- Chemical Biophysics: Quantitative Analysis of Cellular Systems. (with Beard, D.A.)
*Cambridge Texts in Biomedical Engineering*, Cambridge University Press (2008).

- Self-organization, differentiation, and living matters:
Processes on the emergent landscapes of biochemical reaction networks and
heterogeneous cell population dynamics (Review). (with Huang, S., Li, F.
& Zhou, J.X.)
*Journal of the Royal Society Interface*, . - 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). - 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.)
- 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). - 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). - 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). - A discrete
stochastic formulation for reversible bimolecular reactions
via diffusion encounter (with Del Razo, M.J.)
*Communications in Mathematical Sciences*,**14**, 1741-1772 (2016). - Stochastic
dynamics: Markov chains and random
transformations. (with Ye, F. X.-F. & Wang, Y.)
*Discrete and Continuous Dynamical Systems B*,**21**, 2337-2361 (2016). - 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
tether.
*Journal of Mathematical Biology*,**41**, 331-340 (2000). - Hysteresis
in force probe measurements: A dynamic systems perspective.
(with Shapiro, B.E.)
*Journal of Theoretical Biology*,**194**, 551-559 (1998). - 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).

- Maximum entropy
principle, equal probability
*a priori*and Gibbs paradox. (with Ge, H.) - 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.)
- Mesoscopic
kinetic basis of macroscopic chemical thermodynamics: A
mathematical theory. (with Ge, H.)
*Physical Review E*,**94**, 052150 (2016). - 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). - 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). - 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). - Thermodynamics of
the general diffusion process: Equilibrium supercurrent and nonequilibrium
driven circulation with dissipation.
*European Physical Journal Special Topics*,**224**, 781-799 (2015). - Universal ideal behavior
and macroscopic work relation of linear irreversible stochastic
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.
(with Del Razo, M.J., Pan, W.-X. & Lin, G.)
*Journal of Physical Chemistry B*,**108**, 7037-7046 (2014). - Stochastic dynamics
of electrical membrane with voltage-dependent ion channel
fluctuations. (with Zhang, X.-J. & Qian, M.)
*Europhysics Letters*,**106**, 10002 (2014). -
The zeroth law of thermodynamics and volume-preserving conservative
system in equilibrium with stochastic damping.
*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
(with Santillán, M.)
*Physica A: Statistical Mechanics and its Applications*,**392**, 123-135 (2013). - Hill's small
systems nanothermodynamics: A simple macromolecular partition
problem with a statistical perspective.
*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.
(with Santillán, M.)
*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.
(with Ge, H.)
*Physical Review Letters*,**103**, 148103 (2009). - 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). - 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). - 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). - 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). - 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.
(with Miller, G.A., Shi, Y.Y. & Bomsztyk, K.)
*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
cycle kinetics of single enzymes. (with Xie, X.S.)
*Physical Review E*,**74**, 010902(R) (2006). - 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). - Grand canonical
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.
(with Min, W., Jiang, L., Yu, J., Kou, S.C. & Xie, X.S.)
*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.
(with Reluga, T.C.)
*Physical Review Letters*,**94**, 028101 (2005). - Entropy
production of Brownian macromolecules with inertia.
(with Kim, K.H.)
*Physical Review Letters*,**93**, 120602 (2004). - A motor
protein with nonequilibrium potential: Its thermodynamics and efficiency.
*Physical Review E*,**69**, 012901 (2004). -
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). - 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). - Entropy
production and excess entropy in nonequilibrium steady-state of single
macromolecules.
*Physical Review E*,**65**, 021111 (2002). - Mesoscopic
nonequilibrium thermodynamics of single macromolecules and dynamic
entropy-energy compensation.
*Physical Review E*,**65**, 016102 (2002). - Nonequilibrium steady-state circulation and heat dissipation functional.
*Physical Review E*,**64**, 022101 (2001). - Relative
entropy: Free energy associated with equilibrium
fluctuations and nonequilibrium deviations.
*Physical Review E*,**63**, 042103 (2001). - Transformed
Poisson-Boltzmann relations and
ionic distributions. (with Schellman, J.A.)
*Journal of Physical Chemistry B*,**104**, 11528-11540 (2000). - Pumped
biochemical reactions, nonequilibrium circulation, and stochastic
resonance. (with Qian, M.)
*Physical Review Letters*,**84**, 2271-2274 (2000). - Stochastic
fractal behaviour in concentration fluctuation and fluorescence correlation
spectroscopy. (with Raymond, G.M. & Bassingthwaighte, J.B.)
*Biophysical Chemistry*,**80**, 1-5 (1999). - Entropy-enthalpy
compensation: Conformational fluctuation and induced-fit.
*Journal of Chemical Physics*,**109**, 10015-10017 (1998). - Vector field
formalism and analysis for a class of Brownian ratchets.
*Physical Review Letters*,**81**, 3063-3066 (1998). - Entropy-enthalpy
compensation: Perturbation and relaxation in thermodynamic systems.
(with Hopfield, J.J.)
*Journal of Chemical Physics*,**105**, 9292-9296 (1996). - Helix-coil theories: A comparative studies for finite length
polypeptides. (with Schellman, J.A.)
*Journal of Physical Chemistry*,**96**, 3987-3994 (1992). - Analysis
of confocal laser-microscope optics for three-dimensional fluorescence
correlation spectroscopy. (with Elson, E.L.)
*Applied Optics*,**30**, 1185-1195 (1991). - Inverse
Poisson transformation and shot noise filtering.
*Review of Scientific Instruments*,**61**, 2088-2091 (1990). - 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).

- 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.)
- Information and
entropic force: physical description of biological cells, chemical reaction
kinetics, and information theory.
*Scientia Sinica Vitae*[In Chinese], , (). - Actin aggregations mark the sites of neurite
initiation. (with Zhang, S.-X., Duan, L.-H. & Yu, X.)
*Neuroscience Bulletin*,**32**, 1-15(2016). - Nonequilibrium population dynamics
of phenotype conversion of cancer cells.
(with Zhou, J.X., Pisco, A.O. & Huang, S.)
*PLoS ONE*,**9**, e110714 (2014). -
Fitness and entropy production in a cell population dynamics with
epigenetic phenotype switching.
*Quantitative Biology*,**2**, 47-53 (2014). - Stochastic physics,
complex systems and biology.
*Quantitative Biology*,**1**, 50-53 (2013). - 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). - A
stochastic model of DNA fragments rejoining.
(with Li, Y., Wang, Y. & Cucinotta, F.A.)
*PLoS ONE*,**7**, e44293 (2012). - 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). - 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). - Stochastic
ensembles, conformationally adaptive
teamwork and enzymatic detoxification.
(with Atkins, W.M.)
*Biochemistry (New Concept)*,**50**, 3866-3872 (2011). - 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). - Stochastic
bistability and bifurcation in a mesoscopic
signaling system with autocatalytic kinase. (with Bishop, L.M.)
*Biophysical Journal*,**98**, 1-11 (2010). - Open-system
thermodynamic analysis of DNA polymerase fidelity. (with Cady, F.)
*Physical Biology*,**6**, 036011 (2009). - A mechanism
for Src kinase-dependent signaling by noncatalytic receptors.
(with Cooper, J.A.)
*Biochemistry (New Concepts)*,**47**, 5681-5688 (2008). - Temporal cooperativity and sensitivity amplification
in biological signal transduction. (with Cooper, J.A.)
*Biochemistry*,**47**, 2211-2220 (2008). - 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). - 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). - Reducing
intrinsic biochemical noise in cells and its thermodynamic limit.
*Journal of Molecular Biology*,**362**, 387-392 (2006). - 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). - 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). - Chromatin
looping and probability of transcription.
(with Li, Q.-L. & Barkess, G.)
*Trends in Genetics*,**22**, 197-202 (2006). *Ab initio*prediction of thermodynamically feasible reaction directions from biochemical network stoichiometry. (with Yang, F. & Beard, D.A.)*Metabolic Engineering*,**7**, 251-259 (2005).- 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). - 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). - A
stochastic analysis of a Brownian ratchet model for actin-based motility.
*MCB: Mechanics & Chemistry of Biosystems*,**1**, 267-278 (2004). - Sensitivity and
specificity amplification in signal transduction. (with Li, G.-P.)
*Cell Biochemistry and Biophysics*,**39**, 45-60 (2003). - Thermodynamic and kinetic analysis of sensitivity amplification in
biological signal transduction.
*Biophysical Chemistry*[Special Issue in Honor of Walter Kauzmann],**105**, 585-593 (2003). - Amplifying signal transduction specificity without multiple phosphorylation.
*Biophysical Journal*,**84**, 1410 - 1411 (2003). - Stoichiometric network theory for nonequilibrium biochemical
systems. (with Beard, D.A. & Liang, S.-D.)
*European Journal of Biochemistry*,**270**, 415-421 (2003). - Energy
balance for analysis of complex metabolic networks. (with Beard, D.A.
& Liang, S.-D.)
*Biophysical Journal*,**83**, 79-86 (2002). - 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). - 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). - A class
of flow bifurcation models with lognormal distribution and fractal
dispersion. (with Bassingthwaighte, J.B.)
*Journal of Theoretical Biology*,**205**, 261-268 (2000). - A
simple theory of motor protein kinetics and energetics II.
*Biophysical Chemistry*,**83**, 35-43 (2000). - Single-particle tracking: Brownian dynamics of viscoelastic materials.
*Biophysical Journal*,**79**, 137-143 (2000). - 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). - Quantitative
study of polymer conformation and dynamics by single-particle tracking.
(with Elson, E.L.)
*Biophysical Journal*,**76**, 1598-1605 (1999). - Hydrogen
exchange kinetics of proteins in denaturants: A generalized two-process
model. (with Chan, S.I.)
*Journal of Molecular Biology*,**286**, 607-616 (1999). - 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). - Kramers'
diffusion theory applied to gating kinetics of voltage-dependent ion
channels. (with Sigg, D. & Bezanilla, F.)
*Biophysical Journal*,**76**, 782-803 (1999). - Blood
flows and metabolic components of the cardiome. (with Bassingthwaighte,
J.B. & Li, Z.)
*Progress in Biophysics & Molecular Biology*,**69**, 445-461 (1998). - Remarks on discrete and continuous large-scale models of DNA dynamics. (with
Klapper, I.)
*Biophysical Journal*,**74**, 2504-2514 (1998). - 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). - 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). - A simple
theory of motor protein kinetics and energetics.
*Biophysical Chemistry*,**67**, 263-267 (1997). - A
quantitative analysis of single protein-ligand complex separation
with the atomic force microscope. (with Shapiro, B.E.)
*Biophysical Chemistry*,**67**, 211-219 (1997). - Thermodynamic
hierarchy and local energetics of folded proteins.
*Journal of Molecular Biology*,**267**, 198-206 (1997). - 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). - Prediction
of alpha-helices in proteins based on thermodynamic parameters from
solution chemistry.
*Journal of Molecular Biology*,**256**, 663-666 (1996). - Protein hydrogen exchange: Quantitative analysis by a
two-process model. (with Mayo, S.L. & Morton, A.)
*Biochemistry (New Concepts)*,**33**, 8167-8171 (1994). - A
thermodynamic model for helix-coil transition coupled to
dimerization of short coiled-coil peptides.
*Biophysical Journal*,**67**, 349-355 (1994). - 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). - Single-residue substitution in homopolypeptides: Perturbative
helix-coil theory at a single site.
*Biopolymers*,**33**, 1605-1616 (1993). - 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). - 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). - Single particle tracking: Analysis of diffusion and flow in
two dimensional systems. (with Sheetz, M.P. & Elson, E.L.)
*Biophysical Journal*,**60**, 910-921 (1991). - On
the statistics of fluorescence correlation spectroscopy.
*Biophysical Chemistry*,**38**, 49-57 (1990). - 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). - On the analysis of high order moments of fluorescence fluctuations.
(with Elson, E.L.)
*Biophysical Journal*,**57**, 375-380 (1990). - 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). - Cell
poking: Quantitative analysis of indentation of thick viscoelastic layers.
(with Duszyk, M., Schwab, B., Zahalak, G.I. & Elson, E.L.)
*Biophysical Journal*,**55**, 683-690 (1989).

- An analysis of the thermodynamics of hydrophobic solvation based on
scaled particle theory.
*arXiv:physics/0104085*. - 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*. - 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*. - Thermodynamics of Markov processes with non-extensive entropy and
free energy.
*arXiv:1005.1251*.

- 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). - 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). - 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). - 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). - 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). - 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). - Stoichiometric foundation of large-scale biochemical system
analysis. (with Beard, D.A. & Bassingthwaighte, J.B.) In
*Modelling in Molecular Biology*(Natural Computing Series, G. Ciobanu & G. Rozenberg, eds.) Springer, 1-19 (2004). - 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). - 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). - 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). - 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). - Measurements of molecular transport in small systems. (with Elson,
E.L.) In
*Cell Biology*(AMS Lectures on Mathematics in the Life Science, Vol. 24, B. Goldstein & C. Wofsy eds.) American Mathematical Society, 37-49 (1994). - 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). - 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). - 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). - 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).

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

- A Polymer "Sensibility": On the Occasion of My Grandfather's 100th
Birthday.
*Dong Hua Da Xue Bao*,**200**, October, 17 (2007). - Bruno H. Zimm
(1920-2005) (with E.L. Elson and J.M. Schurr)
*Biophysical Chemistry*,**121**, 155-156 (2006). - Mark Greener: Enzymology's New Frontiers.
*The Scientist*,**18**, 16-20 (2004). - John Schellman
and Biophysical Chemistry.
*University of Oregon, Chemistry Department News Letters*,12-13 (2004). - 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).