Computational modeling of macromolecule interactions from droplets to cells

Supervisor: Dr. Styliani (Stella) Constas

Project: Computational modeling of macromolecule interactions from droplets to cells

Can extend to MSc?:  Yes

Project Description (Abstract):

In this project we intend to use Monte Carlo methods developed in the group to study the free energy of conformations of intrinsically disordered proteins under confinement. The sampling of the conformations will take place by using look-ahead Monte Carlo methods [S. Consta et al. “Recoil growth: an efficient simulation method for multi-polymer systems” Journal of Chemical Physics, 110:3220–3228 (1999); “Recoil Growth Algorithm for Chain Molecules with Continuous Interactions” Journal of Molecular Physics, 97:1243-1254 (1999)] that have been developed in the group and they have been shown to be efficient under the stringent conditions of high fluid density. Based on our previous experience on macromolecule-droplet interactions [S. Consta et al. “New mechanisms of macroion-induced disintegration of charged droplets” Chemical Physics Letters-Frontiers 663: 1–12 (2016)] we extend our study into the behaviour of macromolecules in confined environments that mimic cell compartments. The simulations will require the writing of computer codes and usage of already developed codes (NAMD). The student will learn advanced sampling techniques in molecular simulations that go beyond direct molecular dynamics and basic Monte Carlo methods.

 

 

 


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