Research has been carried out on the following topics: 1) First-passage time statistics of a Brownian particle in a quenched random environment and its application tonano-particle tracking in a living cell;2) General relations between energy dissipation, linear response, and thermal fluctuations in small systems with continuous and discrete states and their applications to molecular machines that function in an open thermal environment; 3) Dynamic renormalization group treatment of the entrainment transition in the globally coupled Kuramoto model; 4) fundamental principles underlying non-equilibrium phenomena: macroscopic representation of fluctuation theorems for stochastic systems at macroscopic level, such colloidal suspensions, active matter systems; 5) the microscopic mechanism underlying swarming behavior displayed by a special kind of non-equilibrium systems: active systems where each individual propels itself, and the influence of such swarming behavior to system properties such as viscosity.

We study physical mechanisms of bimolecular systems through quantitative modeling and large scale simulations. We try to understand how biomolecules operate in interactions with one another to achieve their physiological functions. In particular, we focus on studying protein machinery such as RNA polymerases from atomistic scale to their functional level in gene transcription. We also study the functional conformational dynamics of plexin, a signaling protein that plays important roles in neural development. By computationally investigating the mechanochemical coupling and informational control of such systems, we aim to achieved a detailed understanding of how those biomolecular machines and the circuits they belong to function with high efficiency and robustness in the cellular context. The rational can help molecular engineering and support further biomedical research. Moreover, aiming to improve the simulation efficiency in our studies we work on implementing, testing, and improving the Gentlest Ascent Dynamics (GAD) algorithm to realistic biomolecular systems in the framework of all-atomic molecular dynamics simulations.

Collaborating with a large international consortium, we develop software for analyzing experimental data (X-ray scattering, CryoEM, and single molecule tracking), providing interface to computational modeling and simulations to reveal richer dynamics and function information of biomolecules. Research topics include: i) XFEL single particle/molecule structure determination at high resolutions; ii) Algorithms to process noisy CryoEM image data; iii) Diffusion and activity switching of receptor proteins from single-molecule fluorescence microscopy.

Current research in this direction focuses on two aspects: 1) genome-scale analysis and modeling of metabolic flux and proteome data to decipher the gene and pathway regulatory programs in E. coli as the growth rate and nutrient conditions are varied; 2) spatio-temporal patterning of bacterial populations upon reprogramming of cell motility circuit.