A four-year Ph.D Fellowship (FPI contract) is offered at the Soft Matter and Fluids Research Group at UNED, Madrid, Spain in the context of the coordinated project PID2020-117080RB-C54 "Coarse-Graining Theory, and experimental techniques for multiscale biological systems".
The candidate should have a strong inclination to theory and MD simulations. Previous expertise with simulation protocols and languages (C++,Python, LAMMPS, etc) will be highly valued.
Interested candidates should contact Pep Español at [log in para visualizar] as soon as possible (deadline for submission 11/11/2021 !!). Please attach CV, short list of research interests, and one or two names of profesors that can be contacted for reference.
Details on the conditions of the fellowship and administrative procedures can be found in https://tinyurl.com/mdhuv62
Summary of the project:
Theory and simulations within the Theory of Coarse-Graining.
Coarse-Graining Theory (CGT) is a general framework to formulate the dynamics of a set of coarse grained (CG) variables that allow one to describe a system with a reduced number of degrees of freedom. In essence, it models the dynamics of the CG variables in terms of a diffusion process and, hence, it requires a separation of time scales in the evolution of the CG variables. Virtually all dynamic equations in Soft Matter that respect the First and Second Laws of thermodynamics can be deduced from CGT. Our group has pioneered the use of CGT in order to derive dynamic representations of CG complex molecules that go beyond the (incomplete) description in terms of potentials of mean force between, for example, the centers of mass of groups of atoms.
In this project, a first theoretical objective is to introduce additional shape and orientation variables that are crucial when coarse-graining extended objects (from liquid crystals, to macromolecules, to liposomes, etc.). In particular, proteins subject to AFM forcing, and nanoparticles subject to alternating magnetic fields will be the target systems here. As CGT is thermodynamically consistent, it allows one to address the field of nanoscale thermodynamics. Microscopic versions of (static) nano-thermodynamics where the volume of the nano-system is defined through the interaction with the surrounding exist, but the connection of this theory with CGT remains to be explored. Understanding the dynamic equations of such a nano-thermodynamic theory will clarify issues emerging in the field of manipulation of complex molecules (proteins, DNA strands) with external forcings due to AFM and optical tweezers. Also, there is huge interest in the field of micro and nano rheology to address near-contact effects of suspended particles. At these short scales the structure of the fluid manifests itself, as attested by AFM experiments and MD simulations. In addition, the irreversible interaction of the suspended particles can no longer be described by simple hydrodynamic lubrication forces, and there is a need to understand in microscopic terms what may be happening at these scales.
The construction of different theoretical descriptions will be substantiated with computer simulations used to both, extract the microscopically defined building blocks, and to validate the ensuing representations.