and DNA-MoS interaction could regulate the speed of the translocation process. Furthermore, the structure (atom constitution of the nanopore rim) of the nanopore considerably regulated both the translocate process and the ionic current. Thus, MoS nanopores could be employed to sequence DNA with the flexibility to regulate the translocation process and ionic current to yield the optimal sequencing performance.

关键词： DNA sequencing     MoS2     molecular dynamics simulation     nanopore     ionic current    

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Enhanced separation of tetrafluoropropanol from water via carbon nanotubes membranes: insights from moleculardynamics simulations

《环境科学与工程前沿（英文）》 2023年 第17卷 第11期 doi: 10.1007/s11783-023-1740-y

摘要：

● MD simulations unveil the transport mechanism for TFP-water mixture through CNTs.

关键词： Fluorinated alcohol     Carbon nanotube     Molecular simulation     Fluorine modified    

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Evaluation of the compatibility between rubber and asphalt based on molecular dynamics simulation

Fucheng GUO, Jiupeng ZHANG, Jianzhong PEI, Weisi MA, Zhuang HU, Yongsheng GUAN

《结构与土木工程前沿（英文）》 2020年 第14卷 第2期   页码 435-445 doi: 10.1007/s11709-019-0603-x

摘要： Using of rubber asphalt can both promote the recycling of waste tires and improve the performance of asphalt pavement. However, the segregation of rubber asphalt caused by the poor storage stability always appears during its application. Storage stability of asphalt and rubber is related to the compatibility and also influenced by rubber content. In this study, molecular models of different rubbers and chemical fractions of asphalt were built to perform the molecular dynamics simulation. The solubility parameter and binding energy between rubber and asphalt were obtained to evaluate the compatibility between rubber and asphalt as well as the influence of rubber content on compatibility. Results show that all three kinds of rubber are commendably compatible with asphalt, where the compatibility between asphalt and cis-polybutadiene rubber (BR) is the best, followed by styrene-butadiene rubber (SBR), and natural rubber (NR) is the worst. The optimum rubber contents for BR asphalt, SBR asphalt, and NR asphalt were determined as 15%, 15%, and 20%, respectively. In addition, the upper limits of rubber contents were found as between 25% and 30%, between 20% and 25%, and between 25% and 30%, respectively.

关键词： rubber asphalt     compatibility     rubber content     molecular dynamics simulation    

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Molecular dynamics study of water diffusion in an amphiphilic block copolymer with large difference in

Yang Zhou, Phillip Choi

《化学科学与工程前沿（英文）》 2017年 第11卷 第3期   页码 440-447 doi: 10.1007/s11705-017-1626-2

摘要： Isothermal-isobaric molecular dynamics simulation was used to study the diffusion mechanism of water in polyurethane- -poly( -isopropyl acrylamide) (PU- -PNIPAm) with a hydrophobic PU/hydrophilic PNIPAm mass ratio of 1.4 to 1 at 298 K and 450 K. Here, the experimental glass transition temperature ( ) of PU is 243 K while that of PNIPAm is 383 K. Different amounts of water up to 15 wt-% were added to PU- -PNIPAm. We were able to reproduce the specific volumes and glass transition temperatures (250 K and 390 K) of PU- -PNIPAm. The computed self-diffusion coefficient of water increased exponentially with increasing water concentration at both temperatures (i.e., following the free volume model of Fujita). It suggested that water diffusion in PU- -PNIPAm depends only on its fractional free volume despite the free volume inhomogeneity. It is noted that at 298 K, PU is rubbery while PNIPAm is glassy. Regardless of temperature, radial distribution functions showed that water formed clusters with sizes in the range of 0.2–0.4 nm in PU- -PNIPAm. At low water concentrations, more clusters were found in the PU domain but at high water concentrations, more in the PNIPAm domain. It is believed that water molecules diffuse as clusters rather than as individual molecules.

关键词： molecular dynamics simulation     amphiphilic block copolymer     free volume     water diffusivity     fujita model    

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Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

《化学科学与工程前沿（英文）》 2019年 第13卷 第1期   页码 133-139 doi: 10.1007/s11705-018-1737-4

摘要： In , the global transcriptional regulatory factor CodY can interact with the promoter DNA to regulate the growth, metabolism, environmental adaptation and other biological activities of the strains. In order to study the mechanism of interaction between CodY and its target DNA, molecular docking and molecular dynamics simulations were used to explore the binding process at molecular level. Through the calculations of the free energy of binding, hydrogen bonding and energy decomposition, nine key residues of CodY were identified, corresponding to SER184, SER186, SER208, THR217, ARG218, SER219, ASN223, LYS242 and GLY243, among which SER186, ARG218 and LYS242 play a vital role in DNA binding. Our research results provide important theoretical guidance for using wet-lab methods to study and optimize the metabolic network regulated by CodY.

关键词： CodY     DNA     molecular docking     molecular dynamics    

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Advances in molecular dynamics simulation of ultra-precision machining of hard and brittle materials

Xiaoguang GUO,Qiang LI,Tao LIU,Renke KANG,Zhuji JIN,Dongming GUO

《机械工程前沿（英文）》 2017年 第12卷 第1期   页码 89-98 doi: 10.1007/s11465-017-0412-7

摘要：

Hard and brittle materials, such as silicon, SiC, and optical glasses, are widely used in aerospace, military, integrated circuit, and other fields because of their excellent physical and chemical properties. However, these materials display poor machinability because of their hard and brittle properties. Damages such as surface micro-crack and subsurface damage often occur during machining of hard and brittle materials. Ultra-precision machining is widely used in processing hard and brittle materials to obtain nanoscale machining quality. However, the theoretical mechanism underlying this method remains unclear. This paper provides a review of present research on the molecular dynamics simulation of ultra-precision machining of hard and brittle materials. The future trends in this field are also discussed.

关键词： MD simulation     ultra-precision machining     hard and brittle materials     machining mechanism     review    

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parameters to study self-healing and interface properties of crumb rubber modified asphalt based on moleculardynamics simulation

Dongliang HU, Jianzhong PEI, Rui LI, Jiupeng ZHANG, Yanshun JIA, Zepeng FAN

《结构与土木工程前沿（英文）》 2020年 第14卷 第1期   页码 109-122 doi: 10.1007/s11709-019-0579-6

摘要： The thermodynamic property of asphalt binder is changed by the addition of crumb rubber, which in turn influences the self-healing property as well as the cohesion and adhesion within the asphalt-aggregate system. This study investigated the self-healing and interface properties of crumb rubber modified asphalt (CRMA) using thermodynamic parameters based on the molecular simulation approach. The molecular models of CRMA were built with representative structures of the virgin asphalt and the crumb rubber. The aggregate was represented by SiO and Al O crystals. The self-healing capability was evaluated with the thermodynamic parameter wetting time, work of cohesion and diffusivity. The interface properties were evaluated by characterizing the adhesion capability, the debonding potential and the moisture susceptibility of the asphalt-aggregate interface. The self-healing capability of CRMA is found to decrease as the rubber content increases. The asphalt-Al O interface with higher rubber content has stronger adhesion and moisture stability. But the influence of crumb rubber on the interfacial properties of asphalt-SiO interface has no statistical significance. Comparing with the interfacial properties of the asphalt-SiO interface, the asphalt-Al O interface is found to have a stronger adhesion but a worse moisture susceptibility for its enormous thermodynamic potential for water to displace the asphalt binder.

关键词： crumb rubber modified asphalt     surface free energy     self-healing     interface properties     molecular dynamics simulation    

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Study on the gas permeabilities in styrene-butadiene rubber by molecular dynamics simulation

Hailu LIU, Xuejia DING, Jun YI, Liqun ZHANG, Sizhu WU,

《化学科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 257-262 doi: 10.1007/s11705-009-0270-x

摘要： In this research, molecular dynamics (MD)simulations were used to study the transport properties of small gas molecules in the butadiene-styrene copolymer(SBR). The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field was applied. The diffusion coefficients were obtained from MD (NVT ensemble) and the relationship between gas permeability; the chemical structure and free volume of butadiene-styrene copolymer were investigated. The results indicated that the diffusion coefficient of oxygen declined with increasing styrene content. The fraction of free volume (FFV) in butadiene-styrene copolymer was calculated. It was concluded that diffusion coefficient increased as the FFV increases, which is in accordance with the analysis of the small molecular hop through the free volume in polymer matrix. Subsequently, the glass transition temperatures of these copolymers were calculated by MD. The result showed that the glass transition temperature increased with increasing styrene content in polymer.

关键词： diffusion     atomistic simulation     permeability     chemical structure     relationship    

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styrene-butadiene-styrene copolymer on the aging resistance of asphalt: An atomistic understanding from reactive moleculardynamics simulations

《结构与土木工程前沿（英文）》 2021年 第15卷 第5期   页码 1261-1276 doi: 10.1007/s11709-021-0761-5

摘要： To reveal the potential influence of styrene-butadiene-styrene (SBS) polymer modification on the anti-aging performance of asphalt, and its mechanism, we explored the aging characteristics of base asphalt and SBS-modified asphalt by reaction force field (ReaxFF) and classical molecular dynamics simulations. The results illustrate that the SBS asphalt is more susceptible to oxidative aging than the base asphalt under oxygen-deficient conditions due to the presence of unsaturated C=C bonds in the SBS polymer. In the case of sufficient oxygen, the SBS polymer inhibits the oxidation of asphalt by restraining the diffusion of asphalt molecules. Compared with the base asphalt, the SBS asphalt exhibits a higher degree of oxidation at the early stage of pavement service and a lower degree of oxidation in the long run. In addition, SBS polymer degrades into small blocks during aging, thus counteracting the hardening of aged asphalt and partially restoring its low-temperature cracking resistance.

关键词： SBS asphalt     oxidative aging     asphalt hardening     ReaxFF     molecular dynamics    

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Mechanical responses of pristine and defective hexagonal boron-nitride nanosheets: A molecular dynamics

Mohammad SALAVATI, Arvin MOJAHEDIN, Ali Hossein Nezhad SHIRAZI

《结构与土木工程前沿（英文）》 2020年 第14卷 第3期   页码 623-631 doi: 10.1007/s11709-020-0616-5

摘要： In this work we conducted classical molecular dynamics (MD) simulation to investigate the mechanical characteristics and failure mechanism of hexagonal boron-nitride (h-BN) nanosheets. Pristine and defective structure of h-BN nanosheets were considered under the uniaxial tensile loadings at various temperatures. The defective structure contains three types of the most common initial defects in engineering materials that are known as cracks, notches (with various length/size), and point vacancy defects (with a wide range of concentration). MD simulation results demonstrate a high load-bearing capacity of extremely defective (amorphized) h-BN nanosheets. Our results also reveal that the tensile strength decline by increasing the defect content and temperature as well. Our MD results provide a comprehensive and useful vision concerning the mechanical properties of h-BN nanosheets with/without defects, which is very critical for the designing of nanodevices exploiting the exceptional physics of h-BN.

关键词： hexagonal boron-nitride     mechanical properties     crack     notch     point defects     molecular dynamics    

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Temperature difference-powered carbon nanotube bearings

Quanwen HOU, Bingyang CAO, Zengyuan GUO

《能源前沿（英文）》 2011年 第5卷 第1期   页码 49-52 doi: 10.1007/s11708-010-0111-0

摘要： Molecular dynamics simulations are conducted to study the motion of carbon nanotube-based nanobearings powered by temperature difference. When a temperature difference exists between stator nanotubes, the rotor nanotubes acquire a higher temperature, which arises from the interaction between phonon currents and nanotubes. The thermal driving force increases with the increase in temperature difference between the stators, an increase that is nearly proportional to the temperature difference. Confined by the minimum energy track, the (5, 5)@(10, 10) nanotube bearings only translate along the axis direction but without successive rotation.

关键词： temperature difference-induced motion     carbon nanotubes     nanobearing     molecular dynamics simulation    

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Introduction to the special section on the Symposium on Computational Fluid Dynamics and Molecular Simulation

Tianwei TAN, Peiyong QIN,

《化学科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 241-241 doi: 10.1007/s11705-009-0285-3

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标题 作者 时间 类型 操作

Atomistic understanding of interfacial processing mechanism of silicon in water environment: A ReaxFF moleculardynamics simulation

期刊论文

Molecular dynamics simulation of diffusivity

LIU Juanfang, ZENG Danling, LI Qin, GAO Hong

期刊论文

Effect of ligand chain length on hydrophobic charge induction chromatography revealed by molecular dynamics

Lin ZHANG, Yan SUN

期刊论文

Molecular dynamics simulation on DNA translocating through MoS

Daohui Zhao, Huang Chen, Yuqing Wang, Bei Li, Chongxiong Duan, Zhixian Li, Libo Li

期刊论文

Enhanced separation of tetrafluoropropanol from water via carbon nanotubes membranes: insights from moleculardynamics simulations

期刊论文

Evaluation of the compatibility between rubber and asphalt based on molecular dynamics simulation

Fucheng GUO, Jiupeng ZHANG, Jianzhong PEI, Weisi MA, Zhuang HU, Yongsheng GUAN

期刊论文

Molecular dynamics study of water diffusion in an amphiphilic block copolymer with large difference in

Yang Zhou, Phillip Choi

期刊论文

Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

期刊论文

Advances in molecular dynamics simulation of ultra-precision machining of hard and brittle materials

Xiaoguang GUO,Qiang LI,Tao LIU,Renke KANG,Zhuji JIN,Dongming GUO

期刊论文

parameters to study self-healing and interface properties of crumb rubber modified asphalt based on moleculardynamics simulation

Dongliang HU, Jianzhong PEI, Rui LI, Jiupeng ZHANG, Yanshun JIA, Zepeng FAN

期刊论文

Study on the gas permeabilities in styrene-butadiene rubber by molecular dynamics simulation

Hailu LIU, Xuejia DING, Jun YI, Liqun ZHANG, Sizhu WU,

期刊论文

styrene-butadiene-styrene copolymer on the aging resistance of asphalt: An atomistic understanding from reactive moleculardynamics simulations

期刊论文

Mechanical responses of pristine and defective hexagonal boron-nitride nanosheets: A molecular dynamics

Mohammad SALAVATI, Arvin MOJAHEDIN, Ali Hossein Nezhad SHIRAZI

期刊论文

Temperature difference-powered carbon nanotube bearings

Quanwen HOU, Bingyang CAO, Zengyuan GUO

期刊论文

Introduction to the special section on the Symposium on Computational Fluid Dynamics and Molecular Simulation

Tianwei TAN, Peiyong QIN,

期刊论文