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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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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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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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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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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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A review on ductile mode cutting of brittle materials

Elijah Kwabena ANTWI, Kui LIU, Hao WANG

《机械工程前沿（英文）》 2018年 第13卷 第2期   页码 251-263 doi: 10.1007/s11465-018-0504-z

摘要：

Brittle materials have been widely employed for industrial applications due to their excellent mecha-nical, optical, physical and chemical properties. But obtaining smooth and damage-free surface on brittle materials by traditional machining methods like grinding, lapping and polishing is very costly and extremely time consuming. Ductile mode cutting is a very promising way to achieve high quality and crack-free surfaces of brittle materials. Thus the study of ductile mode cutting of brittle materials has been attracting more and more efforts. This paper provides an overview of ductile mode cutting of brittle materials including ductile nature and plasticity of brittle materials, cutting mechanism, cutting characteristics, molecular dynamic simulation, critical undeformed chip thickness, brittle-ductile transition, subsurface damage, as well as a detailed discussion of ductile mode cutting enhancement. It is believed that ductile mode cutting of brittle materials could be achieved when both crack-free and no subsurface damage are obtained simultaneously.

关键词： ductile mode cutting     brittle materials     critical undeformed chip thickness     brittle-ductile transition     subsurface damage     molecular dynamic 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 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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Dynamic simulation based optimized design method of concrete production system for RCC dam

ZHAO Chunju, ZHOU Yihong

《结构与土木工程前沿（英文）》 2007年 第1卷 第4期   页码 405-410 doi: 10.1007/s11709-007-0055-6

摘要： The construction system of roller compacted concrete (RCC) dam is running according to a series of connected procedures which are highly impacted and interacted consisting with the resource level. Therefore, a dynamic simulation mode

关键词： interacted     dynamic simulation     construction     resource     RCC    

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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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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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Effects of a dynamic membrane formed with polyethylene glycol on the ultrafiltration of natural organic

Boksoon KWON, Noeon PARK, Jaeweon CHO,

《环境科学与工程前沿（英文）》 2010年 第4卷 第2期   页码 172-182 doi: 10.1007/s11783-010-0002-y

摘要： The formation of a dynamic membrane (DM) was investigated using polyethylene glycol (PEG) (molecular weight of 35000 g/mol, concentration of 1 g/L). Two natural organic matters (NOM), Dongbok Lake NOM (DLNOM) and Suwannee River NOM (SRNOM) were used in the ultrafiltration experiments along with PEG. To evaluate the effects of the DM with PEG on ultrafiltration, various transport experiments were conducted, and the analyses of the NOM in the membrane feed and permeate were performed using high performance size exclusion chromatography, and the pore size distribution ( PSD) and molecular weight cut off ( MWCO) were determined. The advantages of DM formed with PEG can be summarized as follows: (1) PEG interferes with NOM transmission through the ultrafiltration membrane pores by increasing the retention coefficient of NOM in UF membranes, and (2) low removal of NOM by the DM is affected by external factors, such as pressure increases during UF membrane filtration, which decreases the PSD and MWCO of UF membranes. However, a disadvantage of the DM with PEG was severe flux decline; thus, one must be mindful of both the positive and negative influences of the DM when optimizing the UF performance of the membrane.

关键词： dynamic membrane     natural organic matters     ultrafiltration membrane performance     effective PSD     effective molecular weight cutoff    

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标题 作者 时间 类型 操作

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

Molecular dynamic simulation on the conformation of mouse muscle type nAChR

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

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

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

期刊论文

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

A review on ductile mode cutting of brittle materials

Elijah Kwabena ANTWI, Kui LIU, Hao WANG

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

Dynamic simulation based optimized design method of concrete production system for RCC dam

ZHAO Chunju, ZHOU Yihong

期刊论文

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

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

Effects of a dynamic membrane formed with polyethylene glycol on the ultrafiltration of natural organic

Boksoon KWON, Noeon PARK, Jaeweon CHO,

期刊论文