My first major research project was developing a quantitative, noninvasive, laser-based optical method for characterizing distributions of molecular clusters in solution. Together with Elliot Elson at Washington University School of Medicine, we worked out a theory based on Fluorescence Correlation Spectroscopy (FCS) [#2 and #4 in the List of Publications], which measures fluorescence fluctuations from a small number of clusters, and then experimentally demonstrated the methodology. In order to obtain quantitative results, I thoroughly studied the confocal fluorescence-microscope system using the image-digitization technique [8], and investigated the statistics of shot noise which is inherent in the photon fluctuation measurements [6,7]. These studies eventually enabled us to quantitatively demonstrate the novel method [5]. Measuring single molecular fluorescence has become increasingly promising lately, and FCS has emerged as one of the important high-throughput methods for post-genomic studies of biological cells and macromolecules.

A second project I carried out is measuring and understanding biomolecular movement, by diffusion and active transport, in complex media such as the cell membrane and the cytoskeleton. I have participated in developing the Fluorescence Photobleaching Recovery (FPR) technique [#3 in the list of Proceedings & Chapters] and the Single Particle Tracking (SPT) methodology [9]. Both quantitatively measure transport properties of macromolecules in small biological systems. In collaboration with Michael Sheetz who is now at Columbia University, we have used the SPT technique to study the dynamics of membrane proteins and their interactions with cytoskeleton [3], and in collaboration with Carl Frieden, we also used the FCS to study tracer diffusion in the model system of actin polymer gel in vitro [11]. All these research involve significant theoretical and computational components. The theoretical part of our work has attracted attention from the mathematical biology community [#5 in the list of Proceedings & Chapters]. SPT is now routinely used to study membrane protein dynamics by many laboratories worldwide. Recently, we have proposed using SPT methodology to studying polymer dynamics of single macromolecules such as DNA [34]; and further developed a unifying theoretical framework for interpreting SPT measurements of linear viscoelasticity, also known as microrheology [38].

In 1990 in the laboratory of John Schellman at the University of Oregon and in collaboration with Buzz Baldwin at Stanford University, I started working in the area of protein and peptide physical chemistry. I have developed a set of models for quantitatively interpreting the alpha-helix formation by small peptides in aqueous solution [12], which include the effects of single residue substitutions [13], interaction between charged residues, interaction between charge residue and helix-dipole [14], and coiled-coil dimerization [15]. These studies have provided a quantitative ground for the current experimental studies of peptides in solution [10,14]. In order to understand the energetics and conformational fluctuations within proteins, I have developed a novel protein model which combines both global and local behavior of a protein [16,19]. The model integrates many known experimental observations, including those from small peptides, the recent measurements of hydrogen exchange (HX) rates, and global folding thermodynamics of proteins. A number of useful equations for quantitatively interpreting HX measurements are derived from this model [20]. This study also has led to a new view of molten globular intermediate states in protein folding and unfolding kinetics [33].

Good progress has also been made on several fundamental but unresolved issues in protein physical chemistry: a model for thermodynamics of solvation and hydrophobic effect, a unified interpretation for linear polyelectrolytes based on the Poisson-Boltzmann Equation and the counter-ion condensation theories [42], a comprehensive theory for entropy-enthalpy compensation [17,28], and a simple model for protein folding kinetics [23].

I have long been interested in mathematical biology. When I was with John Hopfield at Caltech and supported by the Program in Mathematics and Molecular Biology (PMMB), I started to apply mathematics to the various biological and biochemical problems of my interests. Several recent publications reflect my current research directions toward developing stochastic theory for the mechanics and kinetics of single macromolecules such as ligand-protein dissociation in solution [21,26,36], motor protein movement along a linear track [22,27,37], and channel protein in membrane [31]. I am also working on the integrated dynamics of purine metabolism, calcium signaling, and mechanics of myocardium [30], the elastic theory of DNA supercoiling [24,29], and statistical thermodynamics of proteins [18,23,28,32].