1. Chemical Biophysics: Quantitative Analysis of Cellular Systems. (with Beard, D.A.) Cambridge Texts in Biomedical Engineering, Cambridge University Press (2008).
  2. Mathematical Kinetic Models: Applications in Biophysics and Biochemistry. [in Chinese] (with Ge, H.) Peking University Series in Contemporary Mathematics, Peking University Press (2017).
  3. Stochastic Chemical Reaction Systems in Biology (with Ge, H.) Lecture Notes on Mathematical Modelling in the Life Sciences, Springer (2021).

  1. Stochastic dynamics: Models for intrinsic and extrinsic noises and their applications (Survey). (with Ma, Y.-A. and Ye, F. X.-F.) Scientia Sinica Mathematica [In Chinese], 47, 1693-1702 (2017).
  2. Processes on the emergent landscapes of biochemical reaction networks and heterogeneous cell population dynamics - Differentiations in living matters (Review). (with Huang, S., Li, F. & Zhou, J.X.) Journal of the Royal Society Interface, 14, 20170097 (2017).
  3. Entropy production in mesoscopic stochastic thermodynamics - Nonequilibrium kinetic cycles driven by chemical potentials, temperatures, and mechanical forces (Topical review). (with Kjelstrup, S., Kolomeisky, A. B. & Bedeaux, D.) Journal of Physics: Condensed Matter, 28, 153004 (2016).
  4. Statistics and related topics in single-molecule biophysics. (with Kou, S.C.) Annual Review of Statistics and Its Application, 1, 465-492 (2014).
  5. Analytical mechanics in stochastic dynamics: Most probable path, large-deviation rate function and Hamilton-Jacobi equation (Review). (with Ge, H.) International Journal of Modern Physics B, 26, 1230012 (2012).
  6. Cooperativity in cellular biochemical processes: Noise-enhanced sensitivity, fluctuating enzyme, bistability with nonlinear feedback, and other mechanisms for sigmoidal responses. Annual Review of Biophysics, 41, 179-204 (2012).
  7. Stochastic theory of nonequilibrium steady states and its applications (Part I). (with Zhang, X.-J. & Qian, M.) Physics Reports, 510, 1-86 (2012).
  8. Stochastic theory of nonequilibrium steady states (Part II): Applications in chemical biophysics. (with Ge, H & Qian, M.) Physics Reports, 510, 87-118 (2012).
  9. Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems - An analytical theory (Invited article). IoP Nonlinearity, 24, R19-R49 (2011).
  10. The chemical master equation approach to nonequilibrium steady-state of open biochemical systems: Linear single-molecule enzyme kinetics and nonlinear biochemical reaction networks (Review). (with Bishop, L.M.) International Journal of Molecular Sciences, 11, 3472-3500 (2010).
  11. Computational cellular dynamics based on the chemical master equation: A challenge for understanding complexity (Survey). (with Liang, J.) Journal of Computer Science and Technology, 25, 154-168 (2010).
  12. Entropy demystified: The ``thermo''-dynamics of stochastically fluctuating systems. Methods in Enzymology, 467, 111-134 (2009).
  13. Cooperativity and specificity in enzyme kinetics: A single-molecule time-based perspective (Mini review). Biophysical Journal, 95, 10-17 (2008).
  14. Phosphorylation energy hypothesis: Open chemical systems and their biological functions. Annual Review of Physical Chemistry, 58, 113-142 (2007).
  15. Open-system nonequilibrium steady-state: Statistical thermodynamics, fluctuations and chemical oscillations (Feature article). Journal of Physical Chemistry B, 110, 15063-15074 (2006).
  16. Cycle kinetics, steady-state thermodynamics and motors -- a paradigm for living matter physics. Journal of Physics: Condensed Matter, 17, S3783-S3794 (2005).
  17. Thermodynamics of stoichiometric biochemical networks in living systems far from equilibrium (Review). (with Beard, D.A.) Biophysical Chemistry, 114, 213-220 (2005).
  18. From discrete protein kinetics to continuous Brownian dynamics: A new perspective (Review). Protein Science, 11, 1-5 (2002).
  19. The mathematical theory of molecular motor movement and chemomechanical energy transduction (Review article). Journal of Mathematical Chemistry, 27, 219-234 (2000).

  1. A Hamiltonian-entropy production connection in the skew-symmetric part of a stochastic dynamics.
  2. Stochastic free energies, conditional probability and Legendre transform for ensemble change (with Santillán, M.)
  3. Estimate exponential memory decay in Hidden Markov Model and its applications (with Ye, F. X.-F. & Ma, Y.-A.).
  4. Intermittent synchronization in finite-state random networks under Markov perturbations (with Berger, A., Wang, S. & Yi, Y.) Communications in Mathematical Physics, 384,1945-1970 (2021).
  5. Asymptotic behavior of a sequence of conditional probability distributions and the canonical ensemble. (with Cheng, Y.-C. & Zhu, Y.) Annales Henri Poincaré, 22, 1561-1627 (2021).
  6. Stochastic limit-cycle oscillations of a nonlinear system under random perturbations. (with Cheng, Y.-C.) Journal of Statistical Physics, 182, 47 (2021).
  7. Bivectorial nonequilibrium thermodynamics: Cycle affinity, vorticity potential, and Onsager's principle. (with Yang, Y.-J.) Journal of Statistical Physics, 182, 46 (2021).
  8. Mathematical representation of Clausius' and Kelvin's statements of the Second law and irreversibility. (with Wang, Y.) Journal of Statistical Physics, 179, 808-837 (2020).
  9. Representations and divergences in the space of probability measures and stochastic thermodynamics (with Hong, L. & Thompson, L.F.) Journal of Computational and Applied Mathematics, 376, 112842 (2020).
  10. Synchronization in discrete-time, discrete-state random dynamical systems. (with Huang, W., Wang, S., Ye, F. X.-F. & Yi, Y.) SIAM Journal on Applied Dynamical Systems, 19, 233-251 (2020).
  11. Entropy productions in dissipative systems. (with Wang, S. & Yi, Y.) Proceedings of the American Mathematical Society, 147, 5209-5225 (2019).
  12. Time dependent saddle node bifurcation: Breaking time and the point of no return in a non-autonomous model of critical transitions. (with Li, J. H., Ye, F. X.-F. & Huang, S.) Physica D: Nonlinear Phenomena, 395, 7-14 (2019).
  13. Stochastic dynamics II: Finite random dynamical systems, linear representation, and entropy production (with Ye, F. X.-F.) Discrete and Continuous Dynamical Systems B, 24, 4341-4366 (2019).
  14. Dynamic looping of a free-draining polymer (with Ye, F. X.-F. & Stinis, P.) SIAM Journal of Applied Mathematics, 78, 104-123 (2018).
  15. Mathematical formalism of nonequilibrium thermodynamics for nonlinear chemical reaction systems with general rate law. (with Ge, H.) Journal of Statistical Physics, 166, 190-209 (2017).
  16. Nonlinear stochastic dynamics of complex systems, II: Potential of entropic force in Markov systems with nonequilibrium steady state, generalized Gibbs function and criticality. (with Thompson, L.F.) Entropy, 18, 309 (2016).
  17. Nonlinear stochastic dynamics of complex systems, III: Noneqilibrium thermodynamics of self-replication kinetics. (with Saakian, D.B.) IEEE Transactions on Molecular, Biological, and Multi-Scale Communications, 2, 40-51 (2016).
  18. A discrete stochastic formulation for reversible bimolecular reactions via diffusion encounter (with Del Razo, M.J.) Communications in Mathematical Sciences, 14, 1741-1772 (2016).
  19. Stochastic dynamics: Markov chains and random transformations. (with Ye, F. X.-F. & Wang, Y.) Discrete and Continuous Dynamical Systems B, 21, 2337-2361 (2016).
  20. A thermodynamic theory of ecology: Helmholtz theorem for Lotka-Volterra equation, extended conservation law, and stochastic predator-prey dynamics. (with Ma, Y.-A.) Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 471, 20150456 (2015).
  21. A decomposition of irreversible diffusion processes without detailed balance. Journal of Mathematical Physics, 54, 053302 (2013).
  22. One-dimensional birth-death process and Delbrück-Gillespie theory of mesoscopic nonlinear chemical reactions. (with Zhang, Y. & Ge, H.) Studies in Applied Mathematics, 129, 328-345 (2012).
  23. Landscapes of non-gradient dynamics without detailed balance: Stable limit cycles and multiple attractors. (with Ge, H.) Chaos: An Interdisciplinary Journal of Nonlinear Science, 22, 023140 (2012).
  24. An information theoretical analysis of kinase activated phosphorylation dephosphorylation cycle. (with Roy, S.) IEEE Transactions on NanoBioscience, 11, 289-295 (2012).
  25. Circular stochastic fluctuations in SIS epidemics with heterogeneous contacts among subpopulations. (with Wang, J.-Z. & Qian, M.) Theoretical Population Biology, 81, 223-231 (2012).
  26. The dynamics of zeroth-order ultrasensitivity: A critical phenomenon in cell biology. (with Huang, Q.) Discrete and Continuous Dynamical Systems S, 4, 1457-1464 (2011).
  27. Nonlinear oscillations and multiscale dynamics in a closed chemical reaction system. (with Li, Y. & Yi, Y.) Journal of Dynamics and Differential Equations [Special Issue in Honor of Jack K. Hale], 22, 491-507 (2010).
  28. On Poincaré-Hill cycle map of rotational random walk: Locating stochastic limit cycle in reversible Schnakenberg model. (with Vellela, M.) Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 466, 771-788 (2010).
  29. Ultrasensitive dual phosphorylation dephosphorylation cycle kinetics exhibits canonical competition behavior. (with Huang, Q.) Chaos: An Interdisciplinary Journal of Nonlinear Science, 19, 033109 (2009).
  30. On the degree properties of generalized random graphs. (with Shi, Y.Y.) Communications in Mathematical Sciences, 7, 175-187 (2009).
  31. Synchronized dynamics and nonequilibrium steady states in a stochastic yeast cell-cycle network. (with Ge, H. & Qian, M.) Mathematical Biosciences, 211, 132-152 (2008).
  32. Quantitative model for binary measurements of protein-protein interactions. (with Shi, Y.Y., Miller, G.A., Denisenko, O. & Bomsztyk, K.) Journal of Computational Biology, 14, 1011-1023 (2007).
  33. On detailed balance and reversibility of semi-Markov processes and single-molecule enzyme kinetics. (with Wang, H.) Journal of Mathematical Physics, 48, 013303 (2007).
  34. On the existence of potential landscape in the evolution of complex systems. (with Ao, P. & Kwon, C.) Complexity, 12, 19-27 (2007).
  35. A quasistationary analysis of a stochastic chemical reaction: Keizer's paradox. (with Vellela, M.) Bulletin of Mathematical Biology, 69, 1727-1746 (2007).
  36. A stochastic model of oscillatory blood testosterone levels. (with Heuett, W.J.) Bulletin of Mathematical Biology, 68, 1383-1399 (2006).
  37. Combining flux and energy balance analysis to model large-scale biochemical networks. (with Heuett, W.J.) Journal of Bioinformatics and Computational Biology, 4, 1227-1243 (2006).
  38. An asymptotic comparative analysis of the thermodynamics of non-covalent association. Journal of Mathematical Biology, 52, 277-289 (2006).
  39. Thermodynamic constraints for biochemical networks. (with Beard, D.A., Babson, E. & Curtis, E.) Journal of Theoretical Biology, 228, 327-333 (2004).
  40. Thermodynamics of the general diffusion process: Time-reversibility and entropy production. (with Qian, M. & Tang, X.) Journal of Statistical Physics, 107, 1129-1141 (2002). [Expanded version]
  41. Mathematical formalism for isothermal linear irreversibility. Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences, 457, 1645-1655 (2001).
  42. A simple method of parameter space determination for diffusion-driven instability with three species. (with Murray, J.D.) Applied Mathematics Letters, 14, 405-411 (2001).
  43. A mathematical analysis of the Brownian dynamics of DNA tether. Journal of Mathematical Biology, 41, 331-340 (2000).
  44. Hysteresis in force probe measurements: A dynamic systems perspective. (with Shapiro, B.E.) Journal of Theoretical Biology, 194, 551-559 (1998).
  45. On 2-dimensional fractional Brownian motion and fractional Browian random field. (with Raymond, G.M. & Bassingthwaighte, J.B.) Journal of Physics A: Mathematical and General, 31, L527-L535 (1998).

  1. Maximum entropy principle, equal probability a priori and Gibbs paradox. (with Ge, H.)
  2. van't Hoff-Arrhenius analysis of transition rate dependence upon system's size: Stochastic vs. nonlinear bistabilities in population dynamics. (with Zhang, Y. & Ge, H.)
  3. Nonequilibrium stationary process and fluctuation-dissipation relations. (with Yang, Y.-J.).
  4. Gibbsian statistical ensemble theory as an emergent limit law in probability. (with Cheng, Y.-C. and Wang, W.).
  5. Stochastic dynamics, large deviation principle, and nonequilibrium thermodynamics. (with Hong, L.) Physical Review E, 104, 044113 (2021).
  6. Universal relation between thermodynamic driving force and one-way fluxes in a nonequilibrium chemical reaction with complex mechanism. (with Peng, Y., Beard, D. A. & Ge, H.) Physical Review Research, 2, 033089 (2020).
  7. Kinematic basis of emergent energetics of complex dynamics. (with Cheng, Y.-C. & Yang, Y.-J.) Europhysics Letters, 131, 50002 (2020).
  8. The statistical foundation of entropy in extended irreversible thermodynamics. (with Hong, L.) Journal of Physics A: Mathematical and Theoretical, 53, 425202 (2020).
  9. Unified formalism for entropy production and fluctuation relations. (with Yang, Y.-J.) Physical Review E, 101, 022129 (2020).
  10. Thermodynamics of Markov processes with nonextensive entropy and free energy. (with Peng, L. & Hong, L.) Physical Review E, 101, 022114 (2020).
  11. Grand canonical diffusion-influenced reactions: A stochastic theory with applications to multiscale reaction-diffusion simulations. (with Del Razo, M.J. & Noé, F.) Journal of Chemical Physics, 149, 044102 (2018).
  12. Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks. (with Jia, C., Chen, M. & Zhang, M.Q.) Journal of Chemical Physics, 148, 095102 (2018).
  13. Extracting hidden weak sinusoidal signal with short duration from noisy data: Analytical theory and computational realization. (with Zhang, Y., Zhang, Z. & Hu, G.) Chinese Physics B, 26, 100508 (2017).
  14. Emergent Lévy behavior in single-cell stochastic gene expression. (with Jia, C. & Zhang, M. Q.) Physical Review E, 96, 040402(R) (2017).
  15. Mesoscopic kinetic basis of macroscopic chemical thermodynamics: A mathematical theory. (with Ge, H.) Physical Review E, 94, 052150 (2016).
  16. Numerical simulations of piecewise deterministic Markov processes with an application to the stochastic Hodgkin-Huxley model. (with Ding, S.-J., Qian, M. & Zhang, X.-J.) Journal of Chemical Physics, 145, 244107, (2016).
  17. A framework towards understanding mesoscopic phenomena: Emergent unpredictability, symmetry breaking and dynamics across scales. (with Ao, P., Tu, Y. & Wang, J.) Chemical Physics Letters, 665, 153-161 (2016).
  18. Nonequilibrium thermodynamic formalism of nonlinear chemical reaction systems with Waage-Guldberg's law of mass action. (with Ge, H.) Chemical Physics, 472, 241-248 (2016).
  19. Thermodynamics of the general diffusion process: Equilibrium supercurrent and nonequilibrium driven circulation with dissipation. European Physical Journal Special Topics, 224, 781-799 (2015).
  20. Universal ideal behavior and macroscopic work relation of linear irreversible stochastic thermodynamics. (with Ma, Y.-A.) New Journal of Physics, 17, 065013 (2015).
  21. Stochastic phenotype transition of a single cell in an intermediate region of gene state switching. (with Ge, H. & Xie, X.S.) Physical Review Letters, 114, 078101 (2015).
  22. Michaelis-Menten kinetics under non-isothermal conditions. (with Lervik, A. & Kjelstrup, S.) Physical Chemistry Chemical Physics, 17, 1317-1324 (2015).
  23. Small open chemical systems theory and its implications to Darwinian evolutionary dynamics, complex self-organization and beyond. Communications in Theoretical Physics, 62, 550-554 (2014).
  24. Fluorescence correlation spectroscopy and nonlinear stochastic reaction-diffusion. (with Del Razo, M.J., Pan, W.-X. & Lin, G.) Journal of Physical Chemistry B, 108, 7037-7046 (2014).
  25. Stochastic dynamics of electrical membrane with voltage-dependent ion channel fluctuations. (with Zhang, X.-J. & Qian, M.) Europhysics Letters, 106, 10002 (2014).
  26. The zeroth law of thermodynamics and volume-preserving conservative system in equilibrium with stochastic damping. Physics Letters A, 378, 609-616 (2014).
  27. Nonlinear biochemical signal processing via noise propagation. (with Kim, K.H. & Sauro, H.M.) Journal of Chemical Physics, 139, 144108 (2013).
  28. Heat dissipation and nonequilibrium thermodynamics of quasi-steady states and open driven steady state. (with Ge, H.) Physical Review E, 87, 062125 (2013).
  29. Stochastic thermodynamics across scales: Emergent inter-attractoral discrete Markov jump process and its underlying continuous diffusion (with Santillán, M.) Physica A: Statistical Mechanics and its Applications, 392, 123-135 (2013).
  30. Hill's small systems nanothermodynamics: A simple macromolecular partition problem with a statistical perspective. Journal of Biological Physics (Springer), 38, 201-207 (2012).
  31. Fixation, transient landscape and diffusion's dilemma in stochastic evolutionary game dynamics. (with Zhou, D.) Physical Review E, 84, 031907 (2011).
  32. Irreversible thermodynamics in multiscale stochastic dynamical systems. (with Santillán, M.) Physical Review E, 83, 041130 (2011).
  33. A perturbation analysis of rate theory of self-regulating genes and signaling networks. (with Shi, P.-Z.) Journal of Chemical Physics, 134, 065104 (2011).
  34. Nonequilibrium phase transition in mesoscoipic biochemical systems: From stochastic to nonlinear dynamics and beyond. (with Ge, H.) Journal of the Royal Society Interface, 8, 107-116 (2011).
  35. Cyclic conformational modification of an enzyme: Serial engagement, energy relay, hysteretic enzyme, and Fischer's hypothesis. Journal of Physical Chemistry B [Robert A. Alberty Festshrift], 114, 16105-16111 (2010).
  36. Cellular biology in terms of stochastic nonlinear biochemical dynamics: Emergent properties, isogenetic variations and chemical system inheritability. Journal of Statistical Physics, 141, 990-1013 (2010).
  37. Simple chemical kinetic model for facilitated transport with an application to Wyman-Murray facilitated diffusion. (with Cole, C.L.) Acta Physico-Chimica Sinica, 26, 2857-2864 (2010).
  38. The physical origins of entropy production, free energy dissipation and their mathematical representations. (with Ge, H.) Physical Review E, 81, 051133 (2010).
  39. Thermodynamic limit of a nonequilibrium steady-state: Maxwell-type construction for a bistable biochemical system. (with Ge, H.) Physical Review Letters, 103, 148103 (2009).
  40. Amplification and detection of single-molecule conformational fluctuation through a protein interaction network with bimodal distributions. (with Wu, Z. & Elgart, V. & Xing, J.) Journal of Physical Chemistry B, 113, 12375-12381 (2009).
  41. Stochastic bifurcation, slow fluctuations, and bistability as an origin of biochemical complexity. (with Shi, P.-Z. & Xing, J.) Physical Chemistry Chemical Physics, 11, 4861-4870 (2009).
  42. Fluctuating enzyme and its biological functions: Positive cooperativity without multiple states. (with Shi, P.-Z.) Journal of Physical Chemistry B (Letters), 113, 2225-2230 (2009).
  43. Stochastic dynamics and nonequilibrium thermodynamics of a bistable chemical system: The Schlögl model revisited. (with Vellela, M.) Journal of the Royal Society Interface, 6, 925-940 (2009).
  44. Oscillations and multiscale dynamics in a closed chemical reaction system: Second law of thermodynamics and temporal complexity. (with Li, Y. & Yi, Y.) Journal of Chemical Physics, 129, 154505 (2008).
  45. Protein-protein interaction networks: Beyond the power-law distribution. (with Miller, G.A., Shi, Y.Y. & Bomsztyk, K.) Physical Review E, 75, 051910 (2007).
  46. Fluctuation theorems of a molecular refrigerator. (with Kim, K.H.) Physical Review E, 75, 022102 (2007).
  47. Relationship between thermodynamic driving force and one-way fluxes in reversible chemical reactions. (with Beard, D.A.) PLoS ONE, 2, e144 (2007).
  48. Continuous time random walks in closed and open single-molecule systems with microscopic reversibility. (with Wang, H.) Europhysics Letters, 76, 15-21 (2006).
  49. Generalized Haldane equation and fluctuation theorem in the steady state cycle kinetics of single enzymes. (with Xie, X.S.) Physical Review E, 74, 010902(R) (2006).
  50. Powering a burnt bridges Brownian ratchet: A model for an extracellular motor driven by proteolysis of collagen. (with Saffarian, S., Collier, I.E., Elson, E.L. & Goldberg G.) Physical Review E, 73, 041909 (2006).
  51. Grand canonical Markov model: A stochastic theory for open nonequilibrium biochemical networks. (with Heuett, W.J.) Journal of Chemical Physics, 124, 044110 (2006).
  52. Nonequilibrium steady state of a nanometric biochemical system: Determining the thermodynamic driving force from single enzyme turnover time traces. (with Min, W., Jiang, L., Yu, J., Kou, S.C. & Xie, X.S.) Nano Letters, 5, 2373-2378 (2005).
  53. Nonequilibrium potential function of chemically driven single macromolecules via Jarzynski-type log-mean-exponential heat. Journal of Physical Chemistry B, 109, 23624-23628 (2005).
  54. Nonequilibrium thermodynamics and nonlinear kinetics in a cellular signaling switch. (with Reluga, T.C.) Physical Review Letters, 94, 028101 (2005).
  55. Entropy production of Brownian macromolecules with inertia. (with Kim, K.H.) Physical Review Letters, 93, 120602 (2004).
  56. A motor protein with nonequilibrium potential: Its thermodynamics and efficiency. Physical Review E, 69, 012901 (2004).
  57. Concentration fluctuations in a mesoscopic oscillating chemical reaction system. (with Saffarian, S. & Elson, E.L.) Proceedings of the National Academy of Sciences USA, 99, 10376-10381 (2002).
  58. Equations for stochastic macromolecular mechanics of single proteins: Equilibrium fluctuations, transient kinetics and nonequilibrium steady-state. Journal of Physical Chemistry B, 106, 2065-2073 (2002).
  59. Entropy production and excess entropy in nonequilibrium steady-state of single macromolecules. Physical Review E, 65, 021111 (2002).
  60. Mesoscopic nonequilibrium thermodynamics of single macromolecules and dynamic entropy-energy compensation. Physical Review E, 65, 016102 (2002).
  61. Nonequilibrium steady-state circulation and heat dissipation functional. Physical Review E, 64, 022101 (2001).
  62. Relative entropy: Free energy associated with equilibrium fluctuations and nonequilibrium deviations. Physical Review E, 63, 042103 (2001).
  63. Transformed Poisson-Boltzmann relations and ionic distributions. (with Schellman, J.A.) Journal of Physical Chemistry B, 104, 11528-11540 (2000).
  64. Pumped biochemical reactions, nonequilibrium circulation, and stochastic resonance. (with Qian, M.) Physical Review Letters, 84, 2271-2274 (2000).
  65. Stochastic fractal behaviour in concentration fluctuation and fluorescence correlation spectroscopy. (with Raymond, G.M. & Bassingthwaighte, J.B.) Biophysical Chemistry, 80, 1-5 (1999).
  66. Entropy-enthalpy compensation: Conformational fluctuation and induced-fit. Journal of Chemical Physics, 109, 10015-10017 (1998).
  67. Vector field formalism and analysis for a class of Brownian ratchets. Physical Review Letters, 81, 3063-3066 (1998).
  68. Entropy-enthalpy compensation: Perturbation and relaxation in thermodynamic systems. (with Hopfield, J.J.) Journal of Chemical Physics, 105, 9292-9296 (1996).
  69. Helix-coil theories: A comparative studies for finite length polypeptides. (with Schellman, J.A.) Journal of Physical Chemistry, 96, 3987-3994 (1992).
  70. Analysis of confocal laser-microscope optics for three-dimensional fluorescence correlation spectroscopy. (with Elson, E.L.) Applied Optics, 30, 1185-1195 (1991).
  71. Inverse Poisson transformation and shot noise filtering. Review of Scientific Instruments, 61, 2088-2091 (1990).
  72. Characterization of the equilibrium distribution of polymer molecular weights by fluorescence distribution spectroscopy - theoretical results. (with Elson, E.L.) Applied Polymer Symposium, 43, 305-314 (1989).

  1. The hidden energy in irreversible temporal fluctuations as the origin of noise induced biochemical phenomena: The case of fluctuation-enhanced sensitivity. (with Bishop, L.M.)
  2. Phosphorylation energy and nonlinear kinetics as key determinants for G2/M transition in fission yeast cell cycle. (with Wang, T., Zhao, J., Ouyang, Q., Fu, Y.V. & Li, F.) bioRxiv 084400.
  3. Counting single cells and computing their heterogeneity: from phenotypic frequencies to mean value of a quantitative biomarker. (with Cheng, Y.-C.) Quantitative Biology, 8, 172-176 (2020).
  4. A model for positive feedback control of the transformation of fibroblasts to myofibroblasts. (with Elson, E.L., Fee, J.A. & Wakatsuki, T.) Progress in Biophysics and Molecular Biology, 144, 30--40 (2019).
  5. Structure for energy cycle: A unique status of the Second Law of thermodynamics for living systems. (Bai, S.-N. & Ge, H.) Science China: Life Sciences, 61, 1266-1273 (2018).
  6. Relatively slow stochastic gene-state switching in the presence of positive feedback significantly broadens the region of bimodality through stabilizing the uninduced phenotypic state. (with Ge, H., Wu, P. & Xie, X.S.) PLoS Computational Biology, 14, e1006051 (2018).
  7. Competition regulation among DNA methylation, nucleotide synthesis and anti-oxidation in cancer vs. normal tissues. (with Cao, S., Zhu, X., Zhang, C., Schuttler, H.-B., Gong, J.-P. & Xu, Y.) Cancer Research, 77, 1-11 (2017).
  8. Information and entropic force: physical description of biological cells, chemical reaction kinetics, and information theory. Scientia Sinica Vitae [In Chinese], 47, 257-261 (2017).
  9. Actin aggregations mark the sites of neurite initiation. (with Zhang, S.-X., Duan, L.-H. & Yu, X.) Neuroscience Bulletin, 32, 1-15(2016).
  10. Nonequilibrium population dynamics of phenotype conversion of cancer cells. (with Zhou, J.X., Pisco, A.O. & Huang, S.) PLoS ONE, 9, e110714 (2014).
  11. Fitness and entropy production in a cell population dynamics with epigenetic phenotype switching. Quantitative Biology, 2, 47-53 (2014).
  12. Stochastic physics, complex systems and biology. Quantitative Biology, 1, 50-53 (2013).
  13. A little engine that could: ATP-powered electrical battery and heater inside cells. (with Autzen, H.E.) Biophysical Journal (New and Notable), 103, 1409-1410 (2012).
  14. A stochastic model of DNA fragments rejoining. (with Li, Y., Wang, Y. & Cucinotta, F.A.) PLoS ONE, 7, e44293 (2012).
  15. Mesoscopic biochemical basis of isogenetic inheritance and canalization: Stochasticity, nonlinearity, and emergent landscape. (with Ge, H.) MCB: Molecular & Cellular Biomechanics [Special Issue in Honor of Shu Chien], 9, 1-30 (2012).
  16. The Brownian ratchet revisited: Diffusion formalism, polymer-barrier attractions, and multiple filamentous bundle growth. (with Cole, C.L.) Biophysical Reviews and Letters, 6, 59-79 (2011).
  17. Stochastic ensembles, conformationally adaptive teamwork and enzymatic detoxification. (with Atkins, W.M.) Biochemistry (New Concept), 50, 3866-3872 (2011).
  18. Delayed onset of positive feedback activation of Rab5 by Rabex-5 and Rabaptin-5 in endocytosis. (with Zhu, H. & Li, G.-P.) PLoS ONE, 5, e9226 (2010).
  19. Stochastic bistability and bifurcation in a mesoscopic signaling system with autocatalytic kinase. (with Bishop, L.M.) Biophysical Journal, 98, 1-11 (2010).
  20. Open-system thermodynamic analysis of DNA polymerase fidelity. (with Cady, F.) Physical Biology, 6, 036011 (2009).
  21. A mechanism for Src kinase-dependent signaling by noncatalytic receptors. (with Cooper, J.A.) Biochemistry (New Concepts), 47, 5681-5688 (2008).
  22. Temporal cooperativity and sensitivity amplification in biological signal transduction. (with Cooper, J.A.) Biochemistry, 47, 2211-2220 (2008).
  23. Linear analysis near a steady-state of biochemical networks: Control analysis, correlation metrics and circuit theory. (with Heuett, W.J. & Beard, D.A.) BMC Systems Biology, 2, 44 (2008).
  24. Viscoelasticity of living materials: Mechanics and chemistry of muscle as an active macromolecular system. MCB: Molecular & Cellular Biomechanics [Special Issue in Honor of Yuan-Cheng Fung], 5, 107-117 (2008).
  25. Reducing intrinsic biochemical noise in cells and its thermodynamic limit. Journal of Molecular Biology, 362, 387-392 (2006).
  26. Metabolic futile cycles and their functions: A systems analysis of energy and control. (with Beard, D.A.) IET Proceedings Systems Biology, 153, 192-200 (2006).
  27. Free energy distribution of binary protein-protein binding suggests cross-species interactome differences. (with Shi, Y.Y., Miller, G.A. & Bomsztyk, K.) Proceedings of the National Academy of Sciences USA, 103, 11527-11532 (2006).
  28. Chromatin looping and probability of transcription. (with Li, Q.-L. & Barkess, G.) Trends in Genetics, 22, 197-202 (2006).
  29. Ab initio prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. (with Yang, F. & Beard, D.A.) Metabolic Engineering, 7, 251-259 (2005).
  30. Thermodynamic-based computational profiling of cellular regulatory control in hepatocyte metabolism. (with Beard, D.A.) American Journal of Physiology: Endocrinology and Metabolism, 288, E633-E644 (2005).
  31. Fluorescence correlation spectroscopy with high-order and dual-color correlation to probe nonequilibrium steady-states. (with Elson, E.L.) Proceedings of the National Academy of Sciences USA, 101, 2828-2833 (2004).
  32. A stochastic analysis of a Brownian ratchet model for actin-based motility. MCB: Mechanics & Chemistry of Biosystems, 1, 267-278 (2004).
  33. Sensitivity and specificity amplification in signal transduction. (with Li, G.-P.) Cell Biochemistry and Biophysics, 39, 45-60 (2003).
  34. Thermodynamic and kinetic analysis of sensitivity amplification in biological signal transduction. Biophysical Chemistry [Special Issue in Honor of Walter Kauzmann], 105, 585-593 (2003).
  35. Amplifying signal transduction specificity without multiple phosphorylation. Biophysical Journal, 84, 1410 - 1411 (2003).
  36. Stoichiometric network theory for nonequilibrium biochemical systems. (with Beard, D.A. & Liang, S.-D.) European Journal of Biochemistry, 270, 415-421 (2003).
  37. Energy balance for analysis of complex metabolic networks. (with Beard, D.A. & Liang, S.-D.) Biophysical Journal, 83, 79-86 (2002).
  38. Single-molecule enzymology: Stochastic Michaelis-Menten kinetics. (with Elson, E.L.) Biophysical Chemistry [Special Issue in Honor of John A. Schellman], 101, 565-576 (2002).
  39. Kinetic timing: A novel mechanism for improving the accuracy of GTPase timers in endosome fusion and other biological processes. (with Li, G.-P.) Traffic, 3, 249-255 (2002).
  40. A class of flow bifurcation models with lognormal distribution and fractal dispersion. (with Bassingthwaighte, J.B.) Journal of Theoretical Biology, 205, 261-268 (2000).
  41. A simple theory of motor protein kinetics and energetics II. Biophysical Chemistry, 83, 35-43 (2000).
  42. Single-particle tracking: Brownian dynamics of viscoelastic materials. Biophysical Journal, 79, 137-143 (2000).
  43. A graphical method for force analysis: Macromolecular mechanics with atomic force microscopy. (with Shapiro, B.E.) Proteins: Structure, Function, and Genetics, 37, 576-581 (1999).
  44. Quantitative study of polymer conformation and dynamics by single-particle tracking. (with Elson, E.L.) Biophysical Journal, 76, 1598-1605 (1999).
  45. Hydrogen exchange kinetics of proteins in denaturants: A generalized two-process model. (with Chan, S.I.) Journal of Molecular Biology, 286, 607-616 (1999).
  46. Hydrogen bonds between short polar side chains and peptide backbone: Prevalence in proteins and effects on helix-forming propensities. (with Vijayakumar, M. & Zhou, H.-X.) Proteins: Structure, Function, and Genetics, 34, 497-507 (1999).
  47. Kramers' diffusion theory applied to gating kinetics of voltage-dependent ion channels. (with Sigg, D. & Bezanilla, F.) Biophysical Journal, 76, 782-803 (1999).
  48. Blood flows and metabolic components of the cardiome. (with Bassingthwaighte, J.B. & Li, Z.) Progress in Biophysics & Molecular Biology, 69, 445-461 (1998).
  49. Remarks on discrete and continuous large-scale models of DNA dynamics. (with Klapper, I.) Biophysical Journal, 74, 2504-2514 (1998).
  50. Terminal twist induced continuous writhe of a circular rod with intrinsic curvature. (with White, J.H.) Journal of Biomolecular Structure and Dynamics, 16, 663-669 (1998).
  51. Local interactions and the optimization of protein folding. (with Doyle, R., Simon, K.T. & Baker, D.) Proteins: Structure, Function, and Genetics, 29, 282-291 (1997).
  52. A simple theory of motor protein kinetics and energetics. Biophysical Chemistry, 67, 263-267 (1997).
  53. A quantitative analysis of single protein-ligand complex separation with the atomic force microscope. (with Shapiro, B.E.) Biophysical Chemistry, 67, 211-219 (1997).
  54. Thermodynamic hierarchy and local energetics of folded proteins. Journal of Molecular Biology, 267, 198-206 (1997).
  55. Interactions between a helical residue and tertiary structures: Helix propensities in small peptides and in native proteins. (with Chan, S.I.) Journal of Molecular Biology, 261, 279-288 (1996).
  56. Prediction of alpha-helices in proteins based on thermodynamic parameters from solution chemistry. Journal of Molecular Biology, 256, 663-666 (1996).
  57. Protein hydrogen exchange: Quantitative analysis by a two-process model. (with Mayo, S.L. & Morton, A.) Biochemistry (New Concepts), 33, 8167-8171 (1994).
  58. A thermodynamic model for helix-coil transition coupled to dimerization of short coiled-coil peptides. Biophysical Journal, 67, 349-355 (1994).
  59. The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide. (with Scholtz, J.M., Robbins, V.H. & Baldwin, R.L.) Biochemistry, 32, 9668-9676 (1993).
  60. Single-residue substitution in homopolypeptides: Perturbative helix-coil theory at a single site. Biopolymers, 33, 1605-1616 (1993).
  61. Studies of the structure of actin gels using time correlation spectroscopy of fluorescence beads. (with Elson, E.L. & Frieden, C.) Biophysical Journal, 63:1000-1010 (1992).
  62. Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water. (with Scholtz, J.M., York, E.J., Stewart, J.M. & Baldwin, R.L.) Biopolymers [Special Issue in Honor of Bruno H. Zimm], 31, 1463-1470 (1991).
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  64. On the statistics of fluorescence correlation spectroscopy. Biophysical Chemistry, 38, 49-57 (1990).
  65. Distribution of molecular aggregation by analysis of fluctuation moments. (with Elson. E.L.) Proceedings of the National Academy of Sciences USA, 87, 5479-5483 (1990).
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  67. Nanometre-level analysis demonstrates that lipid flow does not drive membrane glycoprotein movements. (with Sheetz, M.P., Turney, S. & Elson, E.L.) Nature, 340, 284-288 (1989).
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  1. An analysis of the thermodynamics of hydrophobic solvation based on scaled particle theory. arXiv:physics/0104085.
  2. Characterization of metastatic tumor formation by the colony size distribution. (with S.P. Lee, J.-R. Sun, W.H. McBride & H.R. Withers) arXiv:q-bio.TO/0608024.
  3. An annotated English translation of `Kinetics of stationary reactions' [M. I. Temkin, Dolk. Akad. Nauk SSSR. 152, 156 (1963)]. (with V.V. Levchenko, R. Fleming & D.A. Beard) arXiv:1001.2861.
  4. Thermodynamics of Markov processes with non-extensive entropy and free energy. arXiv:1005.1251.

  1. Chemical master equation. (with Ge, H.) In Springer Encyclopedia of Systems Biology (W. Dubitzky, O. Wolkenhauer, K.-H. Cho & H. Yokota, eds.) Springer, 396-399 (2013).
  2. Stochastic processes, Fokker-Planck equation. (with Ge, H.) In Springer Encyclopedia of Systems Biology (W. Dubitzky, O. Wolkenhauer, K.-H. Cho & H. Yokota, eds.) Springer, 2000-2004 (2013).
  3. Irreversible stochastic processes, coupled diffusions and systems biochemistry. (with Shi, P.-Z.) In Frontiers in Computational and Systems Biology (Computational Biology Series, Vol. 15, J.-F. Feng, W.-J. Fu & F.-Z. Sun, eds.) Springer-Verlag, 175-201 (2010).
  4. Chemical fluxes in cellular steady states measured by fluorescence correlation spectroscopy. (with Elson, E.L.) In Single Molecule Spectroscopy in Chemistry, Physics and Biology (Nobel Symposium: Springer Series in Chemical Physics, Vol. 96, A. Gräslund, R. Rigler & J. Widengren, eds.) Springer, 119-137 (2009).
  5. Multiscale modeling of cardiac cellular energetics. (with Bassingthwaighte, J.B., Chizeck, H.J. & Atlas, L.E.) In The Communicative Cardiac Cell (Annual of the New York Academy of Science, Vol. 1047, S. Sideman, R. Beyar & A. Landesberg, eds.) 395-426 (2005).
  6. Constraint-based modeling of metabolomic systems. (with Beard, D.A.) In Encyclopedia of Genetics, Genomics, Proteomics, and Bioinformatics, Vol. 3: Proteomics (M. Dunn, ed.) Sec. 8: Systems Biology (R.L. Winslow, ed.) John Wiley & Sons, (2005).
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  8. Mathematical Biology. In Dictionary of Applied Math for Engineers and Scientists - A Volume in the Comprehensive Dictionary of Mathematics (E. Previato ed.) CRC Press (2003).
  9. Fractional Brownian motion and fractional Gaussian noise. In Processes with Long-Range Correlations: Theory and Applications (Lecture Notes in Physics, Vol. 621, G. Rangarajan & M.Z. Ding, eds.) Springer, 22-33 (2003).
  10. Strain-dependent fluorescence correlation spectroscopy: proposing a new measurement for conformational fluctuations of biological macromolecules. (with Elson, E.L.) In Fluorescence Correlation Spectroscopy: Theory and Applications (Springer Series in Chemical Physics, Vol. 65, R. Rigler & E.L. Elson eds.) Springer, 65-83 (2001).
  11. The cardiome project: An integrated view of cardiac metabolism and regional mechanical function. (with Bassingthwaighte, J.B. & Li, Z.) In Oxygen Transport to Tissue, Vol. 21, (Advances in Experimental Medicine and Biology, Vol. 471, A. Eke & D.T. Delpy Eds.) Kluwer Academic/Plenum Publishers, 541-553 (1999).
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  13. Characterization of confocal laser based microscope - an optical sectioning microscopy approach. (with Elson, E.L.) In Optical Microscopy for Biology (B. Herman & K.A. Jacobson eds.) Alan R. Liss, 119-130 (1990).
  14. Interpretation of fluorescence correlation spectroscopy and photobleaching recovery in terms of molecular interactions. (with Elson, E.L.) In Quantitative Fluorescence Microscopy - Imaging and Spectroscopy (Methods in Cell Biology, Vol. 30, D.L. Taylor & Y.-L. Wang eds.) Academic Press, 307-332 (1989).
  15. Fluorescence microscopic analysis of molecular interactions in 3-dimensional samples by means of fluorescence correlation spectroscopy and photobleaching recovery. (with Elson, E.L.) Proceedings of Electron Microscopy Society of America, Vol. 46, 38-39 (1988).
  16. 3-D fluorescence correlation spectroscopy in bulk solution. (with Elson, E.L.) Proceedings of the Society of Photo-Optical Instrumentation Engineers, Vol. 909, 352-359 (1988).

  1. Stochastic Chemical Kinetics: Theory and (Mostly) Systems Biology Applications by Péter Érdi and Gárbo Lente, SIAM Review, 57, 475-477 (2015).
  2. Random Perturbations of Dynamical Systems by Mark I. Freidlin and Alexander D. Wentzell, SIAM Review, 55, 569-574 (2013).
  3. Theory and Applications of Stochastic Processes: An Analytical Approach by Zeev Schuss, SIAM Review, 53, 204-207 (2011).
  4. Molecular Modeling and Simulation: An Interdisciplinary Guide by Tamar Schlick, SIAM Review, 47, 843-845 (2005).
  5. Mathematical Physiology by James Keener and James Sneyd, SIAM Review, 46, 587-590 (2004).
  6. Computational Molecular Biology: An Algorithmic Approach by Pavel A. Pevzner, SIAM Review, 43, 733-735(2001).
  7. An Introduction to Chaos in Nonequilibrium Statistical Mechanics by J. R. Dorfman, Bulletin of Mathematical Biology, 63, 597-601 (2001).
  8. Stochastic Processes in Quantum Physics by Masao Nagasawa, SIAM Review, 43, 218-220 (2001).

  1. A Polymer "Sensibility": On the Occasion of My Grandfather's 100th Birthday. Dong Hua Da Xue Bao, 200, October, 17 (2007).
  2. Bruno H. Zimm (1920-2005) (with E.L. Elson and J.M. Schurr) Biophysical Chemistry, 121, 155-156 (2006).
  3. Mark Greener: Enzymology's New Frontiers. The Scientist, 18, 16-20 (2004).
  4. John Schellman and Biophysical Chemistry. University of Oregon, Chemistry Department News Letters,12-13 (2004).
  5. Biophysical Chemistry of Proteins and Nucleic Acids: A Festschrift For John A. Schellman. (with J. Hofrichter and R.L. Baldwin) Biophysical Chemistry, 101, 7-8 (2002).