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Atomistic understanding of interfacial processing mechanism of silicon in water environment: A ReaxFFmolecular dynamics 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 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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Computation of the protein molecular mechanism using adaptive dihedral angle increments

Mikel DIEZ, Victor PETUYA, Mónica URIZAR, Erik MACHO, Oscar ALTUZARRRA

《机械工程前沿（英文）》 2013年 第8卷 第1期   页码 104-108 doi: 10.1007/s11465-013-0360-9

摘要：

Protein motion simulation is still a troublesome problem yet to be solved, especially due to its high computational requirements. The procedure presented in this paper makes use of the proteins’ real degrees of freedom (DOFs). The procedure makes no use of any intermediate energy minimization processes that may alter the motion path or result in very high computational cost requirements. In order to reduce the computational cost, presented algorithms make use of the balls and rods approach for protein structure modelization. Also, structures are normalized in order to minimize inaccuracies introduced by experimental methods, providing a more efficient but still accurate structure for motion simulation.

关键词： kinematics     serial robot     proteins     folding     molecular mechanism    

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Tribological mechanism of carbon group nanofluids on grinding interface under minimum quantity lubricationbased on molecular dynamic 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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Antibiotic resistome of : molecular determinants for the emergence of drug resistance

《医学前沿（英文）》 2021年 第15卷 第5期   页码 693-703 doi: 10.1007/s11684-020-0777-6

摘要： Resistome is a cluster of microbial genes encoding proteins with necessary functions to resist the action of antibiotics. Resistome governs essential and separate biological functions to develop resistance against antibiotics. The widespread clinical and nonclinical uses of antibiotics over the years have combined to select antibiotic-resistant determinants and develop resistome in bacteria. At present, the emergence of drug resistance because of resistome is a significant problem faced by clinicians for the treatment of Salmonella infection. Antibiotic resistome is a dynamic and ever-expanding component in Salmonella. The foundation of resistome in Salmonella is laid long before; therefore, the antibiotic resistome of Salmonella is reviewed, discussed, and summarized. We have searched the literature using PubMed, MEDLINE, and Google Scholar with related key terms (resistome, Salmonella, antibiotics, drug resistance) and prepared this review. In this review, we summarize the status of resistance against antibiotics in S. typhi, highlight the seminal work in the resistome of S. typhi and the genes involved in the antibiotic resistance, and discuss the various methods to identify S. typhi resistome for the proactive identification of this infection and quick diagnosis of the disease.

关键词： S. typhi     antibiotic resistance     mechanism     resistome     identification methods    

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Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecularmechanism of anthocyanin biosynthesis

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

《农业科学与工程前沿（英文）》 2018年 第5卷 第2期   页码 214-225 doi: 10.15302/J-FASE-2018219

摘要： Sweet potato, , is a globally important food crop. The purple-fleshed sweet potato, rich in anthocyanins, has great potential for both nutritional and pharmaceutical uses. In this study, we characterized the root transcriptomes of the purple-fleshed sweet potato cv. Jingshu 6 and its mutant JS6-5 with high anthocyanin content by high-throughput RNA sequencing. A total of 22873364 and 27955097 high quality reads were obtained from Jingshu 6 and JS6-5, respectively, and assembled into 35592 unigenes. In all, we obtained 1566 differentially expressed genes (DEGs). Among them, 994 were upregulated and 572 were downregulated in JS6-5 compared to the expression in Jingshu 6. A total of 1436 DEGs were annotated, in which 847 DEGs had gene ontology (GO) terms and 329 DEGs were assigned to 84 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most importantly, 23 differentially expressed genes and 24 transcription factors were identified as candidate genes involved in anthocyanin biosynthesis. In addition, 2349 SSRs were detected. This study not only provides the candidate genes but also provides insights into the molecular mechanism of anthocyanin biosynthesis in sweet potato.

关键词： anthocyanin     gene expression     mutant     purple-fleshed sweet potato     transcriptome    

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Development, applications and challenges of ReaxFF reactive force field in molecular simulations

You Han, Dandan Jiang, Jinli Zhang, Wei Li, Zhongxue Gan, Junjie Gu

《化学科学与工程前沿（英文）》 2016年 第10卷 第1期   页码 16-38 doi: 10.1007/s11705-015-1545-z

摘要： As an advanced and new technology in molecular simulation fields, ReaxFF reactive force field has been developed and widely applied during the last two decades. ReaxFF bridges the gap between quantum chemistry (QC) and non-reactive empirical force field based molecular simulation methods, and aims to provide a transferable potential which can describe many chemical reactions with bond formation and breaking. This review presents an overview of the development and applications of ReaxFF reactive force field in the fields of reaction processes, biology and materials, including (1) the mechanism studies of organic reactions under extreme conditions (like high temperatures and pressures) related with high-energy materials, hydrocarbons and coals, (2) the structural properties of nanomaterials such as graphene oxides, carbon nanotubes, silicon nanowires and metal nanoparticles, (3) interfacial interactions of solid-solid, solid-liquid and biological/inorganic surfaces, (4) the catalytic mechanisms of many types of metals and metal oxides, and (5) electrochemical mechanisms of fuel cells and lithium batteries. The limitations and challenges of ReaxFF reactive force field are also mentioned in this review, which will shed light on its future applications to a wider range of chemical environments.

关键词： ReaxFF     reaction mechanism     nanomaterials     interfacial interaction     catalyst     fuel cell    

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Room temperature liquid metal: its melting point, dominating mechanism and applications

Junheng FU, Chenglin ZHANG, Tianying LIU, Jing LIU

《能源前沿（英文）》 2020年 第14卷 第1期   页码 81-104 doi: 10.1007/s11708-019-0653-8

摘要： The room temperature liquid metal (LM) is recently emerging as a new class of versatile materials with fascinating characteristics mostly originated from its simultaneous metallic and liquid natures. The melting point is a typical parameter to describe the peculiarity of LM, and a pivotal factor to consider concerning its practical applications such as phase change materials (PCMs) and advanced thermal management. Therefore, the theoretical exploration into the melting point of LM is an essential issue, which can be of special value for the design of new LM materials with desired properties. So far, some available strategies such as molecular dynamics (MD) simulation and classical thermodynamic theory have been applied to perform correlative analysis. This paper is primarily dedicated to performing a comprehensive overview regarding typical theoretical strategies on analyzing the melting points. It, then, presents evaluations on several factors like components, pressure, size and supercooling that may be critical for melting processes of liquid metal. After that, it discusses applications associated with the characteristic of low melting points of LM. It is expected that a great many fundamental and practical works are to be conducted in the coming future.

关键词： melting point     liquid metal     crystal     thermodynamics     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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Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

《工程（英文）》 doi: 10.1016/j.eng.2023.01.015

摘要： The development of effective antifreeze peptides to control ice growth has attracted a significant amount of attention yet still remains a great challenge. Here, we propose a novel design method based on an in-depth investigation of repetitive motifs in various ice-binding proteins (IBPs) with an evolution analysis. In this way, several peptides with notable antifreeze activity were developed. In particular, a designed antifreeze peptide named AVD exhibits ideal ice recrystallization inhibition (IRI), solubility, and biocompatibility, making it suitable for use as a cryoprotective agent (CPA). A mutation analysis and molecular dynamics (MD) simulations indicated that the Thr6 and Asn8 residues of the AVD peptide are fundamental to its ice-binding capacity, while the Ser18 residue can synergistically enhance their interaction with ice, revealing the antifreeze mechanism of AVD. Furthermore, to demonstrate the cryoprotection potential of AVD, the peptide was successfully employed for the cryopreservation of various cells, which demonstrated significant post-freezing cell recovery. This work opens up a new avenue for designing antifreeze materials and provides peptide-based functional modules for synthetic biology.

关键词： Antifreeze peptides     Evolution analysis     Ice recrystallization inhibition     Molecular dynamics simulation     Cryopreservation     Synthetic biology    

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Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

《化学科学与工程前沿（英文）》 2022年 第16卷 第1期   页码 1-3 doi: 10.1007/s11705-021-2134-y

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Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

《化学科学与工程前沿（英文）》 2022年 第16卷 第2期   页码 168-182 doi: 10.1007/s11705-021-2056-8

摘要： Direct application of bio-oil from fast pyrolysis as a fuel has remained a challenge due to its undesirable attributes such as low heating value, high viscosity, high corrosiveness and storage instability. Solvent addition is a simple method for circumventing these disadvantages to allow further processing and storage. In this work, computer-aided molecular design tools were developed to design optimal solvents to upgrade bio-oil whilst having low environmental impact. Firstly, target solvent requirements were translated into measurable physical properties. As different property prediction models consist different levels of structural information, molecular signature descriptor was used as a common platform to formulate the design problem. Because of the differences in the required structural information of different property prediction models, signatures of different heights were needed in formulating the design problem. Due to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular design problem increases with the height of signatures. Thus, a multi-stage framework was developed by developing consistency rules that restrict the number of higher-order signatures. Finally, phase stability analysis was conducted to evaluate the stability of the solvent-oil blend. As a result, optimal solvents that improve the solvent-oil blend properties while displaying low environmental impact were identified.

关键词： computer-aided molecular design     bio-oil additives     molecular signature descriptor    

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Progress on molecular biomarkers and classification of malignant gliomas

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 150-156 doi: 10.1007/s11684-013-0267-1

摘要：

Gliomas are the most common primary intracranial tumors in adults. Anaplastic gliomas (WHO grade III) and glioblastomas (WHO grade IV) represent the major groups of malignant gliomas in the brain. Several diagnostic, predictive, and prognostic biomarkers for malignant gliomas have been reported over the last few decades, and these markers have made great contributions to the accuracy of diagnosis, therapeutic decision making, and prognosis of patients. However, heterogeneity in patient outcomes may still be observed, which highlights the insufficiency of a classification system based purely on histopathology. Great efforts have been made to incorporate new information about the molecular landscape of gliomas into novel classifications that may potentially guide treatment. In this review, we summarize three distinctive biomarkers, three most commonly altered pathways, and three classifications based on microarray data in malignant gliomas.

关键词： malignant glioma     molecular biomarker     IDH1     MGMT     molecular classification    

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Molecular classification and molecular targeted therapy of cancer

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 147-149 doi: 10.1007/s11684-013-0274-2

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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 ReaxFFmolecular dynamics 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

Computation of the protein molecular mechanism using adaptive dihedral angle increments

Mikel DIEZ, Victor PETUYA, Mónica URIZAR, Erik MACHO, Oscar ALTUZARRRA

期刊论文

Tribological mechanism of carbon group nanofluids on grinding interface under minimum quantity lubricationbased on molecular dynamic simulation

期刊论文

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

期刊论文

Antibiotic resistome of : molecular determinants for the emergence of drug resistance

期刊论文

Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecularmechanism of anthocyanin biosynthesis

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

期刊论文

Development, applications and challenges of ReaxFF reactive force field in molecular simulations

You Han, Dandan Jiang, Jinli Zhang, Wei Li, Zhongxue Gan, Junjie Gu

期刊论文

Room temperature liquid metal: its melting point, dominating mechanism and applications

Junheng FU, Chenglin ZHANG, Tianying LIU, Jing LIU

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

Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

期刊论文

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

期刊论文

Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

期刊论文

Progress on molecular biomarkers and classification of malignant gliomas

null

期刊论文

Molecular classification and molecular targeted therapy of cancer

null

期刊论文