We develop methods for constructing kinetic models of biomolecular conformation dynamics from single-molecule experimental data, or by reconciling kinetic experimental data and molecular dynamics simulation data. In the present funding period we aim at developing an approach to directly compute MSMs from single-molecule experiments, with the following main objectives:

1. Estimate conformation dynamics (eigenvalues, eigenvectors of the underlying Markovian dynamics) directly from single-molecule trajectories.
2. Quantify the estimation errors of 1.
3. Applications to optical tweezer data (collaboration with Susan Marqusee).
4. Use 1. to compute improved Markov state models; Applications to simulation data.
5. Provide publicly available software implementation.