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*Cambridge Texts in Biomedical Engineering*, Cambridge University Press (2008).

- Entropy production in mesoscopic stochastic thermodynamics - Nonequilibrium kinetic cycles driven by differences in chemical potential and temperature, or mechanical force. (with Kjelstrup, S., Kolomeisky, A. B. & Bedeaux, D.)
- Statistics and related topics in single-molecule
biophysics. (with Kou, S.C.)
*Annual Review of Statistics and Its Application*,**1**, 465-492 (2014). - 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). - 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).
(with Zhang, X.-J. & Qian, M.)
*Physics Reports*,**510**, 1-86 (2012). - Stochastic
theory of nonequilibrium steady states (Part II): Applications in
chemical biophysics.
(with Ge, H & Qian, M.)
*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).
(with Bishop, L.M.)
*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
equilibrium (Review). (with Beard, D.A.)
*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.)
- Stochastic dynamics: Markov chains and random transformations. (with Ye, F. X.-F. & Wang, Y.)
- 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). - A decomposition of
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.
(with Ge, H.)
*Chaos: An Interdisciplinary Journal of Nonlinear Science*,**22**, 023140 (2012). - An information
theoretical analysis of kinase activated phosphorylation
dephosphorylation cycle. (with Roy, S.)
*IEEE Transactions on NanoBioscience*,**11**, 289-295 (2012). - Circular
stochastic fluctuations in SIS epidemics with heterogeneous
contacts among subpopulations.
(with Wang, J.-Z. & Qian, M.)
*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
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). - 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). - Ultrasensitive
dual phosphorylation dephosphorylation cycle kinetics exhibits
canonical competition behavior.
(with Huang, Q.)
*Chaos: An Interdisciplinary Journal of Nonlinear Science*,**19**, 033109 (2009). - On the degree properties of generalized random
graphs. (with Shi, Y.Y.)
*Communications in Mathematical Sciences*,**7**, 175-187 (2009). - Synchronized dynamics and nonequilibrium steady states in a
stochastic yeast cell-cycle network. (with Ge, H. & Qian, M.)
*Mathematical Biosciences*,**211**, 132-152 (2008). - 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). - On detailed
balance and reversibility of semi-Markov processes
and single-molecule enzyme kinetics. (with Wang, H.)
*Journal of Mathematical Physics*,**48**, 013303 (2007). - On the
existence of potential landscape in the evolution of
complex systems. (with Ao, P. & Kwon, C.)
*Complexity*,**12**, 19-27 (2007). - A
quasistationary analysis of a stochastic
chemical reaction: Keizer's paradox.
(with Vellela, M.)
*Bulletin of Mathematical Biology*,**69**, 1727-1746 (2007). - A
stochastic model of oscillatory blood testosterone levels.
(with Heuett, W.J.)
*Bulletin of Mathematical Biology*,**68**, 1383-1399 (2006). - 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). - An
asymptotic comparative analysis of the thermodynamics of
non-covalent association.
*Journal of Mathematical Biology*,**52**, 277-289 (2006). - Thermodynamic
constraints for biochemical networks.
(with Beard, D.A., Babson, E. & Curtis, E.)
*Journal of Theoretical Biology*,**228**, 327-333 (2004). - 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] - Mathematical
formalism for isothermal linear irreversibility.
*Proceedings of the Royal Society A: Mathematical, Physical and Engineering Sciences*,**457**, 1645-1655 (2001). - 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). - A mathematical
analysis of the Brownian dynamics of DNA
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*Journal of Mathematical Biology*,**41**, 331-340 (2000). - Hysteresis
in force probe measurements: A dynamic systems perspective.
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- A theory of mesoscopic phenomena: Time scales, emergent unpredictability, symmetry breaking and dynamics across different levels. (with Ao, P., Tu, Y. & Wang, J.)
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thermodynamics. (with Ma, Y.-A.)
*New Journal of Physics*,**17**, 065013 (2015). - 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). - Michaelis-Menten kinetics under non-isothermal
conditions. (with Lervik, A. & Kjelstrup, S.)
*Physical Chemistry Chemical Physics*,**17**, 1317-1324 (2015). - 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). - Fluorescence
correlation spectroscopy and nonlinear stochastic reaction-diffusion.
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*Journal of Physical Chemistry B*,**108**, 7037-7046 (2014). - Stochastic dynamics
of electrical membrane with voltage-dependent ion channel
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*Europhysics Letters*,**106**, 10002 (2014). -
The zeroth law of thermodynamics and volume-preserving conservative
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*Physics Letters A*,**378**, 609-616 (2014). - Nonlinear biochemical
signal processing via noise propagation. (with Kim, K.H. & Sauro, H.M.)
*Journal of Chemical Physics*,**139**, 144108 (2013). - Heat dissipation and
nonequilibrium thermodynamics of quasi-steady states and open
driven steady state. (with Ge, H.)
*Physical Review E*,**87**, 062125 (2013). - Stochastic
thermodynamics across scales: Emergent inter-attractoral discrete
Markov jump process and its underlying continuous diffusion
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*Physica A: Statistical Mechanics and its Applications*,**392**, 123-135 (2013). - Hill's small
systems nanothermodynamics: A simple macromolecular partition
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*Journal of Biological Physics*(Springer),**38**, 201-207 (2012). - Fixation,
transient landscape and diffusion's dilemma in stochastic
evolutionary game dynamics. (with Zhou, D.)
*Physical Review E*,**84**, 031907 (2011). - Irreversible
thermodynamics in multiscale stochastic dynamical systems.
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*Physical Review E*,**83**, 041130 (2011). - A
perturbation analysis of rate theory of self-regulating
genes and signaling networks. (with Shi, P.-Z.)
*Journal of Chemical Physics*,**134**, 065104 (2011). - 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). - 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). - 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). - 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). - The physical origins
of entropy production, free energy dissipation and their mathematical
representations. (with Ge, H.)
*Physical Review E*,**81**, 051133 (2010). - Thermodynamic
limit of a nonequilibrium steady-state:
Maxwell-type construction for a bistable biochemical system.
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*Physical Review Letters*,**103**, 148103 (2009). - Amplification
and detection of single-molecule conformational fluctuation through
a protein interaction network with bimodal distributions.
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*Journal of Physical Chemistry B*,**113**, 12375-12381 (2009). - Stochastic
bifurcation, slow fluctuations, and bistability as an origin
of biochemical complexity.
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*Physical Chemistry Chemical Physics*,**11**, 4861-4870 (2009). - Fluctuating
enzyme and its biological functions:
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*Journal of Physical Chemistry B (Letters)*,**113**, 2225-2230 (2009). - Stochastic dynamics and nonequilibrium thermodynamics of
a bistable chemical system: The Schlögl model revisited.
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*Journal of the Royal Society Interface*,**6**, 925-940 (2009). - 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). - Protein-protein
interaction networks: Beyond the power-law distribution.
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*Physical Review E*,**75**, 051910 (2007). - Fluctuation
theorems of a molecular refrigerator. (with Kim, K.H.)
*Physical Review E*,**75**, 022102 (2007). - Relationship between
thermodynamic driving force and one-way fluxes in reversible chemical
reactions. (with Beard, D.A.)
*PLoS ONE*,**2**, e144 (2007). - Continuous
time random walks in closed and open single-molecule systems with
microscopic reversibility. (with Wang, H.)
*Europhysics Letters*,**76**, 15-21 (2006). - Generalized
Haldane equation and fluctuation theorem in the steady state
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*Physical Review E*,**74**, 010902(R) (2006). - Powering
a burnt bridges Brownian ratchet: A model for an extracellular motor
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Markov model: A stochastic theory for open nonequilibrium biochemical
networks. (with Heuett, W.J.)
*Journal of Chemical Physics*,**124**, 044110 (2006). - Nonequilibrium
steady state of a nanometric biochemical system: Determining the
thermodynamic driving force from single enzyme turnover time traces.
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*Nano Letters*,**5**, 2373-2378 (2005). - Nonequilibrium
potential function of chemically driven single
macromolecules via Jarzynski-type log-mean-exponential heat.
*Journal of Physical Chemistry B*,**109**, 23624-23628 (2005). - Nonequilibrium
thermodynamics and nonlinear kinetics in a cellular signaling switch.
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*Physical Review Letters*,**94**, 028101 (2005). - Entropy
production of Brownian macromolecules with inertia.
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*Physical Review Letters*,**93**, 120602 (2004). - A motor
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Concentration fluctuations in a mesoscopic oscillating chemical
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*Physical Review E*,**65**, 021111 (2002). - Mesoscopic
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*Physical Review E*,**65**, 016102 (2002). - Nonequilibrium steady-state circulation and heat dissipation functional.
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*Biophysical Journal (New and Notable)*,**103**, 1409-1410 (2012). - A
stochastic model of DNA fragments rejoining.
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biochemical basis of isogenetic inheritance
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*MCB: Molecular & Cellular Biomechanics*[Special Issue in Honor of Shu Chien],**9**, 1-30 (2012). - The
Brownian ratchet revisited: Diffusion formalism,
polymer-barrier attractions, and multiple filamentous bundle
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ensembles, conformationally adaptive
teamwork and enzymatic detoxification.
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onset of positive feedback activation of
Rab5 by Rabex-5 and Rabaptin-5 in endocytosis. (with Zhu, H. & Li, G.-P.)
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*Biochemistry*,**47**, 2211-2220 (2008). - Linear
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*BMC Systems Biology*,**2**, 44 (2008). - Viscoelasticity
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intrinsic biochemical noise in cells and its thermodynamic limit.
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*American Journal of Physiology: Endocrinology and Metabolism*,**288**, E633-E644 (2005). - Fluorescence correlation spectroscopy with high-order and dual-color correlation to
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*Biophysical Chemistry*[Special Issue in Honor of John A. Schellman],**101**, 565-576 (2002). - Kinetic
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- An analysis of the thermodynamics of hydrophobic solvation based on
scaled particle theory.
*arXiv:physics/0104085*. - Characterization of metastatic tumor formation by the
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