From a (over)simplified point of view, competition between two biological species can be modeled as two types of auto-catalyzed self-replicators (green dimmers and red trimers) competing to convert a shared pool of resource molecules (blue dots) into replications of themselves. These reactions are driven by an external source of energy and thus the system never reaches thermal equilibrium. In this simple regime, we find that the entropy production can provide us an upper bound on the fitness of any given species at the non-equilibrium steady state.

Circadian clocks with autonomous free-running 24-hour rhythms are seen as remarkable examples of evolutionary adaptation while the hourglass-like clocks found in other organisms seem defective in comparison. Here we view these clocks as computational devices to predict the next sunset or sunrise. We find that free running clocks can efficiently project out the fluctuation in the light intensity due to weather patterns (‘external noise’). However, such a feature is necessarily vulnerable to ‘internal noise’. Hence, at sufficiently high internal noise, point attractor-based ‘hourglass’ clocks can outperform free-running clocks.

Recent understanding of Maxwell's demon revealed the relation between information and thermodynamic entropy. In contrast to a thermal engine that is powered by the temperature between two thermal baths, "information engine" trades information for the ability to extract energy from a single heat bath and perform work. We designed mechanical models of information engines (autonomous engine, feedback-control device, and programmable engine) to illustrate the generalized second law of thermodynamics that incorporates both thermodynamic entropy and information. In the future, I aim to study how biological systems acquire and processes information, and understand its associated cost and gain.

It is commonly expected that cooling a hot system takes a longer time than cooling an identical system initiated at a lower temperature. Surprisingly, this is not always the case; in various systems, including water and magnetic alloys, it has been observed that a hot system can be cooled faster (i.e., the so-called Mpemba effect). Using the theory of non-equilibrium thermodynamics, we explored and demonstrated a family of counter-intuitive effects that occurs when the system is far from equilibrium. The processes that we study range from simple physical processes such as cooling and heating to biological dynamics such as cell signaling dynamics and gene regulation.