Hongyun Wang's Publications


  1. H. Zhou, E. Choate and H. Wang (In Press). Optical Fredericks Transition in a Nematic Liquid Crystal Layer. In: Liquid Crystalline Polymers: Processing and Applications, edited by V. K. Thakur. (Springer, New York).

  2. H. Wang and H. Zhou (2015). Computational Studies on Detecting a Diffusing Target in a Square Region by a Stationary or Moving Searcher. American Journal of Operations Research 5(2), 47-68. [PDF of the article ]

  3. J. M. Dahl, H. Wang, J. M. Lazaro, M. Salas, and K. R. Lieberman (2014). Kinetic Mechanisms Governing Stable Ribonucleotide Incorporation in Individual DNA Polymerase Complexes. Biochemistry 53(51), 8061-8076. [PDF of the article ] [Supplemental Information (SI) ]

  4. K. R. Lieberman, J. M. Dahl, and H. Wang (2014). Kinetic Mechanism at the Branchpoint Between the DNA Synthesis and Editing Pathways in Individual DNA Polymerase Complexes. Journal of the American Chemical Society 136(19), 7117-7131. [PDF of the article ] [Supplemental Information (SI) ]

  5. J. M. Dahl, H. Wang, J. M. Lazaro, M. Salas and K. R. Lieberman (2014). Dynamics of Translocation and Substrate Binding in Individual Complexes Formed with Active Site Mutants of Phi29 DNA Polymeras. J. Biol. Chem. 289(10), 6350-6361. [PDF of the article ]

  6. C. R. O'Donnell, H. Wang, and W. B. Dunbar (2013). Error analysis of idealized nanopore sequencing. Electrophoresis 34(15), 2137-2144. [PDF of the article ]

  7. K. R. Lieberman, J. M. Dahl, A. H. Mai, A. Cox, M. Akeson, and H. Wang (2013). Kinetic Mechanism of Translocation and dNTP Binding in Individual DNA Polymerase Complexes. Journal of the American Chemical Society 135(24), 9149-9155. [PDF of the article ] [Supplemental Information (SI) ]

  8. H. Wang and H. Zhou (2013). Parameter estimation for a thin layer by measuring temperature induced by a heat source. Journal of Mathematical and Computational Science 3(6), 1353-1372. [PDF of the article ]

  9. H. Wang, N. Hurt, and W. B. Dunbar (2013). Measuring and Modeling the Kinetics of Individual DNA-DNA Polymerase Complexes on a Nanopore. ACS Nano 7(5), 3876-3886. [PDF of the article ] [Supplemental Information (SI) ]

  10. K. R. Lieberman, J. M. Dahl, A. H. Mai, M. Akeson, and H. Wang (2012). Dynamics of the translocation step measured in individual DNA polymerase complexes. Journal of the American Chemical Society 134(45), 18816-18823. [PDF of the article ] [Supplemental Information (SI) ]

  11. J. M. Dahl, A. H. Mai, G. M. Cherf, N. N. Jetha, D. R. Garalde, A. Marziali, M. Akeson, H. Wang, and K. R. Lieberman (2012). Direct observation of translocation in individual DNA polymerase complexes. J Biol Chem. 287(16), 13407-13421. [PDF of the article ] [Supplemental Information (SI) ]

  12. H. Wang (2011). Effective Diffusion and Effective Drag Coefficient of a Brownian Particle in a Periodic Potential. Acta Mathematica Scientia 31B(6), 2323-2342. [PDF of the article ]

  13. H. Zhou and H. Wang (2011). Stability of Equilibria of Nematic Liquid Crystalline Polymers. Acta Mathematica Scientia 31B(6), 2289-2304. [PDF of the article ]

  14. D. R. Garalde, C. A. Simon, J. M. Dahl, H. Wang, M. Akeson, and K. R. Lieberman (2011). Distinct Complexes of DNA Polymerase I (Klenow Fragment) for Base and Sugar Discrimination During Nucleotide Substrate Selection. J Biol Chem. 286(16), 14480-14492. [PDF of the article ] [Supplemental Information (SI) ]

  15. B. Gyarfas, R. Abu-Shumays, H. Wang and W. B. Dunbar (2011). Measuring single molecule DNA hybridization by active control of DNA in a nanopore. Biophysical Journal 100(6), 1509-1516. [PDF of the article ] [Supplemental Information (SI) ]

  16. H. Wang and H. Zhou (2010). Phase diagram of nematic polymer monolayers with the Onsager interaction potential. Journal of Computational and Theoretical Nanoscience 7, 738-755. [PDF of the article ]

  17. H. Zhou, W. Kang, A. Krener, and H. Wang (2010). Observability of viscoelastic fluids. Journal of Non-Newtonian Fluid Mechanics 165, 425-434. [PDF of the article ]

  18. H. Zhou, M. G. Forest, and H. Wang (2010). Mathematical Studies and Simulations of Nematic Liquid Crystal Polymers and Nanocomposites. Journal of Computational and Theoretical Nanoscience 7, 645-660. [PDF of the article ]

  19. N. A. Wilson, R. Abu-Shumays, B. Gyarfas, H. Wang, K. R. Lieberman, M. Akeson and W. B. Dunbar (2009). Electronic Control of DNA Polymerase Binding and Unbinding to Single DNA Molecules. ACS Nano 3, 995-1003. [PDF of the article ]

  20. N. Hurt, H. Wang, M. Akeson and K. R. Lieberman (2009). Specific Nucleotide Binding and Rebinding to Individual DNA Polymerase Complexes Captured on a Nanopore. Journal of the American Chemical Society 131, 3772-3778. [PDF of the article ] [Supplemental Information (SI) ]

  21. H. Wang (2009). Stokes Efficiency of Molecular Motors with Inertia. Applied Mathematics Letters 22, 79-83. [PDF of the article ]

  22. H. Wang, H. Zhou, and M. G. Forest (2009). Sheared nematic liquid crystal polymer monolayers. Discrete and Continuous Dynamical Systems - Series B 11, 497-517. [PDF of the article ]

  23. H. Wang and H. Zhou (2008). Extendability of equilibria of nematic polymers. Abstract and Applied Analysis 2008, Article 854725. [PDF of the article ]

  24. H. Wang and P. Hoffman (2008). A unified view on the rotational symmetry of equilibria of nematic polymers, dipolar nematic polymers and polymers in higher dimensional space. Communications in Mathematical Sciences 6, 949-974. [PDF of the article ]

  25. H. Wang (2008). Several issues in modeling molecular motors. Journal of Computational and Theoretical Nanoscience 5, 2311-2345. [PDF of the article ]

  26. H. Wang and H. Zhou (2008). Stokes efficiency of molecular motor-cargo systems. Abstract and Applied Analysis 2008, Article 241736. [PDF of the article ]

  27. L. Wilson, H. Zhou, W. Kang, and H. Wang (2008). Controllability of Non-Newtonian Fluids Under Homogeneous Extensional Flow. Applied Mathematical Sciences 2, 2145-2156. [PDF of the article ]

  28. H. Wang and H. Zhou (2008). Multiple branches of ordered states of polymer ensembles with the Onsager excluded volume potential. Physics Letters A 372, 3423-3428. [PDF of the article ]

  29. H. Zhou, W. Kang, A. Krener and H. Wang (2008). Homogeneous flow field effect on the control of Maxwell materials. Journal of Non-Newtonian Fluid Mechanics 150, 104-115. [PDF of the article ]

  30. H. Wang and H. Zhou (2008). Exact solution of a constrained optimization problem in thermoelectric cooling. Applied Mathematical Sciences 2, 177-186. [PDF of the article ]

  31. A. Brandwajn and H. Wang (2008). A Conditional Probability Approach to M/G/1-like Queues. Performance Evaluation 65, 366-381. [PDF of the article ]

  32. H. Wang (2008). An Improved WPE Method for Solving Discontinuous Fokker-Planck Equations. International Journal of Numerical Analysis and Modeling 5, 1-23. [PDF of the article ]

  33. G. Ji, Q. Wang, P. Zhang, H. Wang, and H. Zhou (2007). Steady states and their stability of homogeneous, rigid, extended nematic polymers under imposed magnetic fields. Communications in Mathematical Sciences 5(4), 917-950. [PDF of the article ]

  34. H. Wang (2007). A New Derivation of the Randomness Parameter. Journal of Mathematical Physics 48, Article 103301. [PDF of the article ]
    This paper was included in the October 15, 2007 issue of Virtual Journal of Biological Physics Research

  35. H. Zhou and H. Wang (2007). Elongational perturbations on nematic liquid crystal polymers under a weak shear. Physics of Fluids 19, Article 103107. [PDF of the article ]

  36. H. Wang and H. Zhou (2007). Monotonicity of a key function arised in studies of nematic liquid crystal polymers. Abstract and Applied Analysis 2007, Article 76209. [PDF of the article ]

  37. H. Zhou and H. Wang (2007). Asymptotic study on the extendability of equilibria of nematic polymers. International Journal of Contemporary Mathematical Sciences 2, 1009-1023. [PDF of the article ]

  38. H. Wang (2007). Convergence of a numerical method for solving discontinuous Fokker-Planck equations. SIAM Journal on Numerical Analysis 45, 1425-1452. [PDF of the article ]

  39. Z. Bian, H. Wang, Q. Zhou, and A. Shakouri (2007). Maximum cooling temperature and uniform efficiency criterion for inhomogeneous thermoelectric materials. Physical Review B 75, Article 245208. [PDF of the article ]

  40. H. Zhou, L. Wilson and H. Wang (2007). On the equilibria of the extended nematic polymers under elongational flow. Abstract and Applied Analysis 2007, Article 36267. [PDF of the article ]

  41. H. Wang and T. Elston (2007). Mathematical and computational methods for studying energy transduction in protein motors. Journal of Statistical Physics 128, 35-76. [PDF of the article ]

  42. H. Zhou, H. Wang and Q. Wang (2007). Nonparallel solutions of extended nematic polymers under an external field. Discrete and Continuous Dynamical Systems - Series B 7, 907-929. [PDF of the article ]

  43. H. Zhou and H. Wang (2007). Steady States and Dynamics of 2-D Nematic Polymers Driven by an Imposed Weak Shear. Communications in Mathematical Sciences 5, 113-132. [PDF of the article ]

  44. H. Wang and H. Qian (2007). On Detailed Balance and Reversiblity of Semi-Markov Processes and Single-molecule Enzyme Kinetics. Journal of Mathematical Physics 48, Article 013303. [PDF of the article ]

  45. H. Zhou, H. Wang, Q. Wang and M. G. Forest (2007). Characterization of stable kinetic equilibria of rigid, dipolar rod ensembles for coupled dipole-dipole and Maier-Saupe potentials. Nonlinearity 20, 277-297. [PDF of the article ]

  46. H. Wang (2006). A robust mathematical formulation for studying elastically coupled motor-cargo systems. Journal of Computational and Theoretical Nanoscience 3, 922-932. [PDF of the article ].
    For colored figures, see PDF page proofs of the article.

  47. H. R. Sadjadpour, K. Kim, H. Wang, R. S. Blum and Y. H. Lee (2006). Application of Randomization Techniques to Space-time Convolutional Codes. IEEE Transactions on Signal Processing 54, 4484-4489. [PDF of the article ]

  48. H. Qian and H. Wang (2006). Continuous Time Random Walks in Closed and Open Single-Molecule Systems with Microscopic Reversibility. Europhysics Letters 76, 15-21 . [PDF of the article ]

  49. H. Wang (2006). Motor potential profile and a robust method for extracting it from time series of motor positions. Journal of Theoretical Biology 242, 908-921. [PDF of the article ]

  50. J. Fricks, H. Wang and T. Elston (2006). A numerical algorithm for investigating the role of the motor-cargo linkage in molecular motor-driven transport. Journal of theoretical Biology 239, 33-48. [PDF of the article ]

  51. H. Wang (2005). Chemical and mechanical efficiencies of molecular motors and implications for motor mechanisms. Journal of Physics: Condensed Matter 17, S3997-S4014. [PDF of the article ]

  52. H. Zhou, H. Wang, M. G. Forest and Q. Wang (2005). A new proof on axisymmetric equilibria of a three-dimensional Smoluchowski equation. Nonlinearity 18, 2815-2825. [PDF of the article ]

  53. J. Xing, H. Wang and G. Oster (2005). From Continuum Fokker-Planck Models to Discrete Kinetic Models. Biophysical Journal 89, 1551-1563. [PDF of the article ]

  54. H. R. Sadjadpour, K. Kim, H. Wang, R. S. Blum and Y. H. Lee (2005). Application of randomization techniques to space-time convolutional codes. 2005 International Conference on Wireless Networks, Communications and Mobile Computing 2, 1491-1496. [PDF of the article ]

  55. J. Xing, H. Wang, C. von Ballmoos, P. Dimroth and G. Oster (2004). Torque generation by the Fo motor of the sodium ATPase. Biophysical Journal 87, 2148-2163. [PDF of the article ]

  56. H. R. Sadjadpour and H. Wang (2004). Exploring New Sources of Diversity in Wireless Systems. 2004 IEEE 60th Vehicular Technology Conference 5, 3644-3648 [PDF of the article ]

  57. S. Sun, H. Wang and G. Oster (2004). Asymmetry in the F1-ATPase and its implication for the rotation cycle. Biophysical Journal 86, 1373-1384. [PDF of the article ]

  58. H. Wang and H. Zhou (2003). Slender Vortex Motion. Recent Research Developments in Fluid Dynamics 4, 159-179. [PDF of the article ]

  59. H. Wang (2003). Mathematical theory of molecular motors and a new approach for uncovering motor mechanism. IEE Proceedings Nanobiotechnology 150, 127-133. [PDF of the article ]

  60. I. Antes, D. Chandler, H. Wang and G. Oster (2003). A molecular dynamics study of the unbinding of ATP from F1-ATPase. Biophysical Journal 85, 695-706. [PDF of the article ]

  61. H. Wang, C. Peskin and T. Elston (2003). A robust numerical algorithm for studying biomolecular transport process. Journal of theoretical Biology 221, 491-511. [PDF of the article ]

  62. G. Oster and H. Wang (2003). Rotary protein motors. Trends in Cell Biology 13, 114-121. [PDF of the article ]

  63. G. Oster and H. Wang (2003). How protein motors convert chemical energy into mechanical work. In: Molecular Motors, edited by M. Schliwa. (Wiley-VCH). [PDF of the article ]

  64. H. Wang and G. Oster (2002). Ratchets, power strokes, and molecular motors. Applied Physics A 75, 315-323. [PDF of the article ]

  65. A. Mogilner, T. Elston, H. Wang, and G. Oster (2002). Molecular motors: theory. In: Joel Keizer's Computational Cell Biology, edited by C. Fall, E. Marland, J. Tyson, and J. Wagner. (Springer, New York). [PDF of the article ]

  66. A. Mogilner, T. Elston, H. Wang, and G. Oster (2002). Molecular motors: examples. In: Joel Keizer's Computational Cell Biology, edited by C. Fall, E. Marland, J. Tyson, and J. Wagner. (Springer, New York). [PDF of the article ]

  67. H. Wang and G. Oster (2002). The Stokes efficiency for molecular motors and its applications. Europhysics Letters 57, 134-140. [PDF of the article ]

  68. G. Oster and H. Wang (2000). Why is the mechanical efficiency of F 1 ATPase so high? Journal of Bioenergetics and Biomembranes 32, 459-469. [PDF of the article ]

  69. M. Grabe, H. Wang and G. Oster (2000). The mechanochemistry of the V-ATPase proton pumps. Biophysical Journal 78, 2798-2813. [PDF of the article ]

  70. G. Oster and H. Wang (2000). Reverse engineering a protein: The mechanochemistry of ATP synthase. Biochimica et Biophysica Acta 1458, 482-510. [PDF of the article ]

  71. G. Oster, H. Wang and M. Grabe (2000). How Fo-ATPase generates rotary torque. Reverse engineering a protein: The mechanochemistry of ATP synthase. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 355, 523-528. [PDF of the article ]

  72. G. Oster, H. Wang (1999). ATP synthase: 2 motors, 2 fuels. Structure 7, R67-R72. [PDF of the article ]

  73. P. Dimroth, H. Wang, M. Grabe, G. Oster (1999). Energy transduction in the sodium F-ATPase of Propionigenium modestum. Proceedings of the National Academy of Sciences 96, 4924-4929. [PDF of the article ] [Supplemental Information (SI) ]

  74. G. Oster and H. Wang (1999). ATP Synthase: Two rotary molecular motors working together. In: Encyclopedia of Molecular Biology, edited by T. Creighton. (Wiley, New York). [PDF of the article ]

  75. H. Wang and G. Oster (1998). Energy transduction in the F1 motor of ATP synthase. Nature 396, 279-282. [PDF of the article ] [Supplemental Information (SI) ]

  76. H. Wang (1998). Short wave instability on vortex filaments. Physical Review Letters 80, 4665-4668. [PDF of the article ]

  77. H. Wang, T. Elston, A. Mogilner and G. Oster (1998). Force generation In RNA polymerase. Biophysical Journal 74, 1186-1202. [PDF of the article ]

  78. T. Elston, H. Wang and G. Oster (1998). Energy transduction in ATP synthase. Nature 391, 510-513. [PDF of the article ] [Supplemental Information (SI) ]

  79. H. Wang (1996). A study of short wave instability on vortex filaments. Ph.D. Dissertation, University of California, Berkeley.

  80. H. Wang (1993). A high order vortex method for patches of constant vorticity. LBL report, Lawrence Berkeley National Laboratory.

  81. H. Wang (1987). A simple conservative difference scheme for solving full Euler equations. Chinese Journal Computational Physics 4, 79-84.