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*Annual Review of Statistics and Its Application*,**1**, 465-492 (2014). - Analytical mechanics
in stochastic dynamics: Most probable path, large-deviation rate
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*International Journal of Modern Physics B*,**26**, 1230012 (2012). - 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). - Stochastic
theory of nonequilibrium steady states and its applications (Part I).
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*Physics Reports*,**510**, 1-86 (2012). - Stochastic
theory of nonequilibrium steady states (Part II): Applications in
chemical biophysics.
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*Physics Reports*,**510**, 87-118 (2012). - Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems - An analytical theory (Invited article).
*IoP Nonlinearity*,**24**, R19-R49 (2011). - The
chemical master equation approach to nonequilibrium steady-state
of open biochemical systems: Linear single-molecule enzyme
kinetics and nonlinear biochemical reaction networks (Review).
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*International Journal of Molecular Sciences*,**11**, 3472-3500 (2010). - 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). - Entropy
demystified: The ``thermo''-dynamics of
stochastically fluctuating systems.
*Methods in Enzymology*,**467**, 111-134 (2009). - Cooperativity and specificity in enzyme kinetics: A single-molecule
time-based perspective (Mini review).
*Biophysical Journal*,**95**, 10-17 (2008). - Phosphorylation energy hypothesis: Open chemical systems and their biological
functions.
*Annual Review of Physical Chemistry*,**58**, 113-142 (2007). - Open-system
nonequilibrium steady-state: Statistical thermodynamics, fluctuations
and chemical oscillations (Feature article).
*Journal of Physical Chemistry B*,**110**, 15063-15074 (2006). - Cycle
kinetics, steady-state thermodynamics and motors -- a paradigm
for living matter physics.
*Journal of Physics: Condensed Matter*,**17**, S3783-S3794 (2005). - Thermodynamics
of stoichiometric biochemical networks in living systems far from
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*Biophysical Chemistry*,**114**, 213-220 (2005). - From discrete protein kinetics to continuous Brownian
dynamics: A new perspective (Review).
*Protein Science*,**11**, 1-5 (2002). - The
mathematical theory of molecular motor movement and chemomechanical
energy transduction (Review article).
*Journal of Mathematical Chemistry*,**27**, 219-234 (2000).

- A Hamiltonian-entropy production connection in the skew-symmetric part of a stochastic dynamics.
- Stochastic free energies, conditional probability and Legendre transform for ensemble change (with Santillán, M.)
- The Helmholtz theorem for the Lotka-Volterra equation, the extended conservation relation, and stochastic predator-prey dynamics. (with Ma, Y.)
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irreversible diffusion processes without detailed balance.
*Journal of Mathematical Physics*,**54**, 053302 (2013). - 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). - Landscapes of
non-gradient dynamics without detailed balance: Stable limit
cycles and multiple attractors.
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*Chaos: An Interdisciplinary Journal of Nonlinear Science*,**22**, 023140 (2012). - An information
theoretical analysis of kinase activated phosphorylation
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*IEEE Transactions on NanoBioscience*,**11**, 289-295 (2012). - Circular
stochastic fluctuations in SIS epidemics with heterogeneous
contacts among subpopulations.
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*Theoretical Population Biology*,**81**, 223-231 (2012). - 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). - Nonlinear
oscillations and multiscale dynamics in a closed chemical
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*Journal of Dynamics and Differential Equations*[Special Issue in Honor of Jack K. Hale],**22**, 491-507 (2010). - On
Poincaré-Hill cycle map of rotational random walk:
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*Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences*,**466**, 771-788 (2010). - Ultrasensitive
dual phosphorylation dephosphorylation cycle kinetics exhibits
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*Chaos: An Interdisciplinary Journal of Nonlinear Science*,**19**, 033109 (2009). - On the degree properties of generalized random
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*Communications in Mathematical Sciences*,**7**, 175-187 (2009). - Synchronized dynamics and nonequilibrium steady states in a
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*Mathematical Biosciences*,**211**, 132-152 (2008). - Quantitative
model for binary measurements of protein-protein interactions.
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*Journal of Computational Biology*,**14**, 1011-1023 (2007). - On detailed
balance and reversibility of semi-Markov processes
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*Journal of Mathematical Physics*,**48**, 013303 (2007). - On the
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*Complexity*,**12**, 19-27 (2007). - A
quasistationary analysis of a stochastic
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*Bulletin of Mathematical Biology*,**68**, 1383-1399 (2006). - Combining flux and energy balance analysis to model
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*Journal of Mathematical Biology*,**52**, 277-289 (2006). - Thermodynamic
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*Journal of Theoretical Biology*,**228**, 327-333 (2004). - Thermodynamics
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*Journal of Statistical Physics*,**107**, 1129-1141 (2002). [Expanded version] - Mathematical
formalism for isothermal linear irreversibility.
*Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences*,**457**, 1645-1655 (2001). - A
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*Applied Mathematics Letters*,**14**, 405-411 (2001). - A mathematical
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*Journal of Chemical Physics*,**134**, 065104 (2011). - Nonequilibrium
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*Journal of the Royal Society Interface*,**8**, 107-116 (2011). - Cyclic
conformational modification of an enzyme:
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chemical kinetic model for facilitated transport with
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*Acta Physico-Chimica Sinica*,**26**, 2857-2864 (2010). - The physical origins
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*Journal of Physical Chemistry B*,**113**, 12375-12381 (2009). - Stochastic
bifurcation, slow fluctuations, and bistability as an origin
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*Physical Chemistry Chemical Physics*,**11**, 4861-4870 (2009). - Fluctuating
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*Journal of Physical Chemistry B (Letters)*,**113**, 2225-2230 (2009). - Stochastic dynamics and nonequilibrium thermodynamics of
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*PLoS ONE*,**2**, e144 (2007). - Continuous
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