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- Hongyun Wang, Hong Qian
- 2007

Semi-Markov processes have found increasing applications in modeling the kinet-ics of single enzyme molecules. Detailed balance is a widely accepted condition for Markov models of closed chemical systems and well known to be equivalent to the reversibility of a stationary Markov process. We show that for a semi-Markov process detailed balance is only a… (More)

- H Qian
- Journal of mathematical biology
- 2000

In the single-particle tracking experiment, the internal motion of a single DNA or polymer molecule whose one end is attached to a microsphere (optical marker) and the other end is anchored to a substratum is studied (Finzi and Gelles, 1995). The stochastic Brownian dynamics of the sphere reflect the spontaneous fluctuations, thus the physical… (More)

- Hong Qian, Saveez Saffarian, Elliot L Elson
- Proceedings of the National Academy of Sciences…
- 2002

Under sustained pumping, kinetics of macroscopic nonlinear biochemical reaction systems far from equilibrium either can be in a stationary steady state or can execute sustained oscillations about a fixed mean. For a system of two dynamic species X and Y, the concentrations n(x) and n(y) will be constant or will repetitively trace a closed loop in the (n(x),… (More)

- Hong Qian
- Annual review of biophysics
- 2012

Cooperativity in classical biophysics originates from molecular interactions; nonlinear feedbacks in biochemical networks regulate dynamics inside cells. Using stochastic reaction kinetic theory, we discuss cooperative transitions in cellular biochemical processes at both the macromolecular and the cellular levels. We show that fluctuation-enhanced… (More)

Applying the mathematical circulation theory of Markov chains, we investigate the synchronized stochastic dynamics of a discrete network model of yeast cell-cycle regulation where stochasticity has been kept rather than being averaged out. By comparing the network dynamics of the stochastic model with its corresponding deterministic network counterpart, we… (More)

- Melissa Vellela, Hong Qian
- Journal of the Royal Society, Interface
- 2009

Schlögl's model is the canonical example of a chemical reaction system that exhibits bistability. Because the biological examples of bistability and switching behaviour are increasingly numerous, this paper presents an integrated deterministic, stochastic and thermodynamic analysis of the model. After a brief review of the deterministic and stochastic… (More)

- Hong Qian, Timothy C Reluga
- Physical review letters
- 2005

We develop a rigorous nonequilibrium thermodynamics for an open system of nonlinear biochemical reactions responsible for cell signal processing. We show that the quality of the biological switch consisting of a phosphorylation-dephosphorylation cycle, such as those in protein kinase cascade, is controlled by the available intracellular free energy from the… (More)

- Hong Qian
- 2000

The mathematical formulation of the model for molecular movement of single motor proteins driven by cyclic biochemical reactions in an aqueous environment leads to a drifted Brownian motion characterized by coupled diffusion equations. In this article, we introduce the basic notion for the continuous model and review some asymptotic solutions for the… (More)

- Hong Qian, Pei-Zhe Shi, Jianhua Xing
- Physical chemistry chemical physics : PCCP
- 2009

We present a simple, unifying theory for stochastic biochemical systems with multiple time-scale dynamics that exhibit noise-induced bistability in an open-chemical environment, while the corresponding macroscopic reaction is unistable. Nonlinear stochastic biochemical systems like these are fundamentally different from classical systems in equilibrium or… (More)

- Hong Qian
- Biophysical chemistry
- 2003

Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the free energy from hydrolysis inside cells, DeltaG (phosphorylation potential), controls the amplification and sensitivity… (More)