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Peng Lian
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Peng Lian

1 Bethel Valley Rd.
Bldg. 2040

Oak Ridge , Tennessee 37830
Work: (865) 275-5096

Education:

  1. 2010-2013 Visiting Ph.D., UT/ORNL Center for Molecular Biophysics
  2. 2008-2010 Ph.D., Biomedical Engineering (Bioinformatics), Shanghai Jiao Tong University
  3. 2004-2008 B.Sc., Biotechnology, Shandong University

Biography:

My research interests focus on 1) developing and applying theoretical chemistry and biophysics methods including quantum mechanics/molecular mechanics (QM/MM), molecular dynamics (MD) simulation, molecular docking, datamining etc to investigate the molecular mechanism of macromolecules; 2) developing new accurate computer-aided drug design (CADD) algorithms to improve the efficiency of drug discovery.

 

Selected Publications

Quantum Chemical Calculation of pKas of Environmentally Relevant Functional Groups: Carboxylic Acids, Amines and Thiols in Aqueous Solution. Peng Lian, Ryne C. Johnston, Jerry M. Parks, Jeremy C. Smith. The Journal of Physical Chemistry A, 2018, DOI: 10.1021/acs.jpca.8b01751.

Emerging investigator series: methylmercury speciation and dimethylmercury production in sulfidic solutions. Charlotte R. Kanzler, Peng Lian, Emma Leverich Trainer, Xiaoxuan Yang, Niranjan Govind, Jerry M. Parks and Andrew M. Graham. Environmental Science: Processes & Impacts. 2018, DOI: 10.1039/c7em00533d.

Thermostability mechanism for the hyperthermophilicity of extremophile cellulase TmCel12A: Implied from molecular dynamics simulation.Peng Lian, Congmin Yuan, Qin Xu, Wei Fu. The Journal of Physical Chemistry B. 2016, 120(30) 7346-7352

Higher-affinity agonists of 5-HT1AR discovered through tuning the binding-site flexibility. Peng Lian, Linlang Li, Chuanrong Geng, Xuechu Zhen, Wei Fu. Journal of Chemical Information and Modeling, 2015, 55(8), 1616-1627

X-ray structure of a Hg2+ complex of mercuric reductase (MerA) and QM/MM study of Hg2+ transfer between the C-terminal and buried catalytic site cysteine pairs. Peng Lian, Hao-bo Guo, Susan Miller, Jerry M. Parks, Liyuan Liang, Jeremy C. Smith, Dong-Qing Wei, hong Guo. Biochemistry. Epub 2014 Oct.

Catalytic mechanism and origin of high activity of cellulase TmCel12A at high temperature: a quantum mechanical/molecular mechanical study.Peng Lian, Hao-Bo Guo, Jeremy C. Smith, Dong-Qing Wei, Hong Guo. Cellulose, 2013 1-30 DOI: 10.1007/s10570-013-0011-7
 
Car-Parrinello molecular dynamics / molecular mechanics (CPMD/MM) simulation study of coupling and uncoupling mechanisms of cytochrome P450cam. Peng Lian, Jue Li, Dongqi Wang, Dong-Qing Wei. The Journal of Physical Chemistry B2013117 (26), 7849–7856
 

An allosteric mechanism inferred from molecular dynamics simulations on phospholamban pentamer in lipid membranes. Peng Lian, Dong-Qing Wei, Jing-Fang Wang, Kuo-Chen Chou. PLoS ONE, 2011 6(4): e18587

Thermal decomposition of the solid phase of nitromethane: Ab initio molecular dynamics simulations. Jing Chang, Peng Lian, Dong-Qing Wei, Xiang-Rong Chen, Qing-Ming Zhang, and Zi-Zheng Gong.  Physical Review Letters, 2010, 105(17), 188302.

Tethered-hopping model for protein-DNA binding and unbinding based on Sox2-Oct1-Hoxb1 ternary complex simulations.Peng Lian, Limin Angela Liu, Yongxiang Shi, Yuxiang Bu, Dongqing Wei. Biophysical Journal, 2010, 98(7), 1285-1293

 

Book Chapters:

Chapter 18. An Application of QM/MM Simulation: The Second Protonation of Cytochrome P450Peng Lian and Dongqing Wei, 2015, in Advance in Structural Bioinformatics, 827, 311-324, Springer netherlands.

Molecular Simulation and Computer Aided Drug Design (Chinese). Dongqing Wei, Ruoxu Gu, Peng Lian, Tao Zhang and Ying Wang, 2012, Shanghai Jiao Tong University Press, ISBN: 9787313079800, 731307980X

Protein Structure Modeling and Design (Chinese). Shigao Chen, Chao Cheng, Yan Feng, Rongxiu Li, Peng Lian, Jingfang Wang, Ying Wang, Dongqing Wei, Conghao Zhong (Names are arranged alphabetically). 2011, Chemical Industry Press, ISBN: 978-7-122-10183-9