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Atomistic understanding of interfacial processing mechanism of silicon in water environment: A ReaxFFmolecular dynamics simulation

Frontiers of Mechanical Engineering 2021, Volume 16, Issue 3,   Pages 570-579 doi: 10.1007/s11465-021-0642-6

Abstract: process between silicon and amorphous silica in water environment, exploring the removal and damage mechanism

Keywords： 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

Frontiers of Chemical Science and Engineering 2019, Volume 13, Issue 1,   Pages 133-139 doi: 10.1007/s11705-018-1737-4

Abstract: In order to study the mechanism of interaction between CodY and its target DNA, molecular docking andmolecular dynamics simulations were used to explore the binding process at molecular level.

Keywords： 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

Frontiers of Mechanical Engineering 2013, Volume 8, Issue 1,   Pages 104-108 doi: 10.1007/s11465-013-0360-9

Abstract:

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.

Keywords： 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

Frontiers of Mechanical Engineering 2023, Volume 18, Issue 1, doi: 10.1007/s11465-022-0733-z

Abstract: However, the formation mechanism of lubrication films generated by carbon group nanofluids on MQL grindingHere, molecular dynamic simulations for the abrasive grain/workpiece interface were conducted under nanofluidworkpiece contact states under the different grinding conditions were compared to reveal the formation mechanism

Keywords： 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

Frontiers of Chemical Science and Engineering 2023, Volume 17, Issue 3,   Pages 347-357 doi: 10.1007/s11705-022-2246-z

Abstract: However, to date, the reverse-separation performance of ethanol/water is poor and the separation mechanismmembranes with tunable apertures and functional groups have shown substantial potential for use in molecularUsing molecular dynamics simulations, for the first time, we reveal two-way selectivity in ethanol/waterwater molecules are preferred for hydroxylated graphene membranes because of the synergistic effects of molecularThis study provides new insights into the reverse-selective mechanism of porous graphene membranes and

Keywords： reverse separation     graphene membrane     ethanol/water separation     molecular simulation    

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

Frontiers of Medicine 2021, Volume 15, Issue 5,   Pages 693-703 doi: 10.1007/s11684-020-0777-6

Abstract: 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.

Keywords： 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

Frontiers of Agricultural Science and Engineering 2018, Volume 5, Issue 2,   Pages 214-225 doi: 10.15302/J-FASE-2018219

Abstract: This study not only provides the candidate genes but also provides insights into the molecular mechanism

Keywords： 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

Frontiers of Chemical Science and Engineering 2016, Volume 10, Issue 1,   Pages 16-38 doi: 10.1007/s11705-015-1545-z

Abstract: As an advanced and new technology in molecular simulation fields, ReaxFF reactive force field has beenReaxFF bridges the gap between quantum chemistry (QC) and non-reactive empirical force field based molecularreactive force field in the fields of reaction processes, biology and materials, including (1) the mechanism

Keywords： 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

Frontiers in Energy 2020, Volume 14, Issue 1,   Pages 81-104 doi: 10.1007/s11708-019-0653-8

Abstract: So far, some available strategies such as molecular dynamics (MD) simulation and classical thermodynamic

Keywords： 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

Frontiers of Mechanical Engineering 2017, Volume 12, Issue 1,   Pages 89-98 doi: 10.1007/s11465-017-0412-7

Abstract: 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

Keywords： 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,

Engineering doi: 10.1016/j.eng.2023.01.015

Abstract: A mutation analysis and molecular dynamics (MD) simulations indicated that the Thr6 and Asn8 residuesthe Ser18 residue can synergistically enhance their interaction with ice, revealing the antifreeze mechanism

Keywords： Antifreeze peptides     Evolution analysis     Ice recrystallization inhibition     Molecular dynamics simulation    

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Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

Frontiers of Chemical Science and Engineering 2022, Volume 16, Issue 1,   Pages 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

Frontiers of Chemical Science and Engineering 2022, Volume 16, Issue 2,   Pages 168-182 doi: 10.1007/s11705-021-2056-8

Abstract: In this work, computer-aided molecular design tools were developed to design optimal solvents to upgradeAs different property prediction models consist different levels of structural information, molecularDue to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular

Keywords： computer-aided molecular design     bio-oil additives     molecular signature descriptor    

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Progress on molecular biomarkers and classification of malignant gliomas

Chuanbao Zhang, Zhaoshi Bao, Wei Zhang, Tao Jiang

Frontiers of Medicine 2013, Volume 7, Issue 2,   Pages 150-156 doi: 10.1007/s11684-013-0267-1

Abstract: Great efforts have been made to incorporate new information about the molecular landscape of gliomas

Keywords： malignant glioma     molecular biomarker     IDH1     MGMT     molecular classification    

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Molecular classification and molecular targeted therapy of cancer

Miao Xu, Jianyong Shao, Yixin Zeng

Frontiers of Medicine 2013, Volume 7, Issue 2,   Pages 147-149 doi: 10.1007/s11684-013-0274-2

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Title Author Date Type Operation

Atomistic understanding of interfacial processing mechanism of silicon in water environment: A ReaxFFmolecular dynamics simulation

Journal Article

Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

Journal Article

Computation of the protein molecular mechanism using adaptive dihedral angle increments

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

Journal Article

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

Journal Article

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

Journal Article

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

Journal Article

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

Journal Article

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

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

Journal Article

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

Junheng FU, Chenglin ZHANG, Tianying LIU, Jing LIU

Journal Article

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

Journal Article

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,

Journal Article

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

Journal Article

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

Journal Article

Progress on molecular biomarkers and classification of malignant gliomas

Chuanbao Zhang, Zhaoshi Bao, Wei Zhang, Tao Jiang

Journal Article

Molecular classification and molecular targeted therapy of cancer

Miao Xu, Jianyong Shao, Yixin Zeng

Journal Article