(Chemistry and Physics)
B.S., (Physics) 1984, Jilin University, China
Ph.D. (Astrophysics) 1991, University of Illinois
Post Doctor Research Associate (Chemistry and Biological physics ), 1991-1996, University of Illinois
Phone: (631) 632-1185
Fax: (631) 632-7960
Physics and Chemistry of Biomolecules, Cellular Networks and Single Molecules
The main focus of my research is on the study of the fundamental mechanism of biomolecular folding and recognition, especially protein folding and protein-protein/protein-DNA interactions. Using modern statistical mechanics, molecular simulations and empirical information from protein database, energy landscapes of protein folding and recognition can be mapped. By further studying the detailed structure correlations of the landscape, the fundamental questions such as nucleations and nature of transition state ensemble can be answered for different proteins and biomolecular recognition complexes. The results of the study can be compared with the experiments. The energy landscape description of protein folding and recognition will also provide insight of new algorithms of structure prediction and drug design.
I am also interested in the study of the underlying principles of the cellular networks. In particular, I am interested in the nature of the robustness of the cellular networks in the noisy fluctuating environments. I am also interested in understanding and quantifying the dynamics and pathways of the cellular networks. These studies should lead to optimal design and evolution of the networks.
Another focus of my study is on the reaction dynamics in complex environments, specifically biomolecular reactions and interactions where the reaction happens in a relatively fast or comparable time scale relative to the environmental fluctuations. A path integral formalism is developed for the full treatment of the problem. Potential application of this method includes electron transfer in proteins, ligand binding, reaction dynamics in complex solvents.
I am also interested in the study of single molecule reaction dynamics. The single molecule detection provides us detailed picture of molecular reactions without ensemble average. It is also a sensitive probe to the local environments. It can help us to pin down the reaction pathways. Since the single molecule has only one sample, the statistical fluctuations normally ignored under the situation of large samples may not be neglected. Quantitative study of the statistics of single molecule reaction dynamics is very necessary and underway in order to understand the whole picture.
- Guest Scientist, 1996-1997, National Institutes of Health
- Vice President and Senior Analyst, 1997-2005, Citibank
- Adjunct Professor (Physics and Credit Management), 1997-present, Jilin University, China
- Adjunct Professor (Chemistry), 1999-2004, SUNY Stony Brook
- Adjunct Professor, 2002-present, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences
- National Science Foundation Career Award, 2005
- Adjunct Professor (Applied Mathematics), 2006-present, SUNY Stony Brook
- Adjunct Professor (Harriman College of Business), 2008-present, SUNY Stony Brook
- Fellow of American Physical Society, 2010
110. H. Feng, J. Wang, “ Potential and flux decomposition for dynamical systems and non-equilibrium thermodynamics: Curvature, gauge field, and generalized fluctuation-dissipation theorem”. J. Chem. Phys. 135, 234511 (2011).
109. Q. Lu, N. Nassar, J. Wang, "A mechanism of catalyzed GTP hydrolysis by Ras Protein through magnesium ion". Chem. Phys. Lett. 516, 233-238 (2011).
108. Z.Z. Lai, Q. Lu, J. Wang, " Exploring the Thermodynamic Landscape, Kinetics, and Structural Evolution of a Protein Conformational Transition with a Microscopic Double-Well Model". J. Phys. Chem. B, 115 (14), pp 4147–4159(2011).
107. Wang J, X.K. Chu, Y. Wang, S. Hagen, W. Han, E.K.Wang "Multi-Scaled Explorations of Binding-Induced Folding of Instrinsically Disordered Protein Inhibitor IA3 to its Target Enzyme". PLOS Comp. Biol. 7(4): e1001118 (2011).
106. J. Wang, K. Zhang, L. Xu, E.K. Wang, "Quantifying the Waddington landscape and biological paths for development and differentiation". Proc. Natl. Acad. Sci. USA. 108(20):8257-8262(2011).
105. J. Wang, "Potential Landscape and Flux Framework of Non-Equilibrium Biological Networks". Annual Reports in Computational Chemistry 7, 3-37, (2011).
104. J. Wang, C.H. Li, and E.K. Wang, "A FPT Approach for Predicting Protein Localization from Yeast Genomic Data". PLoS One 6, e14449:1-11 (2011).
103. C.H. Li, E.K. Wang, and J. Wang, "Landscape, Flux, Correlation, Resonance, Coherence, Stability and Key Network Wirings of Stochastic Circadian Oscillation". Biophys. J. 101, 1335-1344(2011).
102. C.H. Li, E.K. Wang, and J. Wang, "Landscape and flux decomposition for exploring global natures of non-equilibrium dynamical systems under intrinsic statistical fluctuations". Chem. Phys. Lett. 505, 75-80 (2011).
101. C.H. Li, E.K. Wang, and J. Wang, "Potential Landscape and Probabilistic Flux of a Predator-Prey Network". PLoS One 6, e17888:1-9 (2011).
100. H.D. Feng and J. Wang, "Correlation function, response function and effective temperature of gene networks", Chem. Phys. Lett. 510, 267 (2011).
99. H.D. Feng and J. Wang, "A new formulation of two-time correlation functions of Markov chains applied to gene networks", Chem. Phys. Lett. 501, 562 (2011).
98. H.D. Feng, Bo Han, and J. Wang, "Adiabatic and Non-Adiabatic Non-Equilibrium Stochastic Dynamics of Single Regulating Genes", J. Phys. Chem. B, 115, 1254 (2011).
97. J.T. Ren, H.X. Qin, J.H. Wang, N. W. Luedtke, E.K. Wang, J. Wang, "Label-free detection of nucleic acids by turn-on and turn-off G-quadruplex-mediated fluorescence". Analytical and Bioanalytical Chemistry, 399(8), 2763-2770(2011)
96. M. Zhou, X.L. Zheng, J. Wang, S.J. Dong, "'Nondestructive' biocomputing security system based on gas-controlled biofuel cell and potentially used for intelligent medical diagnostics". Bioinformatics 27(3): 399-404(2011).
95. J. Wang, K. Zhang, E.K. Wang, "Kinetic paths, time scale, and underlying landscapes: A path integral framework to study global natures of nonequilibrium systems and networks". J. Chem. Phys. 133, 125103 (2010).
94. D. Lepzelter, H. Feng, J. Wang, "Oscillation, cooperativity, and intermediates in the self-repressing gene". Chem. Phys. Lett. 490, 216-220 (2010).
93. C. Marai, S. Mukamel, J. Wang, "Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy: simulation study". PMC Biophysics 3, 8(2010).
92. M. Zhou, X. Zheng, J. Wang and S.J. Dong, "A Self-Powered and Reusable Biocomputing Security Keypad Lock System Based on Biofuel Cells" Chemistry – A European J. 16, 7719–7724(2010).
91. Jin Wang, "Cellular and Biomolecular Recognition: Synthetic and Non-Biological Molecules". J. Am. Chem. Soc., 132 (18), 6611(2010).
90. H. Feng, B. Han and J. Wang, "Dominant Kinetic Paths of Complex Systems: Gene Networks". J. Phys. Chem. Lett., 1, 1836–1840(2010).
89. J. Wang, C. Li, and E.K. Wang, "Potential and flux landscapes quantify the stability and robustness of budding yeast cell cycle network". Proc. Natl. Acad. Sci. USA 107, 8195–8200(2010).
88. R. J. Oliveira,P.C. Whitford, J. Chahine, V.B.P. Leite, Jin Wang, "Coordinate and time-dependent diffusion dynamics in protein folding". Methods 52, 91–98(2010).
87. J. Wang, L. Xu, E.K. Wang, and S. Huang, "The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation". Biophys. J. 99, 29–39(2010).
86. Z. Liu, J. Wang and E.K. Wang, "Direct Binding of Thymopentin to Surface Class II Major Histocompatibility Complex in Living Cells". J. Phys. Chem. B, 114, 638–642(2010).
85. R. J. Oliveira,P.C. Whitford, J. Chahine, Jin Wang, J.N. Onuchic, V.B.P. Leite,"The Origin of Nonmonotonic Complex Behavior and the Effects of Nonnative Interactions on the Diffusive Properties of Protein Folding". Biophys. J. 99, 600–608(2010).
84. D. Li, G. Li, P. Li, L. Zhang, Z. Liu, Jin Wang, E.K. Wang, "The enhancement of transfection efficiency of cationic liposomes by didodecyldimethylammonium bromide coated gold nanoparticles". Biomaterials 31, 1850–1857 (2010).
83. J. Wang, "Potential Landscape Theory of Cellular Networks". in Statistical Mechanics of Cellular Systems and Processes. Ed. M. H. Zaman. Page 74-120. Cambridge University Press. (2009).
82. J. Wang, L. Xu, E. K. Wang, "Robustness and Coherence of a Three-Protein Circadian Oscillator: Landscape and Flux Perspectives" Biophys. J. 97, 3038–3046(2009).
81. Z. Liu, X. Zheng, X. Yang, E.K. Wang, J. Wang, "Affinity and Specificity of Levamlodipine-Human Serum Albumin Interactions: Insights into Its Carrier Function". Biophys. J. 96, 3917–3925(2009).
80. D. Li, P. Li, G. Li, J. Wang, E.K. Wang, "The effect of nocodazole on the transfection efficiency of lipid-bilayer coated gold nanoparticles". Biomaterials 30, 1382–1388 (2009).
79. J. Wang, C. Li, E. K. Wang, X.D. Wang, "Uncovering the rules for protein–protein interactions from yeast genomic data." Proc. Natl. Acad. Sci. 106, 3752–3757 (2009).
78. Q. Lu, and J. Wang, "Kinetics and Statistical Distributions of Single-Molecule Conformational Dynamics." J. Phys. Chem. B, 113, 1517-1521(2009).
77. L. C. Paula, J. Wang, and V. B. P. Leite, "Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study." J. Chem. Phys. 129, 224504 (2008).
76. J. Wang, L. Xu, E.K. Wang, "Robustness, Dissipations and Coherence of the Oscillation of Circadian Clock: Potential Landscape and Flux Perspectives.’’ PMC Biophysics, 1, 7(2008)
75. Y. Chen, J. Jakoncic, J. Wang, X. Zheng, N. Carpino, N. Nassar, "Structural and Functional Characterization of the C-terminal Domain of the Ecdysteroid Phosphate Phosphatase from Bombyx mori reveals a new enzymatic activity’’, Biochemistry 47, 12135-12145 (2008)
74. J. Wang, L. Xu, K. Xue, E.K. Wang, "Exploring the origin of power law distribution in single-molecule conformation dynamics: Energy landscape perspectives’’, Chem. Phys. Lett. 463, 405–409(2008)
73. J. Wang, K. Zhang, and E. K. Wang, "Robustness and dissipation of mitogen-activated protein kinases signal transduction network: Underlying funneled landscape against stochastic fluctuations’’, J. Chem. Phys. 129, 135101(2008).
72. J. Wang, L. Xu, E. K. Wang, "Potential Landscape and Flux Framework of Non-Equilibrium Networks: Robustness, Dissipation and Coherence of Biochemical Oscillations" Proc. Natl. Acad. Sci. 105: 12271-12276. (2008).
71. D. Lepzelter, J. Wang, "Exact probabilistic solution of spatial-dependent stochastics and associated spatial potential landscape for the bicoid protein", Phys. Rev. E. 77, 041917(2008).
70. Q. Lu, J. Wang, "Single Molecule Conformational Dynamics of Adenylate Kinase: Energy Landscape, Structural Correlations, and Transition State Ensembles", J. Amer. Chem. Soc. 130, 4772(2008).
69. S. Lapidus, B. Han, J. Wang, "Intrinsic noise, dissipation cost, and robustness of cellular networks: The underlying energy landscape of MAPK signal transduction", Proc. Natl. Acad. Sci. 105, 6039(2008).
68. B. Han, J. Wang, "Least dissipation cost as a design principle for robustness and function of cellular networks", Phys. Rev. E 77, 031922 (2008).
67. D. Li, G. Li, W. Guo, P. Li, E. Wang, J. Wang, "Glutathione-mediated release of functional plasmid DNA from positively charged quantum dots", Biomaterials 29, 2776–2782(2008).
66. E. Ying, D. Li, S. Guo, S. Dong, J. Wang, "Synthesis and Bio-Imaging Application of Highly Luminescent Mercaptosuccinic Acid-Coated CdTe Nanocrystals", PLOS One, 3, e2222(2008).
65. Z. J. Liu, X. Zheng, J. Wang, E. K. Wang, "Molecular Analysis of Thymopentin Binding to HLA-DR Molecules", PLOS One, 2(12), e1348(2007).
64. J. Wang, X. Zheng, Y. Yang, D. Drueckhammer, W. Yang, G. Verkhivker, E. K. Wang, "Quantifying intrinsic specificity: A potential complement to affinity in drug screening’’, Phys. Rev. Lett. 99, 198101 (2007).
63. J. Chahine, R. J. Oliveira, V. B. P. Leite, and J. Wang, "Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding", Proc. Natl. Acad. Sci. 104, 14646 (2007)
62. D. Lepzelter, K. Kim, J. Wang, "Dynamics and Intrinsic Statistical Fluctuations of a Gene Switch", J. Phys. Chem. B, 111, 10239(2007).
61. J. Wang, L. Xu, E. K. Wang, "Optimal Specificity and Function for Flexible Biomolecular Recognition", Biophys. J. Lett. 92, L109(2007).
60. B. Han, J. Wang, "Quantifying Robustness and Dissipation Cost of Yeast Cell Cycle Network: The Funneled Energy Landscape Perspectives’’, Journal Cover Article, Biophys. J., 92, 3755 (2007).
59. K. Kim, J. Wang, "Potential Energy Landscape and Robustness of A Gene Regulatory Network: Toggle Switch’’, PLOS Comp. Biol., 3, e60 (2007).
58. Q. Lu, P. H. Lu, J. Wang, "Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics’’, Phys. Rev. Lett. 98, 128105(2007).
57. K. Kim, D. Lepzelter, J. Wang, "Single Molecule Dynamics and Statistical Fluctuations of Gene Regulatory Networks: A Repressilator’’, J. Chem. Phys. 126, 034702(2007).
56. J. Wang, K. Zhang, H.Y. Lu, E. K. Wang, "Quantifying the Kinetic Paths of Flexible Biomolecular Recognition", Biophys. J. 91, 866(2006).
55. Y. Wang, L. Gan, H. Chen, S. Dong, J. Wang, "Structure and Identity of 4,4'-Thiobisbenzenethiol Self-Assembled Monolayers", J. Phys. Chem. B. 110, 20418(2006).
54. J. Wang, B. Huang, X. F. Xia, Z. R. Sun, "Funneled Landscape Leads to Robustness of Cell Networks: Yeast Cell Cycle", PLOS Comp. Biol. 2. e147, 1385(2006).
53. J. Wang, Q. Lu, P. Lu, "Single-Molecule Dynamics Reveals Cooperative Binding-Folding in Protein Recognition", PLOS Comp. Biol. 2, e78, 0842(2006)
52. J. Wang, "Diffusion and Single Molecule Dynamics on Biomolecular Interface Binding Energy Landscape", Chem. Phys. Lett. 418, 540(2006).
51. J. Wang, B. Huang, X. F. Xia, Z. R. Sun, "Funneled Landscape Leads to Robustness of Cellular Networks: MAPK Signal Transduction", Biophys. J. Lett. 91, L54(2006).
50. J. Wang, K. Zhang, H. Y. Lu, E. K. Wang, "Identifying the Kinetic Paths on Biomolecular Binding-Folding Energy Landscape", Phys. Rev. Lett. 96, 168101(2006).
49. J. E. M. Hornos, D. Schultz, G. C. P. Innocentini, J. Wang, A. M. Walczak, J. N. Onuchic, and P. G. Wolynes, "Self-Regulating Gene: An Exact Solution," Phys. Rev. E. 72, 051907(2005).
48. V. B. P. Leite, L. C. P. Alonso, M. Newton, and J. Wang, "Single Molecule Electron Transfer Dynamics in Complex Environments ." Phys. Rev. Lett. 95, 118301(2005).
47. J. Wang, K. Zhang, H. Y. Lu, and E.K. Wang, "Quantifying Kinetic Paths of Protein Folding," Biophys. J. 89, 1612–1620(2005).
46. J. Wang, C. Lee, G. Stell, "The cooperative nature of hydrophobic forces and protein folding kinetics," Chemical Physics 316, 53–60(2005).
45. J. Wang, "The Complex Kinetics of Protein Folding in Wide Temperature Ranges," Biophys. J. 87, 2164(2004).
44. J. Wang, W. M. Huang, H. Y. Lu, and E. K. Wang, "Downhill Kinetics of Biomolecular Interface Binding-Global Connected Scenario," Biophys. J. 87, 2187 (2004).
43. V. B.P. Leite, J.N. Onuchic, G. Stell, and J. Wang, "Probing the Kinetics of Single Molecule Protein Folding," Biophys. J. 87, 3633 (2004).
42. Y. Zhou, Q. Zhang, G. Stell, J. Wang, "Temperature Dependence of the distribution of the First Passage Time, Results from Discontinuous Molecular Dynamics Simulations of an All Atom Model of the Second Beta Hairpin Fragment of Protein G", J. Amer. Chem. Soc. 125, 6300(2003)
41. C. L. Lee, C. T. Lin, G. Stell, J. Wang, "Diffusion Dynamics, Moments and Distributions of First Passage Time on Protein Folding Energy Landscapes, with Applications to Single Molecules ", Phys. Rev. E. 67, 41905(2003)
40. J. Wang, G. M. Verkhivker, " Energy Landscape Theory, Funnels, Specificity and Optimal Criterion of Biomolecular Binding", Phys. Rev. Lett. 90, 188101(2003)
39. C. L. Lee, G. Stell, J. Wang, "First Passage Time Distribution and Non-Makovian Dynamics of Protein Folding", J. Chem. Phys. 118, 959(2003)
38. J. Wang , "Statistics, Pathways and Single Molecule Folding", J. Chem. Phys. 118, 952(2003)
37. J. Wang, X. D. Wang, "Some Thoughts on the Credit Bureaus and National Credit Systems in China", China Credit Card, 7(2002).
36. J. Lin, J. Wang, "Demand for Credit Rises in China -But Where Is the Infrastructure?" Credit Risk International, 11, 24(2002).
35. J. Wang, Preface for "Consumer Credit Management’’ by Junyue Lin, Huicheng Credit Management Book Series, China Fangzheng Pub. (2002).
34. J. Wang, P. G. Wolynes, " Reaction Diffusion Description of Intermittency of Single Molecule Reaction Dynamics in Fluctuating Environments ", J. Chem. Phys. 110, 4812, (1999).
33. B. A. Shoemaker, J. Wang, P. G. Wolynes, " Exploring Structures in Protein Folding Funnels with Free Energy Functionals: The Transition State Ensemble", B. A. Shoemaker, J. Wang, P. G. Wolynes, J. Mol. Biology 287, 675 (1999).
32. J. N. Onuchic, J. Wang, P. G. Wolynes, "Analyzing Single Molecule Trajectories on Complex Energy Landscapes Using Replica Correlation Function", Chem. Phys. 247,175 (1999).
31. S. S. Plotkin, J. Wang, P. G. Wolynes, "Statistical Thermodynamics of Correlated Energy Landscape", Physica D 107, 322(1997).
30. S. Okazaki, J. Wang, S. A. Schofield, P. G. Wolynes, "Quantum Twinkling: Fluctuation and Coherence through the High Order Moments of the Wave Function", Chem. Phys. 222, 175(1997).
29. S. S. Plotkin, J. Wang, P. G. Wolynes, "Statistical Mechanics of a Correlated Energy Landscape Model for Protein Folding Funnels", J. Chem. Phys. 106, 2932 (1997).
28. J. Wang, S. S. Plotkin, P. G. Wolynes, " Configurational Diffusion in a Locally Connected Correlated Energy Landscape Model for Random heteropolymers", J. de. Physique. 7, 395(1997).
27. B. A. Shoemaker, J. Wang, P. G. Wolynes, "Structure Correlations in Protein Folding Funnels", Proc. Natl. Acad. Sci. 94, 777(1997).
26. J. Wang, J. G. Saven, P. G. Wolynes, "Kinetics in a Globally Connected, Correlated Random Energy Model", J. Chem. Phys. 105, 11276 (1996).
25. J. Wang, P. G. Wolynes, " Instantons and the Fluctuating Path Description of Reactions in Complex Biological Environments", J. Physical Chemistry, 100, 1129(1996).
24. J. Wang, J. N. Onuchic, P. G. Wolynes, " Statistics and Kinetic Pathways of Protein Folding on Complex Energy Landscapes", Phys. Rev Lett. 76, 4861(1996).
23. S. Plotkin, J. Wang, P. G. Wolynes, " A Correlated Energy Landscape Model for Finite, Random Heteropolymers", Phys. Rev. E. 53, 6271(1996).
22. A. R. Panchenko , J. Wang, G. U. Nienhaus, P. G. Wolynes, " Dynamics of Binding of Myglobin and CO Ligand", Biophys. J. 68, A82 (1995).
21. J. Wang, P. G. Wolynes, "Reaction Dynamics in Fluctuating Proteins", Proceedings of 19th IUPAP on Statistical Physics (1995).
20. A. R. Panchenko, J. Wang, G. U. Nienhaus, P. G. Wolynes, "Analysis of Ligand Binding to Heme Proteins Using a Fluctuating Path Description", J. Phys. Chem. 99, 9278(1995).
19. J. Wang, P. G. Wolynes, "Intermittency of Single Molecule Reaction Dynamics in Fluctuating Environments", Phys. Rev. Lett. 74, 4317 (1995).
18. H. Bohr, J. Wang, P. G. Wolynes, "Growth of Domains in Distance Geometry through Protein Folding", Proceedings of Protein Structure by Distance Analysis, (IOS Press, Amesterdam, 1994).
17. J. Wang, P. G. Wolynes, "Survival Path for Reaction Dynamics in Fluctuating Environment", Chem. Phys. 180, 141(1994).
16. J. G. Saven, J. Wang, P. G. Wolynes, "Kinetics of Protein Folding: the Dynamics of Globally Connected Rough Energy Landscapes with Biases", J. Chem. Phys. 101, 11037(1994).
15. J. Wang, P. G. Wolynes, "Passage Through Fluctuating Barrier-General Gaussian Case", Chem Phys. Lett. 212, 427 (1993).
14. J. Wang, A. Hubler , " Control of Chaos for Solitons", Proceedings of Santa Fe Complex System 1991 Summer School (1992).
13. J. Wang, "Quantum Cosmology of Supersymmetric Strings", Phys. Rev. D. 45, 412 (1992).
12. J. Wang, "Ten Dimensional Supergravity Wormhole", Astrophysics and Space Science 189, 5 (1992).
11. J. Wang, "Constraints of Axion Mass from White Dwarf Cooling", Modern Phys. Lett. A. 7, 1497(1992).
10. J. Wang, "Constraints of Axion Mass from Carbon Oxygen Burning Stage of Stellar Evolution", Phys. Lett. B 291, 97(1992).
9. J. Wang, "Constraints of Neutrino Magnetic Moment from White Dwarf Cooling", Astrophysics and Space Science 189, 1 (1992).
8. J. Wang, S. Mohanty , "Quantum Cosmology of String Theory", Phys. Lett. B. 269, 279 (1991).
7. J. Wang, "Cosmic Strings in the Sun?", Modern Physics Letters A. 6, 2101(1991).
6. J. Wang, "Astrophysical Constraints of Gravitational Constant", Astrophysics and Space Science 184, 31(1991).
5. J. Wang, "Bounds on KSVZ Axions from High Mass Star Evolution", Astrophysics and Space Science 184, 1(1991).
4. J. Wang, "Primordial Magnetic Field and Density Fluctuation from Early Universe Phase Transition" , AIP Proceedings 222 "After the First Three Minutes" (1991).
3. D. Chang, A. Kumar, J. Wang, "Search For Extended Conformal Algebra", Modern Physics Letters. A. 5, 1511(1990).
2. D. Chang, A. Kumar, J. Wang, "Heterotic Conformal Field Theory and Gepner's Construction", Phys. Rev. D. 42, No. 8, 2694 (1990).
1. J. Haglin, S. Kelly, J. Wang, "On the Analysis of Flavour Changing Neutral Current From SUS Y", BNL Workshop Proceedings on Rare K decays and CP violation (1988).