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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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Impacts of cone-structured interface and aperiodicity on nanoscale thermal transport in Si/Ge superlattices

Pengfei JI, Yiming RONG, Yuwen ZHANG, Yong TANG

《能源前沿（英文）》 2018年 第12卷 第1期   页码 137-142 doi: 10.1007/s11708-018-0532-8

摘要： Si/Ge superlattices are promising thermoelectric materials to convert thermal energy into electric power. The nanoscale thermal transport in Si/Ge superlattices is investigated via molecular dynamics (MD) simulation in this short communication. The impact of Si and Ge interface on the cross-plane thermal conductivity reduction in the Si/Ge superlattices is studied by designing cone-structured interface and aperiodicity between the Si and Ge layers. The temperature difference between the left and right sides of the Si/Ge superlattices is set up for nonequilibrium MD simulation. The spatial distribution of temperature is recorded to examine whether the steady-state has been reached. As a crucial factor to quantify thermal transport, the temporal evolution of heat flux flowing through Si/Ge superlattices is calculated. Compared with the even interface, the cone-structured interface contributes remarkable resistance to the thermal transport, whereas the aperiodic arrangement of Si and Ge layers with unequal thicknesses has a marginal influence on the reduction of effective thermal conductivity. The interface with divergent cone-structure shows the most excellent performance of all the simulated cases, which brings a 33% reduction of the average thermal conductivity to the other Si/Ge superlattices with even, convergent cone-structured interfaces and aperiodic arrangements. The design of divergent cone-structured interface sheds promising light on enhancing the thermoelectric efficiency of Si/Ge based materials.

关键词： thermoelectric material     thermal transport     Si/Gesuperlattics     molecular dynamics (MD)    

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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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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 markers and pathogenically targeted therapy in non-small cell lung cancer

Bo PENG BA , Jinnong ZHANG MD , Jamile S. WOODS MD , Wei PENG MD, PhD

《医学前沿（英文）》 2009年 第3卷 第3期   页码 245-255 doi: 10.1007/s11684-009-0044-3

摘要： Lung cancer is one of the most common human cancers and the number one cancer killer in the United States. In general, lung cancer includes small cell lung cancer (SCLC) and non-small cell lung cancer (NSCLC), but NSCLC accounts for approximately 90% of lung cancer. The early diagnosis and therapy of lung cancer still presents a big challenge because validated screening tools, which can improve current early detection to reduce mortality from lung cancer, do not exist. Over the last decade, molecular genetic abnormalities have been described in NSCLC, including chromosomal aberrations, overexpression of oncogenes, and deletion and/or mutations in tumor suppressor genes. These molecular markers in NSCLC demonstrated close associations with the development of lung cancer such as Ras, the epidermal growth factor receptor (EGFR, or c-erbB-1), HER2 (c-erbB-2), c-Met, and Bcl-2. Therefore, this information may be applied for early cancer detection, classification, novel targeted therapy, and prognosis in NSCLC. Recent clinical data have revealed that targeted therapy might be the second-line therapy as an alternative approach. Currently, the targeted therapies are mainly focused on two lung cancer pathways, the EGFR and the vascular endothelial growth factor (VEGF) pathways. Some clinical trials are very encouraging, but some of them are not. However, these trials have not identified a subgroup of NSCLC with biomarkers. Therefore, it is very important to select NSCLC patients with biomarkers to match targeted agents so that we can further identify effectiveness of targeted therapy in the future.

关键词： lung cancer     carcinoma     non-small cell lung cancer     molecular markers     targeted therapy    

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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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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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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 targeted therapy of gynecological malignant tumors: the development and challenge, from laboratory

Pengming SUN PhD, MD , Jalid SEHOULI PhD, MD , Lihui WEI BM ,

《医学前沿（英文）》 2009年 第3卷 第3期   页码 256-264 doi: 10.1007/s11684-009-0052-3

摘要： More and more molecular drugs based on targeted therapy have been utilized in the treatment of gynecologic cancer, especially in ovarian cancer. In this article, we systematically review the current targeted therapeutic trials running in clinic. Large, randomized trials have been conducted in the treatment of ovarian cancer, endometrial cancer and cervical cancer by using small molecule, antisense, mutational gene as well as antibodies. Other planned or ongoing trials currentlytargeted at molecular markers which may play important roles in gynecological carcinogenesis andprogression suggest that combination chemotherapy with molecular targeted therapy will ultimately be an importantoption.

关键词： target therapy     gynecologic malignant tumors     clinical trail     molecular medicine    

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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

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

Impacts of cone-structured interface and aperiodicity on nanoscale thermal transport in Si/Ge superlattices

Pengfei JI, Yiming RONG, Yuwen ZHANG, Yong TANG

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

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

期刊论文

Molecular markers and pathogenically targeted therapy in non-small cell lung cancer

Bo PENG BA , Jinnong ZHANG MD , Jamile S. WOODS MD , Wei PENG MD, PhD

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

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

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

Tianwei TAN, Peiyong QIN,

期刊论文

Molecular targeted therapy of gynecological malignant tumors: the development and challenge, from laboratory

Pengming SUN PhD, MD , Jalid SEHOULI PhD, MD , Lihui WEI BM ,

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