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Department of Mathematical Sciences

Seminar Archives

On this page you can find information about seminars in this and previous academic years, where available on the database.

Biomathematics Seminar: Enhanced sampling methods for exploration of complex (bio-)molecular landscapes

Presented by Dr Ben Leimkuhler, The university of Edinburgh

16 February 2016 14:00 in CM105

Macromolecular models based on classical potentials are a popular starting point for simulation-based studies in chemistry and biology, but the timescales that are typically accessible in molecular dynamics simulation are fairly limited. New algorithms are needed to extend the range of exploration of molecular systems.

In this talk I will describe the development of methods for sampling complex (bio-)molecular systems based on the introduction of auxiliary variables and the incorporation of stochastic perturbations. After some stage-setting, I will focus on two illustrative examples: a method based on kinetic energy constraints for control of resonances in multiple timestep simulations [1], and a continuous tempering method to facilitate rare transitions by varying the temperature along trajectories [2].

[1] B. Leimkuhler, D. Margul and M. Tuckerman, Stochastic resonance-free multiple time-step algorithm for molecular dynamics with very large time steps, Molecular Physics, vol 111, no. 22-23, pp. 3579-3594, 2013.
[2] G. Gobbo and B. Leimkuhler, Extended Hamiltonian approach to continuous tempering
Physical Review E 91, 061301(R), 2015.

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