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Computational work is felt to be more of art than science.


Personal:

I was born in July 1981, Nanjing, P. R. China. I was educated in the same city, initially at
Nanjing University of Science and Technology, and then at Nanjing University, where I read chemistry and conducted doctoral research with Prof. Shuhua Li. I had 3-years postdoctoral training in Prof. Huan-Xiang Zhou's group at Florida State University, where I mainly worked on membrane proteins. I am now a postdoctoral fellow in Prof. Michael L. Klein's group at Temple University. I maintain a steady interest in understanding general questions in both chemical and biological systems by using multi-scale computational methods. I speak Chinese and English, fluent with accent.

Email: donghaonj@gmail.com
Office: Science Education and Research Center, 701A, 1925 N 12th Street, Philadelphia, PA 19122
Phone: (215) 204-4221 (office)





Experience:


2012.1 ~ present   Postdoctoral Fellow
Institute for Computational Molecular Science (ICMS), Temple University, Philadelphia, PA
Supervisor: Prof. Michael L. Klein




2009.1 ~ 2011.12   Postdoctoral Research Associate
Institute of Molecular Biophysics (IMB) & Department of Physics, Florida State University, Tallahassee, FL
Supervisor: Prof. Huan-Xiang Zhou







Education
:


2003.9 ~ 2008.10
   Ph. D.
Institute of Theoretical and Computational Chemistry (ITCC), Key Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing, PR China
Supervisor: Prof. Shuhua Li
Dissertation title: Non-Covalent Interactions in Supra- and Bio-Molecules: from Structure to Reaction Mechanism




1999.9 ~ 2003.6
   B. E.
School of Chemical Engineering, Nanjing University of Science and Technology, Nanjing, PR China







Research Interests:




Publications:

(20) "Proton Release from the Histidine-tetrad in the M2 Channel of the Influenza A Virus"
Hao Dong, Giacomo Fiorin, William F. DeGrado, & Michael L. Klein*
J. Phys. Chem. B 2014, 118, 12644.
Accepted on Christa's 100-day birthday!

(19) "Counterion-assisted Cation Transport in a Biological Calcium Channel"
Hao Dong, Michael L. Klein*, & Giacomo Fiorin
J. Phys. Chem. B 2014118, 9668.

(18) "Pore Waters Regulate Ion Permeation in a Calcium Release-activated Calcium Channel"
Hao Dong*, Giacomo Fiorin, Vincenzo Carnevale, Werner Treptow, & Michael L. Klein*
Proc. Natl. Acad. Sci. USA 2013, 110, 17332.
 
(17) "Exploring Histidine Conformations in the M2 Channel Lumen of the Influenza A Virus at Neutral pH via Molecular Simulations"
Hao Dong, Giacomo Fiorin, William F. DeGrado, & Michael L. Klein*
J. Phys. Chem. Lett. 2013, 4, 3067.
 
(16) "Ab initio Calculations and Validation of the pH-dependent Structures of the His37-Trp41 Quartet, the Heart of Acid Activation and Proton Conductance in the M2 Protein of Influenza A Virus"
Hao Dong, Myunggi Yi, Timothy A. Cross, & Huan-Xiang Zhou*
Chem. Sci. 2013, 4, 2776.
 
(15) "Size Matters in Activation/Inhibition of Ligand-gated Ion Channels"
Juan Du, Hao Dong, & Huan-Xiang Zhou*
Trends Pharmacol. Sci. 2012, 33, 482.

(14) "Glycines: Role in alpha-Helical Membrane Protein Structures and a Potential Indicator for Native Conformation"
Hao Dong, Mukesh Sharma, Huan-Xiang Zhou, & Timothy A. Cross*
Biochemistry 2012, 51, 4779.
Highlighted on Biochemistry Home Page

(13) "Gating Mechanism of a P2X4 Receptor Developed from Normal Mode Analysis and Molecular Dynamics Simulations"
Juan Du, Hao Dong, & Huan-Xiang Zhou*
Proc. Natl. Acad. Sci. USA 2012, 109, 4140.

(12) "M2 Protein from Influenza A: from Multiple Structures to Biophysical and Functional Insights"
Timothy A. Cross*, Hao Dong, Mukesh Sharma, David D. Busath, & Huan-Xiang Zhou
Curr. Opin. Virol. 2012, 2, 128. 

(11) "Atomistic Mechanism for the Activation and Desensitization of an AMPA-Subtype Glutamate Receptor"
Hao Dong, & Huan-Xiang Zhou*
Nature Commun. 2011, 2, 354.
Accepted on Daniel's 60-day birthday!

(10) "Insight into the Mechanism of the Influenza A Proton Channel from a Structure in a Lipid Bilayer"
Mukesh Sharma, Myunggi Yi, Hao Dong, Huajun Qin, Emily Peterson, David D. Busath, Huan-Xiang Zhou*, & Timothy A. Cross*
Science 2010, 330, 509.
[Editors' Choice]    [RSC]    [NBC]

(9) "Effects of Macromolecular Crowding on Protein Conformational Changes"
Hao Dong, Sanbo Qin, & Huan-Xiang Zhou*
PLoS Comput. Biol. 2010, 6, e1000833.
Cover Story on C&E News, 11/29/2010

(8) "A Computational Study towards Understanding the Mechanism of Phosphodiester Cleavage by Two Mononuclear Zn(II) Complexes"
Hao Dong
Phys. Chem. Chem. Phys. 2010, 12, 10434.

(7) "Understanding the Role of Intra- and Intermolecular Interactions in the Formation of Single- and Double-Helical Structures of Aromatic Oligoamides: A Computational Study"
Hao Dong, Shugui Hua, & Shuhua Li*
J. Phys. Chem. A 2009, 113, 1335.

(6) "Unprecedented Immunosuppressive Polyketides from Daldinia eschscholzii, a Mantis-Associated Fungus"
Yinglao Zhang, Huiming Ge, Wei Zhao, Hao Dong, Qiang Xu, Shuhua Li, Jing Li, Jie Zhang, Yongchun Song, & Renxiang Tan*
Angew. Chem. Int. Ed. 2008, 47, 1.

(5) "Temperature Controlled Reversible Change of the Coordination Modes of the Highly Symmetrical Multitopic Ligand To Construct Coordination Assemblies: Experimental and Theoretical Studies"
Bo Zheng, Hao Dong, Junfeng Bai*, Yizhi Li, Shuhua Li*, & Manfred Scheer*
J. Am. Chem. Soc. 2008, 130, 7778.

(4) "Relative Energies of Proteins and Water Clusters Predicted with the Generalized Energy-Based Fragmentation Approach"
Wei Li, Hao Dong, & Shuhua Li*
in Progress in Theoretical Chemistry and Physics. Springer-Verlag, Berlin Heidelberg, 2008, 18, 289.

(3) "A Smart Supramolecular Hydrogel: pH-Modulated Reversibly Viscoelastic Properties"
Naien Shi, Hao Dong, Gui Yin, Zheng Xu*, & Shuhua Li*
Adv. Funct. Mater. 2007, 17, 1837.

(2) "Estimation on the Individual Hydrogen-Bond Strength in Molecules with Multiple Hydrogen Bonds"
Hao Dong, Weijie Hua, & Shuhua Li*
J. Phys. Chem. A 2007, 111, 2941.
One of the Most-Accessed Articles, April-June, 2007

(1) "Theoretical Study toward Understanding the Catalytic Mechanism of Pyruvate Decarboxylase."
Jianyi Wang, Hao Dong, & Shuhua Li*
J. Phys. Chem. B 2005, 109, 18664.
 


Patents:

 (1) 2011  "Membrane proteins, mechanisms of action and uses thereof" (link)
Mukesh Sharma, Myunggi Yi, Hao Dong, Huajun Qin, Emily Peterson, David D. Busath, Huan-Xiang Zhou*, & Timothy A. Cross*
US 20110291652 A1



Awards:

(5) 2009  Excellent Graduate Student Award, Key Laboratory of Mesoscopic Chemistry, Ministry of Education
(4) 2008  Excellent Graduate Student Award, Nanjing University
(3) 2007  Corning Award, US Corning Co.
(2) 2007  Excellent Graduate Student Award, Key Laboratory of Mesoscopic Chemistry, Ministry of Education
(1) 2003  Excellent Undergraduate Thesis Dissertation, Nanjing University of Science and Technology



Conferences & Presentations:

(12) 2014.2   Biophysical Society 58th Annual Meeting, San Francisco, California (poster)
(11) 2013.9   246th ACS National Meeting, Indianapolis, Indiana (oral presentation)
(10) 2013.4   245th ACS National Meeting, New Orleans, Louisiana (oral presentation)
(9)   2012.8   244th ACS National Meeting, Philadelphia, Pennsylvania (oral presentation)
(8)   2011.3   Biophysical Society 55th Annual Meeting, Baltimore, Maryland (poster)
(7)   2010.2   Biophysical Society 54th Annual Meeting, San Francisco, California (poster)
(6)   2008.9   Theory and Applications of Computational Chemistry Conference, Shanghai (poster)
(5)   2008.5   The 10th National Quantum Chemistry Conference, Nanjing
(4)   2007.9   The 3rd Asian Pacific Conference on Theoretical & Computational Chemistry, Beijing (poster)
(3)   2006.11  The 3rd Asian Biological Inorganic Chemistry Conference, Nanjing
(2)   2004.9   EMBO-Course: "Methods for protein simulations and drug design", Shanghai
(1)   2004.5   The 2nd Theoretical & Computational Chemistry Symposium, Nanjing