Chara Alexiou joined the group of Soft Matter Theory and Simulation initially in November 2021 and has been working on the development of reduced, coarsegrained (CG) levels of description, suitable to address the large length scales relevant to the DNA kinetoplast, a unique mitochondrial structure formed by thousands of interlinked DNA-mini-rings.
Following the completion of her PhD at the Department of Chemical Engineering at the University of Patras, focused on the theoretical modeling and computational simulation of the interaction between a Newtonian fluid and a permeable, poroelastic cellular medium, Chara shifted the focus of her research interest to much finer scales of resolution through the implementation of atomistic detail Molecular Dynamics for the investigation of the conformational and dynamic properties of DNA duplexes, both in aqueous solutions and in binary fluid mixtures. Chara’s research expertise spans from continuum (finite element modelling of flow through permeable elastic bodies) to discrete particle simulation methods (molecular dynamics for DNA systems), as well as to upscaling techniques (volume averaging) and coarse-grained or mesoscopic methods (Brownian and Dissipative Particle Dynamics).
The expertise of the host group at the faculty of physics, headed by Prof. Christos Likos, will play an essential role in the project, in particular in the accurate coarse graining of these complex, multicomponent soft matter systems. At the same time, Chara will bring to the group her skills on atomistic molecular dynamics of biopolymers, initiating novel research directions in the group.
Complementary to the computational approach of the Soft Matter Theory and Simulation group, a collaboration with the experimental group of Prof. Alex Klotz has been established, to provide a means of validation. Recent experimental work has established some fascinating facts about the mesoscopic structure of the kinetoplast, yet very little is known from the theoretical point of view. This work will contribute to the understanding of the physical mechanisms that determine the self-organization and the elastic properties of 2D catenated ring polymer systems such as the kinetoplast by employing accurate modeling across the scales.