Hongyun Wang

Summary

Affiliation: University of California
Country: USA

Publications

  1. ncbi request reprint A robust numerical algorithm for studying biomolecular transport processes
    Hongyun Wang
    Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA 95064, USA
    J Theor Biol 221:491-511. 2003
  2. ncbi request reprint Motor potential profile and a robust method for extracting it from time series of motor positions
    Hongyun Wang
    Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA 95064, USA
    J Theor Biol 242:908-21. 2006
  3. pmc Dynamics of the translocation step measured in individual DNA polymerase complexes
    Kate R Lieberman
    Biomolecular Engineering, University of California, Santa Cruz, 95064, United States
    J Am Chem Soc 134:18816-23. 2012
  4. pmc Direct observation of translocation in individual DNA polymerase complexes
    Joseph M Dahl
    Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 287:13407-21. 2012
  5. pmc Kinetic mechanism of translocation and dNTP binding in individual DNA polymerase complexes
    Kate R Lieberman
    Department of Biomolecular Engineering, University of California, Santa Cruz, Baskin School of Engineering, 1156 High Street, MS SOE2, Santa Cruz, California 95064, USA
    J Am Chem Soc 135:9149-55. 2013
  6. pmc Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection
    Daniel R Garalde
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 286:14480-92. 2011
  7. pmc From continuum Fokker-Planck models to discrete kinetic models
    Jianhua Xing
    Departments of Molecular and Cellular Biology and Environmental Science, University of California, Berkeley, California, USA
    Biophys J 89:1551-63. 2005
  8. pmc Measuring and modeling the kinetics of individual DNA-DNA polymerase complexes on a nanopore
    Hongyun Wang
    Department of Applied Mathematics and Statistics, University of California, Santa Cruz, California 95064, United States
    ACS Nano 7:3876-86. 2013
  9. pmc Error analysis of idealized nanopore sequencing
    Christopher R O'Donnell
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA, USA
    Electrophoresis 34:2137-44. 2013
  10. pmc Measuring single-molecule DNA hybridization by active control of DNA in a nanopore
    Brett Gyarfas
    Department of Computer Engineering, University of California at Santa Cruz, Santa Cruz, California, USA
    Biophys J 100:1509-16. 2011

Collaborators

Detail Information

Publications14

  1. ncbi request reprint A robust numerical algorithm for studying biomolecular transport processes
    Hongyun Wang
    Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA 95064, USA
    J Theor Biol 221:491-511. 2003
    ..We provide several simple examples of how to implement the algorithm. All the MATLAB functions files needed to reproduce the results presented in the article are available from www.amath.unc.edu/Faculty/telston/matlab_functions...
  2. ncbi request reprint Motor potential profile and a robust method for extracting it from time series of motor positions
    Hongyun Wang
    Department of Applied Mathematics and Statistics, University of California, Santa Cruz, CA 95064, USA
    J Theor Biol 242:908-21. 2006
    ..For a macroscopic motor, the variation of driving force within a cycle is smoothed out by the large inertia...
  3. pmc Dynamics of the translocation step measured in individual DNA polymerase complexes
    Kate R Lieberman
    Biomolecular Engineering, University of California, Santa Cruz, 95064, United States
    J Am Chem Soc 134:18816-23. 2012
    ..The analysis reveals that active-site proximal DNA sequences influence the depth of the pre-translocation and post-translocation state energy wells and affect the location of the transition state along the direction of the translocation...
  4. pmc Direct observation of translocation in individual DNA polymerase complexes
    Joseph M Dahl
    Department of Biomolecular Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 287:13407-21. 2012
    ....
  5. pmc Kinetic mechanism of translocation and dNTP binding in individual DNA polymerase complexes
    Kate R Lieberman
    Department of Biomolecular Engineering, University of California, Santa Cruz, Baskin School of Engineering, 1156 High Street, MS SOE2, Santa Cruz, California 95064, USA
    J Am Chem Soc 135:9149-55. 2013
    ..This combined experimental and theoretical approach and the results obtained provide a framework for separately evaluating the effects of biological variables on the translocation transitions and their effects on dNTP binding...
  6. pmc Distinct complexes of DNA polymerase I (Klenow fragment) for base and sugar discrimination during nucleotide substrate selection
    Daniel R Garalde
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, California 95064, USA
    J Biol Chem 286:14480-92. 2011
    ..These results imply that nucleotide selection proceeds through a series of complexes of increasing stability in which substrates with the correct moiety promote the forward transitions...
  7. pmc From continuum Fokker-Planck models to discrete kinetic models
    Jianhua Xing
    Departments of Molecular and Cellular Biology and Environmental Science, University of California, Berkeley, California, USA
    Biophys J 89:1551-63. 2005
    ..Several numerical examples are given to illustrate the performance of the method...
  8. pmc Measuring and modeling the kinetics of individual DNA-DNA polymerase complexes on a nanopore
    Hongyun Wang
    Department of Applied Mathematics and Statistics, University of California, Santa Cruz, California 95064, United States
    ACS Nano 7:3876-86. 2013
    ..Our method provides a tool for measuring pre-equilibrium kinetics one molecule at a time, serially and for tens of thousands of single-molecule events, and can be used for other polynucleotide-binding enzymes...
  9. pmc Error analysis of idealized nanopore sequencing
    Christopher R O'Donnell
    Department of Computer Engineering, Baskin School of Engineering, University of California, Santa Cruz, CA, USA
    Electrophoresis 34:2137-44. 2013
    ....
  10. pmc Measuring single-molecule DNA hybridization by active control of DNA in a nanopore
    Brett Gyarfas
    Department of Computer Engineering, University of California at Santa Cruz, Santa Cruz, California, USA
    Biophys J 100:1509-16. 2011
    ..The control method is unique in its ability to detect single-molecule complex assembly in the bulk phase, free from external force and with a broad (millisecond-to-second) temporal range...
  11. pmc Torque generation by the Fo motor of the sodium ATPase
    Jianhua Xing
    Department of Molecular Biology, Policy and Management, University of California, Berkeley, California 94720 3112, USA
    Biophys J 87:2148-63. 2004
    ..This work also illustrates how to extract a motor mechanism from dynamical experimental observations in the absence of complete structural information...
  12. pmc The unbinding of ATP from F1-ATPase
    Iris Antes
    Department of Chemistry, University of California, Berkeley, California 94720, USA
    Biophys J 85:695-706. 2003
    ..Our results for the energetics during rotation suggest that the nucleotide's coordination with Mg(2+) during binding and release is necessary to account for the observed high efficiency of the motor...
  13. ncbi request reprint A numerical algorithm for investigating the role of the motor-cargo linkage in molecular motor-driven transport
    John Fricks
    Department of Mathematics, University of North Carolina, Chapel Hill, NC 27599 3250, USA
    J Theor Biol 239:33-48. 2006
    ..The MATLAB code used in this paper is available at: http://www.unc.edu/approximatelytelston/code/...
  14. pmc Asymmetry in the F1-ATPase and its implications for the rotational cycle
    Sean X Sun
    Department of Mechanical Engineering and Whitaker Institute of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
    Biophys J 86:1373-84. 2004
    ....