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Mechanism of ethanol/water reverse separation through a functional graphene membrane: a molecular simulation

《化学科学与工程前沿（英文）》 2023年 第17卷 第3期   页码 347-357 doi: 10.1007/s11705-022-2246-z

摘要： Reverse-selective membranes have attracted considerable interest for bioethanol production. However, to date, the reverse-separation performance of ethanol/water is poor and the separation mechanism is unclear. Graphene-based membranes with tunable apertures and functional groups have shown substantial potential for use in molecular separation. Using molecular dynamics simulations, for the first time, we reveal two-way selectivity in ethanol/water separation through functional graphene membranes. Pristine graphene (PG) exhibits reverse-selective behavior with higher ethanol fluxes than water, resulting from the preferential adsorption for ethanol. Color flow mappings show that this ethanol-permselective process is initiated by the presence of ethanol-enriched and water-barren pores; this has not been reported in previous studies. In contrast, water molecules are preferred for hydroxylated graphene membranes because of the synergistic effects of molecular sieving and functional-group attraction. A simulation of the operando condition shows that the PG membrane with an aperture size of 3.8 Å achieves good separation performance, with an ethanol/water separation factor of 34 and a flux value of 69.3 kg∙m‒2∙h‒1∙bar‒1. This study provides new insights into the reverse-selective mechanism of porous graphene membranes and a new avenue for efficient biofuel production.

关键词： reverse separation     graphene membrane     ethanol/water separation     molecular simulation    

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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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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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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 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 molecular

《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 size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

《化学科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 250-256 doi: 10.1007/s11705-009-0281-7

摘要： Two kinds of heavy oils were fractionated into eight fractions by Liquid-Solid Adsorption Chromatography, respectively, and samples were collected to measure properties. According to the elemental analysis, molecular weight and H-NMR data, average molecular structures of polycyclic aromatic and heavy resin were constructed with improved Brown-Ladner (B-L) method and several corrections. And then, the most stable conformations of polycyclic aromatic and heavy resin in vacuum and toluene solution were obtained by molecular dynamic simulation, and the molecular size was gotten via the radius of gyration analysis. The results showed that the radius of gyration of polycyclic aromatic and heavy resin was 0.55–0.70 nm in vacuum and 0.60–0.90 nm in toluene solution. With molecular weight increasing, the molecular size in vacuum and toluene solution also increased. Due to the swelling behavior of solvent, the alkyl side chains of heavy oil molecule in solution were more stretched. Thus, the molecular size in toluene solution was larger than that in vacuum.

关键词： dynamic simulation     molecular dynamic     behavior     molecule     Adsorption Chromatography    

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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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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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Integration of molecular dynamic simulation and free volume theory for modeling membrane VOC/gas separation

Bo Chen, Yan Dai, Xuehua Ruan, Yuan Xi, Gaohong He

《化学科学与工程前沿（英文）》 2018年 第12卷 第2期   页码 296-305 doi: 10.1007/s11705-018-1701-3

摘要： Gas membrane separation process is highly unpredictable due to interacting non-ideal factors, such as composition/pressure-dependent permeabilities and real gas behavior. Although molecular dynamic (MD) simulation can mimic those complex effects, it cannot precisely predict bulk properties due to scale limitations of calculation algorithm. This work proposes a method for modeling a membrane separation process for volatile organic compounds by combining the MD simulation with the free volume theory. This method can avoid the scale-up problems of the MD method and accurately simulate the performance of membranes. Small scale MD simulation and pure gas permeation data are employed to correlate pressure-irrelevant parameters for the free volume theory; by this approach, the microscopic effects can be directly linked to bulk properties (non-ideal permeability), instead of being fitted by a statistical approach. A lab-scale hollow fiber membrane module was prepared for the model validation and evaluation. The comparison of model predictions with experimental results shows that the deviations of product purity are reduced from 10% to less than 1%, and the deviations of the permeate and residue flow rates are significantly reduced from 40% to 4%, indicating the reliability of the model. The proposed method provides an efficient tool for process engineering to simulate the membrane recovery process.

关键词： membrane vapor separation     membrane process modeling     process engineering     free volume theory     volatile organic compound    

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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 dynamic simulation on the conformation of mouse muscle type nAChR

Shengai SUN, Rilei YU, Yanhui ZHANG, Yanni LI,

《化学科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 348-352 doi: 10.1007/s11705-009-0284-4

摘要： A mouse muscle type nAChR model ((α1)βδγ) was built based on the cryoelectron microscopic structure of intact nAChR and the high resolution crystal structure of nAChR-α1 subunit. The conformation of the pentameric nAChR model was investigated by molecular dynamic simulation. The function of water molecule in the hydrophilic interior was clarified. The reason for Tyr127 showing two alternative conformations was discussed in detail.

关键词： pentameric     hydrophilic     Tyr127     cryoelectron microscopic     conformation    

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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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mechanism of carbon group nanofluids on grinding interface under minimum quantity lubrication based on moleculardynamic simulation

《机械工程前沿（英文）》 2023年 第18卷 第1期 doi: 10.1007/s11465-022-0733-z

摘要： Carbon group nanofluids can further improve the friction-reducing and anti-wear properties of minimum quantity lubrication (MQL). However, the formation mechanism of lubrication films generated by carbon group nanofluids on MQL grinding interfaces is not fully revealed due to lack of sufficient evidence. Here, molecular dynamic simulations for the abrasive grain/workpiece interface were conducted under nanofluid MQL, MQL, and dry grinding conditions. Three kinds of carbon group nanoparticles, i.e., nanodiamond (ND), carbon nanotube (CNT), and graphene nanosheet (GN), were taken as representative specimens. The [BMIM]BF4 ionic liquid was used as base fluid. The materials used as workpiece and abrasive grain were the single-crystal Ni–Fe–Cr series of Ni-based alloy and single-crystal cubic boron nitride (CBN), respectively. Tangential grinding force was used to evaluate the lubrication performance under the grinding conditions. The abrasive grain/workpiece contact states under the different grinding conditions were compared to reveal the formation mechanism of the lubrication film. Investigations showed the formation of a boundary lubrication film on the abrasive grain/workpiece interface under the MQL condition, with the ionic liquid molecules absorbing in the groove-like fractures on the grain wear’s flat face. The boundary lubrication film underwent a friction-reducing effect by reducing the abrasive grain/workpiece contact area. Under the nanofluid MQL condition, the carbon group nanoparticles further enhanced the tribological performance of the MQL technique that had benefited from their corresponding tribological behaviors on the abrasive grain/workpiece interface. The behaviors involved the rolling effect of ND, the rolling and sliding effects of CNT, and the interlayer shear effect of GN. Compared with the findings under the MQL condition, the tangential grinding forces could be further reduced by 8.5%, 12.0%, and 14.1% under the diamond, CNT, and graphene nanofluid MQL conditions, respectively.

关键词： grinding     minimum quantity lubrication     carbon group nanofluid     tribological mechanism    

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水泥基材料及其性能的分子模拟研究 Review

Ashraf A. Bahraq, Mohammed A. Al-Osta, Omar S. Baghabra Al-Amoudi, I.B. Obot,Mohammed Maslehuddin, Habib-ur-Rehman Ahmed, Tawfik A. Saleh

《工程（英文）》 2022年 第15卷 第8期   页码 165-178 doi: 10.1016/j.eng.2021.06.023

摘要：

Hydrated cement is one of the complex composite systems due to the presence of multi-scale phases with varying morphologies. Calcium silicate hydrate (C–S–H), which is the principal binder phase in the hydrated cement, is responsible for the stiffness, strength, and durability of Portland cement concrete. To understand the mechanical and durability behavior of concrete, it is important to investigate the interactions of hydrated cement phases with other materials at the nanoscale. In this regard, the molecular simulation of cement-based materials is an effective approach to study the properties and interactions of the cement system at the fundamental scale. Recently, many studies have been published regarding atomistic simulations to investigate the cement phases to define/explain the microscopic physical and chemical properties, thereby improving the macroscopic performance of hardened binders. The research in molecular simulation of cementitious systems involves researchers with multidisciplinary backgrounds, mainly in two areas: ① cement chemistry, where the hydration reactions govern most of the chemical and physical properties at the atomic scale; and ② computational materials science and engineering, where the bottom-up approach is required. The latter approach is still in its infancy, and as such, a study of the prevailing knowledge is useful, namely through an exhaustive literature review. This state-of-the-art report provides a comprehensive survey on studies that were conducted in this area and cites the important findings.

关键词： Atomistic simulation     Molecular dynamics     Cement phases     Hydration products     Nanoengineering    

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标题 作者 时间 类型 操作

Mechanism of ethanol/water reverse separation through a functional graphene membrane: a molecular simulation

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

Molecular dynamics simulation of diffusivity

LIU Juanfang, ZENG Danling, LI Qin, GAO Hong

期刊论文

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

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 molecular

期刊论文

Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

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

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

Integration of molecular dynamic simulation and free volume theory for modeling membrane VOC/gas separation

Bo Chen, Yan Dai, Xuehua Ruan, Yuan Xi, Gaohong He

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 dynamic simulation on the conformation of mouse muscle type nAChR

Shengai SUN, Rilei YU, Yanhui ZHANG, Yanni LI,

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

mechanism of carbon group nanofluids on grinding interface under minimum quantity lubrication based on moleculardynamic simulation

期刊论文

水泥基材料及其性能的分子模拟研究

Ashraf A. Bahraq, Mohammed A. Al-Osta, Omar S. Baghabra Al-Amoudi, I.B. Obot,Mohammed Maslehuddin, Habib-ur-Rehman Ahmed, Tawfik A. Saleh

期刊论文