Ioan Andricioaei

University of California, Irvine, USA - Andricioaei Lab

Computing large-and-slow DNA motions from fast sampling of rare conformational transitions

Abstract

The molecular machinery of biological cells works on one DNA at a time, and therefore these processes are to be fundamentally understood at the single-molecule level. In my talk, I will present computer simulation results obtained by my research team that adress two difficulties in modeling such events. They stem from the long spatial scales on which the DNA strand relaxes and, separately, from the long relaxation time of the undelrying kinetics.

Two frameworks, both based on path integrals, developed for these two problems will be showcased. One uses molecular-dynamics derived parameters to scale up the dynamics on the micrometer-microsecond scale via the Kirchhoff theory for elastic rods. The other allows for the enhanced calculation of long-time kinetics in complex systems and is based on a stochastic path integral formalism: assigning weights to trajectories of artificially biased dynamics allows for the calculation of time-correlation functions for the unbiased system of interest via reweighting.

Biography

Ioan Andricioaei, a native of Romania, studied physics and biophysics at the A. I. Cuza University of Iasi. He then pursued graduate studies at Boston University and completed his Ph.D. in 1999 under the supervision of John Straub, followed by postdoctoral work at Harvard University with Martin Karplus. Andricioaei was then on the faculty at the University of Michigan, before moving to the University of California, Irvine in 2008, where he is Professor of Chemistry. His research explores theoretical topics at the interface between molecular biophysics and physical chemistry.