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Molecular level simulations on multi-component systems —a morphology prediction method

C. SCHMIDT, J. ULRICH

《化学科学与工程前沿（英文）》 2013年 第7卷 第1期   页码 49-54 doi: 10.1007/s11705-013-1307-8

摘要： The crystal morphology grown from a solution composed of an organic solvent, solute and additive can be predicted reliably by a computational method. Modeling the supersaturated solution as liquid phase is achieved by employing commercial software. The molecular composition of this solution is a required input parameter. The face specific diffusion coefficient of the solid (crystal surface) and liquid (solution) system is determined using the molecular dynamics procedure. The obtained diffusion coefficient is related to the specific face growth rate via the attachment energy of the pure morphology. The significant improvements are achieved in the morphology prediction because the investigation on the face growth rates in a complex growth environment (as multi-component solutions with additives) can be carried out based on the diffusion coefficients.

关键词： crystallization     morphology     molecular dynamics     solution    

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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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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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Molecular dynamics simulations of initial Pd and PdO nanocluster growth in a magnetron gas aggregation

Pascal Brault, William Chamorro-Coral, Sotheara Chuon, Amaël Caillard, Jean-Marc Bauchire, Stève Baranton, Christophe Coutanceau, Erik Neyts

《化学科学与工程前沿（英文）》 2019年 第13卷 第2期   页码 324-329 doi: 10.1007/s11705-019-1792-5

摘要： Molecular dynamics simulations are carried out for describing growth of Pd and PdO nanoclusters using the ReaxFF force field. The resulting nanocluster structures are successfully compared to those of nanoclusters experimentally grown in a gas aggregation source. The PdO structure is quasi-crystalline as revealed by high resolution transmission microscope analysis for experimental PdO nanoclusters. The role of the nanocluster temperature in the molecular dynamics simulated growth is highlighted.

关键词： molecular dynamics     cluster growth     plasma sputtering     nanocatalyst    

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Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ protein

《环境科学与工程前沿（英文）》 2023年 第17卷 第2期 doi: 10.1007/s11783-023-1615-2

摘要：

● B[a]P, nicotine and phenanthrene molecules altered the secondary structure of Aβ42.

关键词： Polycyclic aromatic hydrocarbons     Nicotine     toxicology     Aβ42 peptide     Alzheimer’s disease     Molecular dynamics simulations     Environmental pollution    

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

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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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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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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聚酰胺反渗透膜中水传递阻力的分子模拟——界面阻力和内部阻力 Article

宋阳, 魏明杰, 徐放, 汪勇

《工程（英文）》 2020年 第6卷 第5期   页码 577-584 doi: 10.1016/j.eng.2020.03.008

摘要：

在分子水平上理解水分子在聚酰胺（PA）反渗透（RO）膜中的传递阻力对于这些膜的设计、制备和应用具有非常重要的指导意义。本文通过分子模拟来计算总传递阻力，并将其分成两部分——内部阻力和界面阻力。内部阻力取决于PA层的厚度，而界面阻力则不然。基于5 nm 厚的PA层的模拟显示界面阻力对总阻力的贡献率很大（> 62%）。然而，现实世界中，对于具有200 nm PA层的RO膜，界面阻力起次要作用，其贡献率低于10%。这表明，当使用典型方法估算RO膜的传递阻力时，存在不准确的风险，因为该方法简单地将5 nm厚的PA层的总阻力进行倍增，使得界面阻力被错误放大。此外，界面阻力和内部阻力均取决于PA层的化学性质。我们的模拟显示，减少PA层中剩余羧基的数量会导致内部阻力降低，因此，可以在不牺牲离子截留的情况下改善水的渗透性，这与实验结果高度吻合。

关键词： 传递阻力     反渗透     非平衡分子动力学     水分子亲水性     建模    

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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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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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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 dynamics investigation of mechanical properties of single-layer phagraphene

Ali Hossein Nezhad SHIRAZI

《结构与土木工程前沿（英文）》 2019年 第13卷 第2期   页码 495-503 doi: 10.1007/s11709-018-0492-4

摘要： Phagraphene is a very attractive two-dimensional (2D) full carbon allotrope with very interesting mechanical, electronic, optical, and thermal properties. The objective of this study is to investigate the mechanical properties of this new graphene like 2D material. In this work, mechanical properties of phagraphene have been studied not only in the defect-free form, but also with the critical defect of line cracks, using the classical molecular dynamics simulations. Our study shows that the pristine phagraphene in zigzag direction experience a ductile behavior under uniaxial tensile loading and the nanosheet in this direction are less sensitive to temperature changes as compared to the armchair direction. We studied different crack lengths to explore the influence of defects on the mechanical properties of phagraphene. We also investigated the temperature effect on the mechanical properties of pristine and defective phagraphene. Our classical atomistic simulation results confirm that larger cracks can reduce the strength of the phagraphene. Moreover, it was shown the temperature has a considerable weakening effect on the tensile strength of phagraphene. The results of this study may be useful for the design of nano-devices using the phagraphene.

关键词： phaqraphene     mechanical properties     crack propaqation     molecular dynamics     thermal effects    

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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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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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标题 作者 时间 类型 操作

Molecular level simulations on multi-component systems —a morphology prediction method

C. SCHMIDT, J. ULRICH

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

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

期刊论文

Molecular dynamics simulations of initial Pd and PdO nanocluster growth in a magnetron gas aggregation

Pascal Brault, William Chamorro-Coral, Sotheara Chuon, Amaël Caillard, Jean-Marc Bauchire, Stève Baranton, Christophe Coutanceau, Erik Neyts

期刊论文

Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ protein

期刊论文

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

Lin ZHANG, Yan SUN

期刊论文

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

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

聚酰胺反渗透膜中水传递阻力的分子模拟——界面阻力和内部阻力

宋阳, 魏明杰, 徐放, 汪勇

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

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

Tianwei TAN, Peiyong QIN,

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 dynamics investigation of mechanical properties of single-layer phagraphene

Ali Hossein Nezhad SHIRAZI

期刊论文

Molecular dynamics simulation of diffusivity

LIU Juanfang, ZENG Danling, LI Qin, GAO Hong

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