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Ying-Jen Yang

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Published work

3 published item(s)

preprint2026arXiv

Nonequilibrium Theory for Molecular Machine Design

Modeling the dynamical flows on networks of biomolecular machines often entails computing node populations and edge fluxes with Master Equations and correlating machine performance with entropy production. But this alone is not sufficient for design, optimization and evolution because it doesn't treat cost-benefit tradeoffs, or small-system misflows (backsteps, futile cycles, ineffective actions), or differential properties for flow design. Here we develop CFT Design, based on the recently developed Caliber Force Theory (CFT). We apply it to: designing faster molecular motors through ``traffic control''; optimizing speed, energy, and accuracy in kinetic proofreaders; and designing better enzyme inhibitors. CFT Design provides a general framework for optimizing nonequilibrium flow networks.

preprint2020arXiv

Unified formalism for entropy productions and fluctuation relations

Stochastic entropy production, which quantifies the difference between the probabilities of trajectories of a stochastic dynamics and its time reversals, has a central role in nonequilibrium thermodynamics. In the theory of probability, the change in the statistical properties of observables can be represented by a change in the probability measure. We consider operators on the space of probability measure that induce changes in the statistical properties of a process, and formulate entropy productions in terms of these change-of-probability-measure (CPM) operators. This mathematical underpinning of the origin of entropy productions allows us to achieve an organization of various forms of fluctuation relations: All entropy productions have a non-negative mean value, admit the integral fluctuation theorem, and satisfy a rather general fluctuation relation. Other results such as the transient fluctuation theorem and detailed fluctuation theorems then are derived from the general fluctuation relation with more constraints on the operator. We use a discrete-time, discrete-state-space Markov process to draw the contradistinction among three reversals of a process: time reversal, protocol reversal and the dual process. The properties of their corresponding CPM operators are examined, and the domains of validity of various fluctuation relations for entropy productions in physics and chemistry are revealed. We also show that our CPM operator formalism can help us rather easily extend other fluctuations relations for excess work and heat, discuss the martingale properties of entropy productions, and derive the stochastic integral formulas for entropy productions in constant-noise diffusion process with Girsanov theorem. Our formalism provides a general and concise way to study the properties of entropy-related quantities in stochastic thermodynamics and information theory.

preprint2015arXiv

Adaptive Synchronization and Anticipatory Dynamical System

Many biological systems can sense periodical variations in a stimulus input and produce well-timed, anticipatory responses after the input is removed. Such systems show memory effects for retaining timing information in the stimulus and cannot be understood from traditional synchronization consideration of passive oscillatory systems. To understand this anticipatory phenomena, we consider oscillators built from excitable systems with the addition of an adaptive dynamics. With such systems, well-timed post-stimulus responses similar to those from experiments can be obtained. Furthermore, a well-known model of working memory is shown to possess similar anticipatory dynamics when the adaptive mechanism is identified with synaptic facilitation. The last finding suggests that this type of oscillators can be common in neuronal systems with plasticity.