PUBLICATIONS
LIST
BOOKS
 Chemical Biophysics: Quantitative Analysis of Cellular Systems. (with Beard, D.A.)
Cambridge Texts in Biomedical Engineering,
Cambridge University Press (2008).
REVIEWS and
FEATURE
ARTICLES
 Statistics and related topics in singlemolecule
biophysics. (with Kou, S.C.)
Annual Review of Statistics and Its Application,
1, 465492 (2014).
 Analytical mechanics
in stochastic dynamics: Most probable path, largedeviation rate
function and HamiltonJacobi equation (Review).
(with Ge, H.) International Journal of Modern Physics B,
26, 1230012 (2012).
 Cooperativity in cellular biochemical processes: Noiseenhanced
sensitivity, fluctuating enzyme, bistability with nonlinear feedback,
and other mechanisms for sigmoidal responses.
Annual Review of Biophysics, 41, 179204 (2012).
 Stochastic
theory of nonequilibrium steady states and its applications (Part I).
(with Zhang, X.J. & Qian, M.)
Physics Reports, 510, 186 (2012).
 Stochastic
theory of nonequilibrium steady states (Part II): Applications in
chemical biophysics.
(with Ge, H & Qian, M.)
Physics Reports, 510, 87118 (2012).
 Nonlinear stochastic dynamics of mesoscopic homogeneous biochemical reaction systems  An analytical theory (Invited article). IoP Nonlinearity, 24,
R19R49 (2011).
 The
chemical master equation approach to nonequilibrium steadystate
of open biochemical systems: Linear singlemolecule enzyme
kinetics and nonlinear biochemical reaction networks (Review).
(with Bishop, L.M.)
International Journal of Molecular Sciences,
11, 34723500 (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, 154168 (2010).
 Entropy
demystified: The ``thermo''dynamics of
stochastically fluctuating systems. Methods in Enzymology,
467, 111134 (2009).
 Cooperativity and specificity in enzyme kinetics: A singlemolecule
timebased perspective (Mini review). Biophysical Journal, 95,
1017 (2008).
 Phosphorylation energy hypothesis: Open chemical systems and their biological
functions. Annual Review of Physical Chemistry, 58,
113142 (2007).
 Opensystem
nonequilibrium steadystate: Statistical thermodynamics, fluctuations
and chemical oscillations (Feature article).
Journal of Physical Chemistry B, 110,
1506315074 (2006).
 Cycle
kinetics, steadystate thermodynamics and motors  a paradigm
for living matter physics. Journal of Physics: Condensed Matter,
17, S3783S3794 (2005).
 Thermodynamics
of stoichiometric biochemical networks in living systems far from
equilibrium (Review). (with Beard, D.A.) Biophysical Chemistry,
114, 213220 (2005).
 From discrete protein kinetics to continuous Brownian
dynamics: A new perspective (Review). Protein Science,
11, 15 (2002).
 The
mathematical theory of molecular motor movement and chemomechanical
energy transduction (Review article). Journal of Mathematical Chemistry, 27, 219234 (2000).
APPLIED MATHEMATICS
 A Hamiltonianentropy
production connection in the skewsymmetric part of a
stochastic dynamics.
 Stochastic free
energies, conditional probability and Legendre transform for ensemble
change (with Santillán, M.)
 The Helmholtz theorem
for the LotkaVolterra equation, the extended conservation
relation, and stochastic predatorprey dynamics. (with Ma, Y.)
 A decomposition of
irreversible diffusion processes without detailed balance.
Journal of Mathematical Physics, 54, 053302 (2013).
 Onedimensional
birthdeath process and DelbrückGillespie theory of mesoscopic
nonlinear chemical reactions. (with Zhang, Y. & Ge, H.)
Studies in Applied Mathematics, 129, 328345 (2012).
 Landscapes of
nongradient 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, 289295 (2012).
 Circular
stochastic fluctuations in SIS epidemics with heterogeneous
contacts among subpopulations.
(with Wang, J.Z. & Qian, M.)
Theoretical Population Biology, 81, 223231 (2012).
 The dynamics of
zerothorder ultrasensitivity: A critical phenomenon in cell
biology. (with Huang, Q.)
Discrete and Continuous Dynamical
Systems S, 4, 14571464 (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, 491507 (2010).
 On
PoincaréHill 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, 771788 (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, 175187 (2009).
 Synchronized dynamics and nonequilibrium steady states in a
stochastic yeast cellcycle network. (with Ge, H. & Qian, M.)
Mathematical Biosciences, 211, 132152 (2008).
 Quantitative
model for binary measurements of proteinprotein interactions.
(with Shi, Y.Y., Miller, G.A., Denisenko, O. & Bomsztyk, K.)
Journal of Computational Biology, 14, 10111023
(2007).
 On detailed
balance and reversibility of semiMarkov processes
and singlemolecule 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, 1927 (2007).
 A
quasistationary analysis of a stochastic
chemical reaction: Keizer's paradox.
(with Vellela, M.) Bulletin of Mathematical Biology,
69, 17271746 (2007).
 A
stochastic model of oscillatory blood testosterone levels.
(with Heuett, W.J.) Bulletin of Mathematical Biology,
68, 13831399 (2006).
 Combining flux and energy balance analysis to model
largescale biochemical networks. (with Heuett, W.J.)
Journal of Bioinformatics and Computational Biology,
4, 12271243 (2006).
 An
asymptotic comparative analysis of the thermodynamics of
noncovalent association. Journal of Mathematical Biology,
52, 277289 (2006).
 Thermodynamic
constraints for biochemical networks.
(with Beard, D.A., Babson, E. & Curtis, E.) Journal of Theoretical
Biology, 228, 327333 (2004).
 Thermodynamics
of the general diffusion process: Timereversibility and entropy
production. (with Qian, M. & Tang, X.) Journal of Statistical
Physics, 107, 11291141 (2002).
[Expanded version]
 Mathematical
formalism for isothermal linear irreversibility. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences,
457, 16451655 (2001).
 A
simple method of parameter space determination for diffusiondriven
instability with three species. (with Murray, J.D.)
Applied Mathematics Letters, 14, 405411 (2001).
 A mathematical
analysis of the Brownian dynamics of DNA
tether. Journal of Mathematical Biology, 41, 331340 (2000).
 Hysteresis
in force probe measurements: A dynamic systems perspective.
(with Shapiro, B.E.) Journal of Theoretical Biology, 194,
551559 (1998).
 On 2dimensional
fractional Brownian motion and fractional Browian random field.
(with Raymond, G.M. & Bassingthwaighte, J.B.) Journal of Physics A:
Mathematical and General, 31, L527L535 (1998).
PHYSICS and PHYSICAL CHEMISTRY
 A theory of
mesoscopic phenomena: Time scales,
emergent unpredictability, symmetry breaking and dynamics across
different levels. (with Ao, P., Tu, Y. & Wang, J.)
 Maximum entropy
principle, equal probability a priori and Gibbs paradox.
(with Ge, H.)
 van't HoffArrhenius
analysis of transition rate dependence upon system's size:
Stochastic vs. nonlinear bistabilities in population dynamics.
(with Zhang, Y. & Ge, H.)
 Fluorescence
correlation spectroscopy and nonlinear stochastic reactiondiffusion.
(with Del Razo, M.J., Pan, W.X. & Lin, G.)
Journal of Physical Chemistry B, to appear.
 Small open chemical
systems theory and its implications to Darwinian evolutionary dynamics,
complex selforganization and beyond.
Communications in Theoretical Physics, to appear.
 Stochastic dynamics
of electrical membrane with voltagedependent ion channel
fluctuations. (with Zhang, X.J. & Qian, M.)
Europhysics Letters, 106, 10002 (2014).

The zeroth law of thermodynamics and volumepreserving conservative
system in equilibrium with stochastic damping.
Physics Letters A, 378, 609616 (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 quasisteady states and open
driven steady state. (with Ge, H.)
Physical Review E, 87, 062125 (2013).
 Stochastic
thermodynamics across scales: Emergent interattractoral discrete
Markov jump process and its underlying continuous diffusion
(with Santillán, M.)
Physica A:
Statistical Mechanics and its Applications, 392,
123135 (2013).
 Hill's small
systems nanothermodynamics: A simple macromolecular partition
problem with a statistical perspective.
Journal of Biological Physics (Springer), 38, 201207 (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 selfregulating
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, 107116 (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, 1610516111 (2010).
 Cellular
biology in terms of stochastic nonlinear biochemical dynamics:
Emergent properties, isogenetic variations and chemical system
inheritability. Journal of Statistical Physics,
141, 9901013 (2010).
 Simple
chemical kinetic model for facilitated transport with
an application to WymanMurray facilitated diffusion.
(with Cole, C.L.) Acta PhysicoChimica Sinica, 26,
28572864 (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 steadystate:
Maxwelltype construction for a bistable biochemical system.
(with Ge, H.)
Physical Review Letters, 103, 148103 (2009).
 Amplification
and detection of singlemolecule conformational fluctuation through
a protein interaction network with bimodal distributions.
(with Wu, Z. & Elgart, V. & Xing, J.)
Journal of Physical Chemistry B, 113, 1237512381 (2009).
 Stochastic
bifurcation, slow fluctuations, and bistability as an origin
of biochemical complexity.
(with Shi, P.Z. & Xing, J.)
Physical Chemistry Chemical Physics, 11, 48614870 (2009).
 Fluctuating
enzyme and its biological functions:
Positive cooperativity without multiple states.
(with Shi, P.Z.)
Journal of Physical Chemistry B (Letters),
113, 22252230 (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, 925940 (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).
 Proteinprotein
interaction networks: Beyond the powerlaw 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 oneway fluxes in reversible chemical
reactions. (with Beard, D.A.) PLoS ONE, 2, e144 (2007).
 Continuous
time random walks in closed and open singlemolecule systems with
microscopic reversibility. (with Wang, H.)
Europhysics Letters, 76, 1521 (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, 23732378 (2005).
 Nonequilibrium
potential function of chemically driven single
macromolecules via Jarzynskitype logmeanexponential heat.
Journal of Physical Chemistry B, 109, 2362423628 (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,
1037610381 (2002).
 Equations
for stochastic macromolecular mechanics of single proteins:
Equilibrium fluctuations, transient kinetics
and nonequilibrium steadystate. Journal of Physical Chemistry B,
106, 20652073 (2002).
 Entropy
production and excess entropy in nonequilibrium steadystate of single
macromolecules. Physical Review E,
65, 021111 (2002).
 Mesoscopic
nonequilibrium thermodynamics of single macromolecules and dynamic
entropyenergy compensation. Physical Review E, 65,
016102 (2002).
 Nonequilibrium steadystate 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
PoissonBoltzmann relations and
ionic distributions. (with Schellman, J.A.)
Journal of Physical Chemistry B, 104, 1152811540 (2000).
 Pumped
biochemical reactions, nonequilibrium circulation, and stochastic
resonance. (with Qian, M.) Physical Review Letters,
84, 22712274 (2000).
 Stochastic
fractal behaviour in concentration fluctuation and fluorescence correlation
spectroscopy. (with Raymond, G.M. & Bassingthwaighte, J.B.)
Biophysical Chemistry, 80, 15 (1999).
 Entropyenthalpy
compensation: Conformational fluctuation and inducedfit.
Journal of Chemical Physics, 109, 1001510017 (1998).
 Vector field
formalism and analysis for a class of Brownian ratchets.
Physical Review Letters, 81, 30633066 (1998).
 Entropyenthalpy
compensation: Perturbation and relaxation in thermodynamic systems.
(with Hopfield, J.J.) Journal of Chemical Physics,
105, 92929296 (1996).
 Helixcoil theories: A comparative studies for finite length
polypeptides. (with Schellman, J.A.) Journal of Physical Chemistry,
96, 39873994 (1992).
 Analysis
of confocal lasermicroscope optics for threedimensional fluorescence
correlation spectroscopy. (with Elson, E.L.) Applied
Optics, 30, 11851195 (1991).
 Inverse
Poisson transformation and shot noise filtering. Review
of Scientific Instruments, 61, 20882091 (1990).
 Characterization of the equilibrium distribution of polymer molecular
weights by fluorescence distribution spectroscopy  theoretical results.
(with Elson, E.L.) Applied Polymer Symposium, 43, 305314 (1989).
BIOCHEMISTRY, BIOPHYSICS and LIFE SCIENCES
 Analysis of chromatin immunoprecipitated RNA
polymerase II using a simple stochastic model of inducible
transcription. (with Miller, G.A., Krassovsky, K., Shi, Y.Y.,
Flanagin, S., Ruzzo, W.L. & Bomsztyk, K.)
 The hidden energy in irreversible temporal fluctuations
as the origin of noise induced biochemical phenomena:
The case of fluctuationenhanced sensitivity.
(with Bishop, L.M.)

Fitness and entropy production in a cell population dynamics with
epigenetic phenotype switching.
Quantitative Biology, 2, 4753 (2014).
 Stochastic physics,
complex systems and biology.
Quantitative Biology, 1, 5053 (2013).
 A little
engine that could: ATPpowered electrical battery
and heater inside cells. (with Autzen, H.E.)
Biophysical Journal (New and Notable), 103, 14091410 (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, 130 (2012).
 The
Brownian ratchet revisited: Diffusion formalism,
polymerbarrier attractions, and multiple filamentous bundle
growth. (with Cole, C.L.) Biophysical Reviews and Letters,
6, 5979 (2011).
 Stochastic
ensembles, conformationally adaptive
teamwork and enzymatic detoxification.
(with Atkins, W.M.) Biochemistry (New Concept),
50, 38663872 (2011).
 Delayed
onset of positive feedback activation of
Rab5 by Rabex5 and Rabaptin5 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, 111 (2010).
 Opensystem
thermodynamic analysis of DNA polymerase fidelity. (with Cady, F.)
Physical Biology, 6, 036011 (2009).
 A mechanism
for Src kinasedependent signaling by noncatalytic receptors.
(with Cooper, J.A.) Biochemistry (New Concepts),
47, 56815688 (2008).
 Temporal cooperativity and sensitivity amplification
in biological signal transduction. (with Cooper, J.A.)
Biochemistry, 47, 22112220 (2008).
 Linear
analysis near a steadystate 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 YuanCheng Fung], 5, 107117 (2008).
 Reducing
intrinsic biochemical noise in cells and its thermodynamic limit.
Journal of Molecular Biology, 362, 387392 (2006).
 Metabolic
futile cycles and their functions: A systems analysis of
energy and control. (with Beard, D.A.)
IET Proceedings Systems Biology, 153, 192200 (2006).
 Free
energy distribution of binary proteinprotein binding suggests
crossspecies interactome differences. (with Shi, Y.Y.,
Miller, G.A. & Bomsztyk, K.) Proceedings of the National
Academy of Sciences USA, 103, 1152711532 (2006).
 Chromatin
looping and probability of transcription.
(with Li, Q.L. & Barkess, G.) Trends in Genetics, 22,
197202 (2006).
 Ab
initio prediction of thermodynamically feasible reaction directions
from biochemical network stoichiometry. (with Yang, F. & Beard, D.A.)
Metabolic Engineering, 7, 251259 (2005).
 Thermodynamicbased computational profiling of cellular regulatory
control in hepatocyte metabolism. (with Beard, D.A.) American Journal
of Physiology: Endocrinology and Metabolism, 288, E633E644 (2005).
 Fluorescence correlation spectroscopy with highorder and dualcolor correlation to
probe nonequilibrium steadystates.
(with Elson, E.L.) Proceedings of the National Academy of
Sciences USA, 101, 28282833 (2004).
 A
stochastic analysis of a Brownian ratchet model for actinbased motility.
MCB: Mechanics & Chemistry of Biosystems, 1, 267278 (2004).
 Sensitivity and
specificity amplification in signal transduction. (with Li, G.P.)
Cell Biochemistry and Biophysics, 39, 4560 (2003).
 Thermodynamic and kinetic analysis of sensitivity amplification in
biological signal transduction. Biophysical Chemistry [Special Issue in Honor of Walter Kauzmann], 105, 585593 (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, 415421 (2003).
 Energy
balance for analysis of complex metabolic networks. (with Beard, D.A.
& Liang, S.D.) Biophysical Journal, 83, 7986 (2002).
 Singlemolecule enzymology: Stochastic MichaelisMenten kinetics.
(with Elson, E.L.) Biophysical Chemistry [Special
Issue in Honor of John A. Schellman], 101,
565576 (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, 249255 (2002).
 A class
of flow bifurcation models with lognormal distribution and fractal
dispersion. (with Bassingthwaighte, J.B.)
Journal of Theoretical Biology, 205, 261268 (2000).
 A
simple theory of motor protein kinetics and energetics II.
Biophysical Chemistry, 83, 3543 (2000).
 Singleparticle tracking: Brownian dynamics of viscoelastic materials.
Biophysical Journal, 79, 137143 (2000).
 A graphical method for force analysis: Macromolecular mechanics with
atomic force microscopy. (with Shapiro, B.E.) Proteins: Structure,
Function, and Genetics, 37, 576581 (1999).
 Quantitative
study of polymer conformation and dynamics by singleparticle tracking.
(with Elson, E.L.) Biophysical Journal, 76, 15981605 (1999).
 Hydrogen
exchange kinetics of proteins in denaturants: A generalized twoprocess
model. (with Chan, S.I.) Journal of Molecular Biology,
286, 607616 (1999).
 Hydrogen bonds between short polar side chains and peptide
backbone: Prevalence in proteins and effects on helixforming propensities.
(with Vijayakumar, M. & Zhou, H.X.) Proteins: Structure,
Function, and Genetics, 34, 497507 (1999).
 Kramers'
diffusion theory applied to gating kinetics of voltagedependent ion
channels. (with Sigg, D. & Bezanilla, F.)
Biophysical Journal, 76, 782803 (1999).
 Blood
flows and metabolic components of the cardiome. (with Bassingthwaighte,
J.B. & Li, Z.) Progress in Biophysics & Molecular Biology,
69, 445461 (1998).
 Remarks on discrete and continuous largescale models of DNA dynamics. (with
Klapper, I.) Biophysical Journal, 74, 25042514 (1998).
 Terminal twist induced continuous writhe of a circular rod
with intrinsic curvature. (with White, J.H.) Journal of Biomolecular
Structure and Dynamics, 16, 663669 (1998).
 Local interactions and the optimization of protein folding.
(with Doyle, R., Simon, K.T. & Baker, D.) Proteins: Structure, Function, and
Genetics, 29, 282291 (1997).
 A simple
theory of motor protein kinetics and energetics. Biophysical
Chemistry, 67, 263267 (1997).
 A
quantitative analysis of single proteinligand complex separation
with the atomic force microscope. (with Shapiro, B.E.) Biophysical
Chemistry, 67, 211219 (1997).
 Thermodynamic
hierarchy and local energetics of folded proteins. Journal of
Molecular Biology, 267, 198206 (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, 279288 (1996).
 Prediction
of alphahelices in proteins based on thermodynamic parameters from
solution chemistry. Journal of Molecular Biology,
256, 663666 (1996).
 Protein hydrogen exchange: Quantitative analysis by a
twoprocess model. (with Mayo, S.L. & Morton, A.) Biochemistry
(New Concepts),
33, 81678171 (1994).
 A
thermodynamic model for helixcoil transition coupled to
dimerization of short coiledcoil peptides. Biophysical Journal,
67, 349355 (1994).
 The energetics of ionpair and hydrogenbonding interactions
in a helical peptide. (with Scholtz, J.M., Robbins, V.H. & Baldwin,
R.L.) Biochemistry, 32, 96689676 (1993).
 Singleresidue substitution in homopolypeptides: Perturbative
helixcoil theory at a single site. Biopolymers, 33,
16051616 (1993).
 Studies of the structure of actin gels using time correlation
spectroscopy of fluorescence beads. (with Elson, E.L. & Frieden, C.)
Biophysical Journal, 63:10001010 (1992).
 Parameters
of helixcoil transition theory for alaninebased 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, 14631470 (1991).
 Single particle tracking: Analysis of diffusion and flow in
two dimensional systems. (with Sheetz, M.P. & Elson, E.L.) Biophysical
Journal, 60, 910921 (1991).
 On
the statistics of fluorescence correlation spectroscopy.
Biophysical Chemistry, 38, 4957 (1990).
 Distribution of molecular aggregation by analysis of fluctuation
moments. (with Elson. E.L.) Proceedings of the National Academy of
Sciences USA, 87, 54795483 (1990).
 On the analysis of high order moments of fluorescence fluctuations.
(with Elson, E.L.) Biophysical Journal, 57, 375380 (1990).
 Nanometrelevel analysis demonstrates that lipid flow does not
drive membrane glycoprotein movements. (with Sheetz, M.P., Turney, S.
& Elson, E.L.)
Nature, 340, 284288 (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, 683690 (1989).
EPRINTS
 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:qbio.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 nonextensive entropy and
free energy.
arXiv:1005.1251.
PROCEEDINGS and CHAPTERS
 Chemical master equation. (with Ge, H.) In Springer Encyclopedia of Systems Biology (W. Dubitzky, O. Wolkenhauer, K.H. Cho & H. Yokota, eds.) Springer, 396399 (2013).
 Stochastic processes, FokkerPlanck equation. (with Ge, H.) In
Springer Encyclopedia of Systems Biology (W. Dubitzky, O. Wolkenhauer, K.H. Cho & H. Yokota, eds.) Springer, 20002004 (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.)
SpringerVerlag, 175201 (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, 119137 (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.) 395426 (2005).
 Constraintbased 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 largescale biochemical system
analysis. (with Beard, D.A. & Bassingthwaighte, J.B.) In
Modelling in Molecular Biology (Natural Computing
Series, G. Ciobanu & G. Rozenberg, eds.) Springer, 119 (2004).
 Mathematical Biology. In Dictionary of Applied Math for Engineers and Scientists
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BOOK
REVIEWS
 Random Perturbations of Dynamical Systems by
Mark I. Freidlin and Alexander D. Wentzell, SIAM Review,
55, 569574 (2013).
 Theory and Applications of Stochastic Processes:
An Analytical Approach by Zeev Schuss, SIAM Review, 53,
204207 (2011).
 Molecular Modeling and Simulation: An Interdisciplinary
Guide by Tamar Schlick, SIAM Review, 47, 843845 (2005).
 Mathematical Physiology by James Keener and James Sneyd,
SIAM Review, 46, 587590 (2004).
 Computational Molecular Biology: An Algorithmic Approach
by Pavel A. Pevzner, SIAM Review, 43, 733735(2001).

An Introduction to Chaos in Nonequilibrium Statistical Mechanics by J. R. Dorfman, Bulletin of Mathematical Biology, 63,
597601 (2001).
 Stochastic Processes in Quantum Physics by Masao Nagasawa,
SIAM Review, 43, 218220 (2001).
OTHER
MISCELLANEA
 A Polymer "Sensibility": On the Occasion of My Grandfather's 100th
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 Bruno H. Zimm
(19202005) (with E.L. Elson and J.M. Schurr) Biophysical Chemistry, 121, 155156 (2006).
 Mark Greener: Enzymology's New Frontiers.
The Scientist, 18, 1620 (2004).
 John Schellman
and Biophysical Chemistry. University of Oregon, Chemistry Department
News Letters,1213 (2004).
 Biophysical
Chemistry of Proteins and Nucleic Acids: A Festschrift For John A. Schellman. (with J. Hofrichter and R.L. Baldwin) Biophysical Chemistry, 101,
78 (2002).