Alex Dickson Email & Phone Number

East Lansing, Mi, Us

East Lansing, Mi, Us

East Lansing, Michigan, United States

East Lansing, Mi

Asst. Prof. in the Department of Biochemistry and Molecular Biology (BMB), with an appointment in the new Department of Computational Science, Mathematics and Engineering (CMSE).

In my postdoctoral work I developed techniques to analyze the dynamics of biomolecules with configuration space networks. Using such network graphs, one can visualize the entire landscape of possible configurations of a molecule (such as a protein, or an RNA), and how these configurations are connected. I also developed enhanced sampling methods for molecular dynamics algorithms that can be used to build these networks in an efficient manner.

Chicago, Il

Molecular simulations are achieved by starting with an initial structure and taking very small steps forward in time (~ 1 femtosecond). It then takes a lot of steps to reach timescales that are physically or biologically relevant. There are clever ways to speed up these simulations that are collectively referred to as "enhanced sampling methods". In my PhD I focused on analyzing and developing enhanced sampling algorithms for application to nonequilibrium systems, which involve flows of energy or matter, like a waterfall. Molecular examples of nonequilibrium systems include proteins under a shear flow (such as hemoglobin in a blood vessel) and processes that occur only in one direction (such as translation of a protein by a ribosome). In Chicago I focused mostly on model systems, but always with an eye towards more complicated, multi-dimensional systems like biomolecules. My final project there was to simulate the folding and unfolding of a tethered RNA molecule under shear flow. We found, surprisingly, that there were multiple mechanisms of folding and unfolding, and you could tune between them by adjusting the flow speed.

Ph.D., Chemistry

Hon. B. Sc., Chemical Physics