PUBLICATIONS
LIST
BOOKS |
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- 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,
Springer (2021).
|
REVIEWS and
FEATURE
ARTICLES |
|
- Statistical chemical thermodynamics and energetic behavior of counting: Gibbs' theory revisited. (Review). Journal of Chemical Theory and Computation, 18, 6421-6436 (2022).
- Stochastic
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).
- Processes
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,
20170097 (2017).
- 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).
|
APPLIED MATHEMATICS |
|
- 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.)
- Estimate
exponential memory decay in hidden Markov model and its
applications to inference (with Ye, F. X.-F. & Ma, Y.-A.) Physica D: Nonlinear Phenomena, 460, 134053 (2024).
- 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).
- Asymptotic
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).
- Stochastic
limit-cycle oscillations of a nonlinear system under random perturbations. (with Cheng, Y.-C.)
Journal of Statistical Physics, 182, 47 (2021).
- Bivectorial
nonequilibrium thermodynamics: Cycle affinity, vorticity potential, and
Onsager's principle. (with Yang, Y.-J.)
Journal of Statistical Physics, 182, 46 (2021).
- Mathematical
representation of Clausius' and Kelvin's statements of the
Second law and irreversibility. (with Wang, Y.)
Journal of Statistical Physics, 179, 808-837 (2020).
- Representations
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).
- Entropy
productions in dissipative systems.
(with Wang, S. & Yi, Y.)
Proceedings of the American Mathematical Society,
147, 5209-5225 (2019).
- Time
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).
- Stochastic
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).
- 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).
|
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.).
- Emergence and breaking of duality symmetry in generalized fundamental thermodynamic relations. (with Lu, Z.) Physical Review Letters, 128, 150603 (2022).
- 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).
- Kinematic
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).
- Unified
formalism for entropy production and fluctuation relations.
(with Yang, Y.-J.) Physical Review E, 101, 022129 (2020).
- Thermodynamics
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).
- Emergent
Lévy behavior in single-cell stochastic gene expression.
(with Jia, C. & Zhang, M. Q.) Physical Review E,
96, 040402(R) (2017).
- 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).
|
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.)
- Phosphorylation
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.)
bioRxiv 084400.
- Counting
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
(2019).
- Structure
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
(2018).
- 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).
- 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
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Cell Biochemistry and Biophysics, 39, 45-60 (2003).
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biological signal transduction. Biophysical Chemistry [Special Issue in Honor of Walter Kauzmann], 105, 585-593 (2003).
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- Stoichiometric network theory for nonequilibrium biochemical
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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
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- 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
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- Parameters
of helix-coil transition theory for alanine-based peptides
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(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.)
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- Cell
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(with Duszyk, M., Schwab, B., Zahalak, G.I. & Elson, E.L.) Biophysical Journal,
55, 683-690 (1989).
|
E-PRINTS |
|
- 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.
|
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).
- 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).
|
BOOK
REVIEWS |
|
- 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).
|
OTHER
MISCELLANEA |
|
- 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).
|