- Chemical Biophysics: Quantitative Analysis of Cellular Systems. (with Beard, D.A.)
Cambridge Texts in Biomedical Engineering,
Cambridge University Press (2008).
- Mathematical Kinetic Models: Applications in
Biophysics and Biochemistry. [in Chinese] (with Ge, H.)
Peking University Series in Contemporary Mathematics,
Peking University Press (2017).
- Stochastic Chemical Reaction Systems in Biology (with Ge, H.)
Lecture Notes on Mathematical Modelling in the Life Sciences,
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).
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,
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).
theory of nonequilibrium steady states and its applications (Part I).
(with Zhang, X.-J. & Qian, M.)
Physics Reports, 510, 1-86 (2012).
theory of nonequilibrium steady states (Part II): Applications in
(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,
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).
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).
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,
- Phosphorylation energy hypothesis: Open chemical systems and their biological
functions. Annual Review of Physical Chemistry, 58,
nonequilibrium steady-state: Statistical thermodynamics, fluctuations
and chemical oscillations (Feature article).
Journal of Physical Chemistry B, 110,
kinetics, steady-state thermodynamics and motors -- a paradigm
for living matter physics. Journal of Physics: Condensed Matter,
17, S3783-S3794 (2005).
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).
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 free
energies, conditional probability and Legendre transform for ensemble
change (with Santillán, M.)
exponential memory decay in Hidden Markov Model and its
applications (with Ye, F. X.-F. & Ma, Y.-A.).
- 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).
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).
limit-cycle oscillations of a nonlinear system under random perturbations. (with Cheng, Y.-C.)
Journal of Statistical Physics, 182, 47 (2021).
nonequilibrium thermodynamics: Cycle affinity, vorticity potential, and
Onsager's principle. (with Yang, Y.-J.)
Journal of Statistical Physics, 182, 46 (2021).
representation of Clausius' and Kelvin's statements of the
Second law and irreversibility. (with Wang, Y.)
Journal of Statistical Physics, 179, 808-837 (2020).
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).
- 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).
productions in dissipative systems.
(with Wang, S. & Yi, Y.)
Proceedings of the American Mathematical Society,
147, 5209-5225 (2019).
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).
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).
- Dynamic looping of a
free-draining polymer (with Ye, F. X.-F. & Stinis, P.)
SIAM Journal of Applied Mathematics, 78, 104-123 (2018).
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).
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).
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).
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).
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).
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).
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).
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
- 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).
quasistationary analysis of a stochastic
chemical reaction: Keizer's paradox.
(with Vellela, M.) Bulletin of Mathematical Biology,
69, 1727-1746 (2007).
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).
asymptotic comparative analysis of the thermodynamics of
non-covalent association. Journal of Mathematical Biology,
52, 277-289 (2006).
constraints for biochemical networks.
(with Beard, D.A., Babson, E. & Curtis, E.) Journal of Theoretical
Biology, 228, 327-333 (2004).
of the general diffusion process: Time-reversibility and entropy
production. (with Qian, M. & Tang, X.) Journal of Statistical
Physics, 107, 1129-1141 (2002).
formalism for isothermal linear irreversibility. Proceedings of
the Royal Society A: Mathematical, Physical and Engineering Sciences,
457, 1645-1655 (2001).
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).
in force probe measurements: A dynamic systems perspective.
(with Shapiro, B.E.) Journal of Theoretical Biology, 194,
- 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).
|PHYSICS and PHYSICAL CHEMISTRY
- 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.)
- Nonequilibrium stationary process and fluctuation-dissipation relations.
(with Yang, Y.-J.).
- Gibbsian statistical
ensemble theory as an emergent limit law in probability.
(with Cheng, Y.-C. and Wang, W.).
- Stochastic dynamics, large deviation principle, and nonequilibrium thermodynamics.
(with Hong, L.) Physical Review E, 104, 044113 (2021).
- 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).
basis of emergent energetics of complex dynamics. (with Cheng, Y.-C. &
Yang, Y.-J.) Europhysics Letters, 131, 50002 (2020).
- The statistical foundation of entropy in extended irreversible thermodynamics. (with Hong, L.) Journal of Physics A: Mathematical and Theoretical, 53, 425202 (2020).
formalism for entropy production and fluctuation relations.
(with Yang, Y.-J.) Physical Review E, 101, 022129 (2020).
of Markov processes with nonextensive entropy and free energy.
(with Peng, L. & Hong, L.) Physical Review E, 101, 022114 (2020).
- 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).
- 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).
- 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).
Lévy behavior in single-cell stochastic gene expression.
(with Jia, C. & Zhang, M. Q.) Physical Review E,
96, 040402(R) (2017).
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).
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,
- 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).
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).
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).
transient landscape and diffusion's dilemma in stochastic
evolutionary game dynamics. (with Zhou, D.)
Physical Review E, 84, 031907 (2011).
thermodynamics in multiscale stochastic dynamical systems.
(with Santillán, M.)
Physical Review E, 83, 041130 (2011).
perturbation analysis of rate theory of self-regulating
genes and signaling networks. (with Shi, P.-Z.)
Journal of Chemical Physics, 134, 065104 (2011).
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).
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).
biology in terms of stochastic nonlinear biochemical dynamics:
Emergent properties, isogenetic variations and chemical system
inheritability. Journal of Statistical Physics,
141, 990-1013 (2010).
chemical kinetic model for facilitated transport with
an application to Wyman-Murray facilitated diffusion.
(with Cole, C.L.) Acta Physico-Chimica Sinica, 26,
- The physical origins
of entropy production, free energy dissipation and their mathematical
representations. (with Ge, H.)
Physical Review E, 81, 051133 (2010).
limit of a nonequilibrium steady-state:
Maxwell-type construction for a bistable biochemical system.
(with Ge, H.)
Physical Review Letters, 103, 148103 (2009).
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).
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).
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).
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).
interaction networks: Beyond the power-law distribution.
(with Miller, G.A., Shi, Y.Y. & Bomsztyk, K.)
Physical Review E, 75, 051910 (2007).
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).
time random walks in closed and open single-molecule systems with
microscopic reversibility. (with Wang, H.)
Europhysics Letters, 76, 15-21 (2006).
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).
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).
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).
potential function of chemically driven single
macromolecules via Jarzynski-type log-mean-exponential heat.
Journal of Physical Chemistry B, 109, 23624-23628 (2005).
thermodynamics and nonlinear kinetics in a cellular signaling switch.
(with Reluga, T.C.) Physical Review Letters, 94, 028101 (2005).
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,
for stochastic macromolecular mechanics of single proteins:
Equilibrium fluctuations, transient kinetics
and nonequilibrium steady-state. Journal of Physical Chemistry B,
106, 2065-2073 (2002).
production and excess entropy in nonequilibrium steady-state of single
macromolecules. Physical Review E,
65, 021111 (2002).
nonequilibrium thermodynamics of single macromolecules and dynamic
entropy-energy compensation. Physical Review E, 65,
- Nonequilibrium steady-state circulation and heat dissipation functional.
Physical Review E, 64, 022101 (2001).
entropy: Free energy associated with equilibrium
fluctuations and nonequilibrium deviations. Physical Review E,
63, 042103 (2001).
Poisson-Boltzmann relations and
ionic distributions. (with Schellman, J.A.)
Journal of Physical Chemistry B, 104, 11528-11540 (2000).
biochemical reactions, nonequilibrium circulation, and stochastic
resonance. (with Qian, M.) Physical Review Letters,
84, 2271-2274 (2000).
fractal behaviour in concentration fluctuation and fluorescence correlation
spectroscopy. (with Raymond, G.M. & Bassingthwaighte, J.B.)
Biophysical Chemistry, 80, 1-5 (1999).
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).
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).
of confocal laser-microscope optics for three-dimensional fluorescence
correlation spectroscopy. (with Elson, E.L.) Applied
Optics, 30, 1185-1195 (1991).
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).
|BIOCHEMISTRY, BIOPHYSICS and LIFE SCIENCES
- 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.)
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.)
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).
- 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
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
- 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).
- 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).
- Information and
entropic force: physical description of biological cells, chemical reaction
kinetics, and information theory.
Scientia Sinica Vitae [In Chinese], 47, 257-261 (2017).
- 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).
stochastic model of DNA fragments rejoining.
(with Li, Y., Wang, Y. & Cucinotta, F.A.)
PLoS ONE, 7, e44293 (2012).
biochemical basis of isogenetic inheritance
and canalization: Stochasticity, nonlinearity, and emergent
landscape. (with Ge, H.)
Molecular & Cellular Biomechanics
[Special Issue in Honor of Shu Chien], 9, 1-30 (2012).
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).
ensembles, conformationally adaptive
teamwork and enzymatic detoxification.
(with Atkins, W.M.) Biochemistry (New Concept),
50, 3866-3872 (2011).
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).
bistability and bifurcation in a mesoscopic
signaling system with autocatalytic kinase. (with Bishop, L.M.)
Biophysical Journal, 98, 1-11 (2010).
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).
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).
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).
intrinsic biochemical noise in cells and its thermodynamic limit.
Journal of Molecular Biology, 362, 387-392 (2006).
futile cycles and their functions: A systems analysis of
energy and control. (with Beard, D.A.)
IET Proceedings Systems Biology, 153, 192-200 (2006).
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).
looping and probability of transcription.
(with Li, Q.-L. & Barkess, G.) Trends in Genetics, 22,
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).
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).
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,
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).
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).
study of polymer conformation and dynamics by single-particle tracking.
(with Elson, E.L.) Biophysical Journal, 76, 1598-1605 (1999).
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).
diffusion theory applied to gating kinetics of voltage-dependent ion
channels. (with Sigg, D. & Bezanilla, F.)
Biophysical Journal, 76, 782-803 (1999).
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).
quantitative analysis of single protein-ligand complex separation
with the atomic force microscope. (with Shapiro, B.E.) Biophysical
Chemistry, 67, 211-219 (1997).
hierarchy and local energetics of folded proteins. Journal of
Molecular Biology, 267, 198-206 (1997).
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).
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
33, 8167-8171 (1994).
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,
- 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).
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).
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).
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.
- Characterization of metastatic tumor formation by the
colony size distribution. (with S.P. Lee, J.-R. Sun, W.H. McBride &
- An annotated English translation of `Kinetics of
[M. I. Temkin, Dolk. Akad. Nauk SSSR. 152, 156 (1963)].
(with V.V. Levchenko, R. Fleming & D.A. Beard)
- Thermodynamics of Markov processes with non-extensive entropy and
|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, 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).
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
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).
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).
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,
- 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,
- 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).
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,
- 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,
- 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).
Chemistry of Proteins and Nucleic Acids: A Festschrift For John A. Schellman. (with J. Hofrichter and R.L. Baldwin) Biophysical Chemistry, 101,