papers
Publications (70)
cond-mat.stat-mech2009
The Physical Origins of Entropy Production, Free Energy Dissipation and their Mathematical Representations
Hao Ge, Hong Qian
q-bio.PE2011
Circular Stochastic Fluctuations in SIS Epidemics with Heterogeneous Contacts Among Sub-populations
Jia-Zeng Wang, Min Qian, Hong Qian
nlin.AO2012
Stochastic Physics, Complex Systems and Biology
Hong Qian
q-bio.MN2015
Stochastic phenotype transition of a single cell in an intermediate region of gene-state switching
Hao Ge, Hong Qian, Sunney Xiaoliang Xie
physics.bio-ph2009
Nonequilibrium phase transition in a mesoscopic biochemical system: From stochastic to nonlinear dynamics and beyond
Hao Ge, Hong Qian
q-bio.CB2018
Both cellular ATP level and ATP hydrolysis free energy determine energetically the calcium oscillation in pancreatic $β$-cell
Yunsheng Sun, Congjian Ni, Yingda Ge +3
physics.chem-ph2019
Grand canonical diffusion-influenced reactions: a stochastic theory with applications to multiscale reaction-diffusion simulations
Mauricio J. del Razo, Hong Qian, Frank Noé
q-bio.MN2008
Sensitivity Regulation based on Noise Propagation in Stochastic Reaction Networks
Kyung Hyuk Kim, Hong Qian, Herbert M. Sauro
cond-mat.stat-mech2006
Generalized Haldane Equation and Fluctuation Theorem in the Steady State Cycle Kinetics of Single Enzymes
Hong Qian, X. Sunney Xie
cond-mat.stat-mech2016
Nonlinear Stochastic Dynamics of Complex Systems, I: A Chemical Reaction Kinetic Perspective with Mesoscopic Nonequilibrium Thermodynamics
Hong Qian
cond-mat.stat-mech2001
The Mathematical Theory of Molecular Motor Movement and Chemomechanical Energy Transduction
Hong Qian
physics.class-ph2006
Fluctuation Theorems of Brownian Particles Controlled by a Maxwell's Demon
Kyung Hyuk Kim, Hong Qian
q-bio.QM2006
Free-energy distribution of binary protein-protein binding suggests cross-species interactome differences
Yi Y. Shi, Gerald A. Miller, Hong Qian +1
q-bio.MN2018
Relaxation rates of gene expression kinetics reveal the feedback signs of autoregulatory gene networks
Chen Jia, Hong Qian, Min Chen +1
physics.class-ph2004
Entropy Production of Brownian Macromolecules with Inertia
Kyung Hyuk Kim, Hong Qian
math-ph2012
Analytical Mechanics in Stochastic Dynamics: Most Probable Path, Large-Deviation Rate Function and Hamilton-Jacobi Equation
Hao Ge, Hong Qian
q-bio.SC2011
An Information Theoretical Analysis of Kinase Activated Phosphorylation Dephosphorylation Cycle
Hong Qian, Sumit Roy
cond-mat.stat-mech2001
Mesoscopic Nonequilibrium Thermodynamics of Single Macromolecules and Dynamic Entropy-Energy Compensation
Hong Qian
physics.bio-ph2001
Equations for Stochastic Macromolecular Mechanics of Single Proteins: Equilibrium Fluctuations, Transient Kinetics and Nonequilibrium Steady-State
Hong Qian
q-bio.TO2006
Characterization of Metastatic Tumor Formation by the Colony Size Distribution
Steve P. Lee, Ji-Rong Sun, Hong Qian +2
cond-mat.stat-mech2011
Maximum Entropy Principle, Equal Probability a Priori and Gibbs Paradox
Hao Ge, Hong Qian
physics.chem-ph2010
van't Hoff-Arrhenius Analysis of Mesoscopic and Macroscopic Dynamics of Simple Biochemical Systems: Stochastic vs. Nonlinear Bistabilities
Yunxin Zhang, Hao Ge, Hong Qian
q-bio.MN2009
Synchronized Dynamics and Nonequilibrium Steady States in a Stochastic Yeast Cell-Cycle Network
Hao Ge, Hong Qian, Min Qian
physics.bio-ph2001
From Discrete Protein Kinetics to Continuous Brownian Dynamics: A New Perspective
Hong Qian
cond-mat.stat-mech2015
Universal Ideal Behavior and Macroscopic Work Relation of Linear Irreversible Stochastic Thermodynamics
Yi-An Ma, Hong Qian
q-bio.SC2012
The Dynamics of Zeroth-Order Ultrasensitivity: A Critical Phenomenon in Cell Biology
Qingdao Huang, Hong Qian
cond-mat.stat-mech2015
Stochastic Free Energies, Conditional Probability and Legendre Transform for Ensemble Change
Moisés Santillán, Hong Qian
cond-mat.stat-mech2011
Irreversible Thermodynamics in Multiscale Stochastic Dynamical Systems
Moises Santillan, Hong Qian
q-bio.SC2006
Relationship between Thermodynamic Driving Force and One-Way Fluxes in Reversible Chemical Reactions
Daniel A. Beard, Hong Qian
math-ph2015
Thermodynamics of the General Diffusion Process: Equilibrium Supercurrent and Nonequilibrium Driven Circulation with Dissipation
Hong Qian
cond-mat.stat-mech2019
Ternary Representation of Stochastic Change and the Origin of Entropy and Its Fluctuations
Hong Qian, Yu-Chen Cheng, Lowell F. Thompson
cond-mat.stat-mech2011
Thermodynamics and Geometry of Reversible and Irreversible Markov Processes
Hao Ge, Woo H. Kim, Hong Qian
math-ph2013
A Hamiltonian-Entropy Production Connection in the Skew-symmetric Part of a Stochastic Dynamics
Hong Qian
q-bio.MN2017
Emergent Lévy behavior in single-cell stochastic gene expression
Chen Jia, Michael Q. Zhang, Hong Qian
physics.bio-ph2003
Thermodynamic and Kinetic Analysis of Sensitivity Amplification in Biological Signal Transduction
Hong Qian
physics.bio-ph2011
Hill's Small Systems Nanothermodynamics: A Simple Macromolecular Partition Problem with a Statistical Perspective
Hong Qian
physics.bio-ph2014
Fluorescence Correlation Spectroscopy and Nonlinear Stochastic Reaction-Diffusion
Mauricio J. Del Razo, Wenxiao Pan, Hong Qian +1
math-ph2015
A Thermodynamic Theory of Ecology: Helmholtz Theorem for Lotka-Volterra Equation, Extended Conservation Law, and Stochastic Predator-Prey Dynamics
Yi-An Ma, Hong Qian
q-bio.PE2011
Fixation, transient landscape and diffusion's dilemma in stochastic evolutionary game dynamics
Da Zhou, Hong Qian
cond-mat.stat-mech2005
Nonequilibrium Potential Function of Chemically Driven Single Macromolecules via Jarzynski-Type Log-Mean-Exponential Work
Hong Qian
physics.chem-ph2016
Mesoscopic Kinetic Basis of Macroscopic Chemical Thermodynamics: A Mathematical Theory
Hao Ge, Hong Qian
q-bio.BM2009
Amplification and detection of single molecule conformational fluctuation through a protein interaction network with bimodal distributions
Zhanghan Wu, Vlad Elgart, Hong Qian +1
cond-mat.stat-mech2012
Stochastic Thermodynamics Across Scales: Emergent Inter-attractoral Discrete Markov Jump Process and Its Underlying Continuous Diffusion
Moises Santillan, Hong Qian
physics.chem-ph2014
Small Open Chemical Systems Theory and Its Implications to Darwinian Evolutionary Dynamics, Complex Self-Organization and Beyond
Hong Qian
math-ph2001
Relative Entropy: Free Energy Associated with Equilibrium Fluctuations and Nonequilibrium Deviations
Hong Qian
physics.bio-ph2014
Stochastic Dynamics of Electrical Membrane with Voltage-Dependent Ion Channel Fluctuations
Hong Qian, Xue-Juan Zhang, Min Qian
q-bio.SC2012
Mesoscopic Biochemical Basis of Isogenetic Inheritance and Canalization: Stochasticity, Nonlinearity, and Emergent Landscape
Hong Qian, Hao Ge
math-ph2013
The Zeroth Law of Thermodynamics and Volume-Preserving Conservative Dynamics with Equilibrium Stochastic Damping
Hong Qian
physics.chem-ph2010
An annotated English translation of `Kinetics of stationary reactions' [M. I. Temkin, Dolk. Akad. Nauk SSSR. 152, 156 (1963)]
Vladislav V. Levchenko, Ronan Fleming, Hong Qian +1
math-ph2001
Mathematical Formalism for Isothermal Linear Irreversibility
Hong Qian
q-bio.QM2007
Clustering Coefficients of Protein-Protein Interaction Networks
Gerald A. Miller, Yi Y. Shi, Hong Qian +1
physics.chem-ph2016
Nonequilibrium Thermodynamic Formalism of Nonlinear Chemical Reaction Systems with Waage-Guldberg's Law of Mass Action
Hao Ge, Hong Qian
cond-mat.stat-mech2016
Entropy Production in Mesoscopic Stochastic Thermodynamics: Nonequilibrium Kinetic Cycles Driven by Chemical Potentials, Temperatures, and Mechanical Forces
Hong Qian, Signe Kjelstrup, Anatoly B. Kolomeisky +1
math-ph2016
Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law
Hao Ge, Hong Qian
cond-mat.stat-mech2016
A Discrete Stochastic Formulation for Reversible Bimolecular Reactions via Diffusion Encounter
Mauricio J. Del Razo, Hong Qian
q-bio.PE2014
Fitness and entropy production in a cell population dynamics with epigenetic phenotype switching
Hong Qian
math-ph2013
A Decomposition of Irreversible Diffusion Processes Without Detailed Balance
Hong Qian
cond-mat.stat-mech2013
Dissipation, Generalized Free Energy, and a Self-consistent Nonequilibrium Thermodynamics of Chemically Driven Open Subsystems
Hao Ge, Hong Qian
math-ph2002
Statistical Thermodynamics of General Minimal Diffusion Processes: Constuction, Invariant Density, Reversibility and Entropy Production
Hong Qian, Min Qian, Xiang Tang
physics.chem-ph2009
Thermodynamic Limit of a Nonequilibrium Steady-State: Maxwell-Type Construction for a Bistable Biochemical System
Hao Ge, Hong Qian
physics.bio-ph2001
An Analysis of the Thermodynamics of Hydrophobic Solvation Based on Scaled Particle Theory
Hong Qian
cond-mat.stat-mech2016
Nonlinear Stochastic Dynamics of Complex Systems, III: Noneqilibrium Thermodynamics of Self-Replication Kinetics
David B. Saakian, Hong Qian
math-ph2012
Landscapes of Non-gradient Dynamics Without Detailed Balance: Stable Limit Cycles and Multiple Attractors
Hao Ge, Hong Qian
cs.NE2014
The Sampling-and-Learning Framework: A Statistical View of Evolutionary Algorithms
Yang Yu, Hong Qian
q-bio.SC2006
Metabolic Futile Cycles and Their Functions: A Systems Analysis of Energy and Control
Hong Qian, Daniel A. Beard
q-bio.QM2013
Nonlinear Biochemical Signal Processing via Noise Propagation
Kyung Hyuk Kim, Hong Qian, Herbert M. Sauro
cond-mat.stat-mech2016
Nonlinear Stochastic Dynamics of Complex Systems, II: Potential of Entropic Force in Markov Systems with Nonequilibrium Steady State, Generalized Gibbs Function and Criticality
Lowell F. Thompson, Hong Qian
math.DS2012
One-Dimensional Birth-Death Process and Delbrück-Gillespie Theory of Mesoscopic Nonlinear Chemical Reactions
Yunxin Zhang, Hao Ge, Hong Qian
cond-mat.stat-mech2016
A framework towards understanding mesoscopic phenomena: Emergent unpredictability, symmetry breaking and dynamics across scales
Hong Qian, Ping Ao, Yuhai Tu +1
cond-mat.stat-mech2001
A Stochastic Analysis of a Brownian Ratchet Model for Actin-Based Motility and Integrate-and-Firing Neurons
Hong Qian