Samuel C. Kou

Learn More
We introduce a new sampling algorithm, the equi-energy sampler, for efficient statistical sampling and estimation. Complementary to the widely used temperature-domain methods, the equi-energy sampler, utilizing the temperature-energy duality, targets the energy directly. The focus on the energy function not only facilitates efficient sampling, but also(More)
Enzymes are biological catalysts vital to life processes and have attracted century-long investigation. The classic Michaelis-Menten mechanism provides a highly satisfactory description of catalytic activities for large ensembles of enzyme molecules. Here we tested the Michaelis-Menten equation at the single-molecule level. We monitored long time traces of(More)
This paper summarizes our present theoretical understanding of single-molecule kinetics associated with the Michaelis-Menten mechanism of enzymatic reactions. Single-molecule enzymatic turnover experiments typically measure the probability density f(t) of the stochastic waiting time t for individual turnovers. While f(t) can be reconciled with ensemble(More)
The fluctuation of the distance between a fluorescein-tyrosine pair within a single protein complex was directly monitored in real time by photoinduced electron transfer and found to be a stationary, time-reversible, and non-Markovian Gaussian process. Within the generalized Langevin equation formalism, we experimentally determine the memory kernel K(t),(More)
Recent advances in experimental technologies allow scientists to follow biochemical processes on a single-molecule basis, which provides much richer information about chemical dynamics than traditional ensemble-averaged experiments but also raises many new statistical challenges. The paper provides the first likelihood-based statistical analysis of the(More)
Advances in nanotechnology enable scientists for the first time to study biological processes on a nanoscale molecule-by-molecule basis. A surprising discovery from recent nanoscale single-molecule biophysics experiments is that biological reactions involving enzymes behave fundamentally differently from what classical theory predicts. In this article we(More)
The characteristics of the inducible galactose system in Saccharomyces cerevisiae were studied by using the nonmetabolized galactose analogues, l-arabinose and d-fucose, and galactokinaseless and transportless mutants. Induced wild-type cells transport l-arabinose by facilitated diffusion. Transportless cells transport neither galactose nor l-arabinose(More)
It is known that DNA-binding proteins can slide along the DNA helix while searching for specific binding sites, but their path of motion remains obscure. Do these proteins undergo simple one-dimensional (1D) translational diffusion, or do they rotate to maintain a specific orientation with respect to the DNA helix? We measured 1D diffusion constants as a(More)
Enzymes are dynamic entities: both their conformation and catalytic activity fluctuate over time. When such fluctuations are relatively fast, it is not surprising that the classical Michaelis-Menten (MM) relationship between the steady-state enzymatic velocity and the substrate concentration still holds. However, recent single-molecule experiments have(More)
By introducing fractional Gaussian noise into the generalized Langevin equation, the subdiffusion of a particle can be described as a stationary Gaussian process with analytical tractability. This model is capable of explaining the equilibrium fluctuation of the distance between an electron transfer donor and acceptor pair within a protein that spans a(More)