Discrete flux and velocity fields of probability and their global maps in reaction systems

Remarks on the chemical Fokker-Planck and Langevin equations: Nonphysical currents at equilibrium

(2018) Alessandro Ceccato et al.   JOURNAL OF CHEMICAL PHYSICS

An adaptive solution to the chemical master equation using tensors

(2017) Huy D. Vo et al.   JOURNAL OF CHEMICAL PHYSICS

Potential landscape of high dimensional nonlinear stochastic dynamics with large noise

(2017) Ying Tang et al.   Scientific Reports

State Space Truncation with Quantified Errors for Accurate Solutions to Discrete Chemical Master Equation

(2016) Youfang Cao et al.   BULLETIN OF MATHEMATICAL BIOLOGY

Construction of the landscape for multi-stable systems: Potential landscape, quasi-potential, A-type integral and beyond

(2016) Peijie Zhou et al.   JOURNAL OF CHEMICAL PHYSICS

Accurate Chemical Master Equation Solution Using Multi-Finite Buffers

(2016) Youfang Cao et al.   MULTISCALE MODELING & SIMULATION

DNA-Binding Kinetics Determines the Mechanism of Noise-Induced Switching in Gene Networks

(2015) Margaret J. Tse et al.   BIOPHYSICAL JOURNAL

Evaluation of reaction fluxes in stationary and oscillating far-from-equilibrium biological systems

(2015) C. Bianca et al.   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Noise-induced multistability in chemical systems: Discrete versus continuum modeling

(2015) Andrew Duncan et al.   PHYSICAL REVIEW E

An energetic variational approach for ion transport

(2014) Shixin Xu et al.   Communications in Mathematical Sciences

The role of non-equilibrium fluxes in the relaxation processes of the linear chemical master equation

(2014) Luciana Renata de Oliveira et al.   JOURNAL OF CHEMICAL PHYSICS

Quantifying the underlying landscape and paths of cancer

(2014) C. Li et al.   Journal of the Royal Society Interface

Nonequilibrium work relation beyond the Boltzmann-Gibbs distribution

(2014) Ying Tang et al.   PHYSICAL REVIEW E

Landscape and flux reveal a new global view and physical quantification of mammalian cell cycle

(2014) Chunhe Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Thermodynamics with Continuous Information Flow

(2014) Jordan M. Horowitz et al.   Physical Review X

Adaptively biased sequential importance sampling for rare events in reaction networks with comparison to exact solutions from finite buffer dCME method

(2013) Youfang Cao et al.   JOURNAL OF CHEMICAL PHYSICS

Exploring a noisy van der Pol type oscillator with a stochastic approach

(2013) Ruoshi Yuan et al.   PHYSICAL REVIEW E

Stability and Multiattractor Dynamics of a Toggle Switch Based on a Two-Stage Model of Stochastic Gene Expression

(2012) Michael Strasser et al.   BIOPHYSICAL JOURNAL

Bistability in the chemical master equation for dual phosphorylation cycles

(2012) Armando Bazzani et al.   JOURNAL OF CHEMICAL PHYSICS

The energy pump and the origin of the non-equilibrium flux of the dynamical systems and the networks

(2012) Liufang Xu et al.   JOURNAL OF CHEMICAL PHYSICS

Landscape, Flux, Correlation, Resonance, Coherence, Stability, and Key Network Wirings of Stochastic Circadian Oscillation

(2011) Chunhe Li et al.   BIOPHYSICAL JOURNAL

Automated estimation of rare event probabilities in biochemical systems

(2011) Bernie J. Daigle et al.   JOURNAL OF CHEMICAL PHYSICS

How accurate are the nonlinear chemical Fokker-Planck and chemical Langevin equations?

(2011) Ramon Grima et al.   JOURNAL OF CHEMICAL PHYSICS

Stochastic theory of nonequilibrium steady states and its applications. Part I

(2011) Xue-Juan Zhang et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Stochastic theory of nonequilibrium steady states. Part II: Applications in chemical biophysics

(2011) Hao Ge et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

The Potential Landscape of Genetic Circuits Imposes the Arrow of Time in Stem Cell Differentiation

(2010) Jin Wang et al.   BIOPHYSICAL JOURNAL

Solving the chemical master equation using sliding windows

(2010) Verena Wolf et al.   BMC Systems Biology

Nonlinear Langevin model with product stochasticity for biological networks: The case of the Schnakenberg model

(2010) Youfang Cao et al.   Journal of Systems Science & Complexity

Probability landscape of heritable and robust epigenetic state of lysogeny in phage lambda

(2010) Y. Cao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Optimal enumeration of state space of finitely buffered stochastic molecular networks and exact computation of steady state landscape probability

(2008) Youfang Cao et al.   BMC Systems Biology

Stochastic dynamics and non-equilibrium thermodynamics of a bistable chemical system: the Schlogl model revisited

(2008) M. Vellela et al.   Journal of the Royal Society Interface

Colored extrinsic fluctuations and stochastic gene expression

(2008) Vahid Shahrezaei et al.   Molecular Systems Biology

Potential landscape and flux framework of nonequilibrium networks: Robustness, dissipation, and coherence of biochemical oscillations

(2008) J. Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extinction and resurrection in gene networks

(2008) D. Schultz et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA