Hong Qian

Personal Home Page

http://www.amath.washington.edu/people/faculty/qian/

Articles in Scholarly Journals [Incomplete List]

  1. Quantitative Model for Binary Measurements of Protein-Protein Interactions
    Journal of Computational Biology, vol. 14, no. 7, pp. 1011–1023, 2007
  2. Clustering coefficients of protein-protein interaction networks
    Physical Review E, vol. 75, no. 5, 2007
  3. Journal of Bioinformatics and Computational Biology, vol. 4, no. 6, p. 1227, 2006
  4. Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen
    Physical Review E, vol. 73, no. 4, 2006
  5. Generalized Haldane equation and fluctuation theorem in the steady-state cycle kinetics of single enzymes
    Physical Review E, vol. 74, no. 1, 2006
  6. Journal of Physical Chemistry B, vol. 110, no. 31, pp. 15063–15074, 2006
  7. Grand canonical Markov model: A stochastic theory for open nonequilibrium biochemical networks
    The Journal of Chemical Physics, vol. 124, no. 4, p. 044110, 2006
  8. Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences
    Proceedings of the National Academy of Sciences, vol. 103, no. 31, pp. 11527–11532, 2006
  9. A Stochastic Model of Oscillatory Blood Testosterone Levels
    Bulletin of Mathematical Biology, vol. 68, no. 6, pp. 1383–1399, 2006
  10. Reducing Intrinsic Biochemical Noise in Cells and Its Thermodynamic Limit
    Journal of Molecular Biology, vol. 362, no. 3, pp. 387–392, 2006
  11. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium
    Biophysical Chemistry, vol. 114, no. 2-3, pp. 213–220, 2005
  12. An Asymptotic Comparative Analysis of the Thermodynamics of Non-Covalent Association
    Journal of Mathematical Biology, vol. 52, no. 3, pp. 277–289, 2005
  13. Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry
    Metabolic Engineering, vol. 7, no. 4, pp. 251–259, 2005
  14. The Journal of Physical Chemistry B, vol. 109, no. 49, pp. 23624–23628, 2005
  15. Nano Letters, vol. 5, no. 12, pp. 2373–2378, 2005
  16. Cycle kinetics, steady state thermodynamics and motors—a paradigm for living matter physics
    Journal of Physics: Condensed Matter, vol. 17, no. 47, pp. S3783–S3794, 2005
  17. Multiscale Modeling of Cardiac Cellular Energetics
    Annals of the New York Academy of Sciences, vol. 1047, no. 1, pp. 395–426, 2005
  18. Nonequilibrium Thermodynamics and Nonlinear Kinetics in a Cellular Signaling Switch
    Physical Review Letters, vol. 94, no. 2, 2005
  19. Entropy Production of Brownian Macromolecules with Inertia
    Physical Review Letters, vol. 93, no. 12, 2004
  20. Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism
    AJP: Endocrinology and Metabolism, vol. 288, no. 3, pp. E633–E644, 2004
  21. Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady states
    Proceedings of the National Academy of Sciences, vol. 101, no. 9, pp. 2828–2833, 2004
  22. Motor protein with nonequilibrium potential: Its thermodynamics and efficiency
    Physical Review E, vol. 69, no. 1, 2004
  23. Thermodynamic constraints for biochemical networks
    Journal of Theoretical Biology, vol. 228, no. 3, pp. 327–333, 2004
  24. Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction
    Biophysical Chemistry, vol. 105, no. 2-3, pp. 585–593, 2003
  25. Stoichiometric network theory for nonequilibrium biochemical systems
    European Journal of Biochemistry, vol. 270, no. 3, pp. 415–421, 2003
  26. Sensitivity and Specificity Amplification in Signal Transduction
    Cell Biochemistry and Biophysics, vol. 39, no. 1, pp. 45–60, 2003
  27. Concentration fluctuations in a mesoscopic oscillating chemical reaction system
    Proceedings of the National Academy of Sciences, vol. 99, no. 16, pp. 10376–10381, 2002
  28. Entropy production and excess entropy in a nonequilibrium steady-state of single macromolecules
    Physical Review E, vol. 65, no. 2, 2002
  29. Single-molecule enzymology: stochastic Michaelis–Menten kinetics
    Biophysical Chemistry, vol. 101-102, pp. 565–576, 2002
  30. Biophysical chemistry of proteins and nucleic acids: a festschrift for John A. Schellman
    Biophysical Chemistry, vol. 101-102, pp. 7–8, 2002
  31. Journal of Statistical Physics, vol. 107, no. 5/6, pp. 1129–1141, 2002
  32. The Journal of Physical Chemistry B, vol. 106, no. 8, pp. 2065–2073, 2002
  33. A simple method of parameter space determination for diffusion-driven instability with three species
    Applied Mathematics Letters, vol. 14, no. 4, pp. 405–411, 2001
  34. Mathematical formalism for isothermal linear irreversibility
    Proceedings: Mathematical, Physical and Engineering Sciences, vol. 457, no. 2011, pp. 1645–1655, 2001
  35. Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation
    Physical Review E, vol. 65, no. 1, 2001
  36. The Journal of Physical Chemistry B, vol. 104, no. 48, pp. 11528–11540, 2000
  37. Journal of Mathematical Chemistry, vol. 27, no. 3, pp. 219–234, 2000
  38. A simple theory of motor protein kinetics and energetics. II
    Biophysical Chemistry, vol. 83, no. 1, pp. 35–43, 2000
  39. A mathematical analysis for the Brownian dynamics of a DNA tether
    Journal of Mathematical Biology, vol. 41, no. 4, pp. 331–340, 2000
  40. A Class of Flow Bifurcation Models with Lognormal Distribution and Fractal Dispersion
    Journal of Theoretical Biology, vol. 205, no. 2, pp. 261–268, 2000
  41. Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix-forming propensities
    Proteins: Structure, Function, and Genetics, vol. 34, no. 4, pp. 497–507, 1999
  42. Graphical method for force analysis: Macromolecular mechanics with atomic force microscopy
    Proteins: Structure, Function, and Genetics, vol. 37, no. 4, pp. 576–581, 1999
  43. Hydrogen exchange kinetics of proteins in denaturants: a generalized two-process model ,
    Journal of Molecular Biology, vol. 286, no. 2, pp. 607–616, 1999
  44. Stochastic fractal behavior in concentration fluctuation and fluorescence correlation spectroscopy
    Biophysical Chemistry, vol. 80, no. 1, pp. 1–5, 1999
  45. Journal of Physics A: Mathematical and General, vol. 31, no. 28, pp. L527–L535, 1999
  46. Entropy-enthalpy compensation: Conformational fluctuation and induced-fit
    The Journal of Chemical Physics, vol. 109, no. 22, p. 10015, 1998
  47. Vector Field Formalism and Analysis for a Class of Thermal Ratchets
    Physical Review Letters, vol. 81, no. 15, pp. 3063–3066, 1998
  48. Blood flows and metabolic components of the cardiome
    Progress in Biophysics and Molecular Biology, vol. 69, no. 2-3, pp. 445–461, 1998
  49. Hysteresis in Force Probe Measurements: a Dynamical Systems Perspective
    Journal of Theoretical Biology, vol. 194, no. 4, pp. 551–559, 1998
  50. Thermodynamic hierarchy and local energetics of folded proteins
    Journal of Molecular Biology, vol. 267, no. 1, pp. 198–206, 1997
  51. Local interactions and the optimization of protein folding
    Proteins: Structure, Function, and Genetics, vol. 29, no. 3, pp. 282–291, 1997
  52. A quantitative analysis of single protein-ligand complex separation with the atomic force microscope
    Biophysical Chemistry, vol. 67, no. 1-3, pp. 211–219, 1997
  53. A simple theory of motor protein kinetics and energetics
    Biophysical Chemistry, vol. 67, no. 1-3, pp. 263–267, 1997
  54. Prediction of a-Helices in Proteins Based on Thermodynamic Parameters from Solution Chemistry
    Journal of Molecular Biology, vol. 256, no. 4, pp. 663–666, 1996
  55. Interactions Between a Helical Residue and Tertiary Structures: Helix Propensities in Small Peptides and in Native Proteins
    Journal of Molecular Biology, vol. 261, no. 2, pp. 279–288, 1996
  56. Entropy-enthalpy compensation: Perturbation and relaxation in thermodynamic systems
    The Journal of Chemical Physics, vol. 105, no. 20, p. 9292, 1996
  57. Biochemistry, vol. 33, no. 27, pp. 8167–8171, 1994
  58. Single-residue substitution in homopolypeptides: Perturbative helix-coil theory at a single site
    Biopolymers, vol. 33, no. 10, pp. 1605–1616, 1993
  59. Helix-coil theories: a comparative study for finite length polypeptides
    Journal of Physical Chemistry, vol. 96, no. 10, pp. 3987–3994, 1992
  60. Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water
    Biopolymers, vol. 31, no. 13, pp. 1463–1470, 1991
  61. Nanometre-level analysis demonstrates that lipid flow does not drive membrane glycoprotein movements
    Nature, vol. 340, no. 6231, Article ID 340284a0, 4 pages, 1989