Multiscale modeling of soft matter and biological systems

Molecular systems with low interaction energies explore many different configurations and it is difficult to predict which effective behavior emerges on larger time and length scales. The natural framework to connect the molecular and macroscopic worlds is statistical mechanics, but its formalism can be completely analyzed only for simple model systems like the van der Waals gas. For complex systems, one is left with computer simulations, which however are informed by statistical mechanics, most prominently by the Mori-Zwanzig formalism, which projects the dynamics of a system with many constituents on a few coarse-grained degrees of freedom. Repeated coarse-graining is also the main idea of renormalization group theory.

In this seminar, we discuss the full range of concepts and models that have been developed for multiscale modelling and coarse-graining. We start from soft matter systems like polymers and membranes, which can be simulated as strings and sheets of particles, respectively. We then discuss the extremely important field of proteins, which in the cell tend to form larger complexes such as centrioles, cytoskeletal filaments or virus capsids. All-atom molecular dynamics simulations are the method of choice, but can only cover microsecond time and tens of nanometers length scales. For larger time and length scales, many different coarse-graining strategies have been developed, including elastic networks, the Martini force field or force matching. For protein-protein interaction networks, we discuss the challenge to implement detailed balance, such that statistical mechanics is obeyed. Finally we turn to the emergence of hydrodynamics, discussing particle-based methods such as dissipative particle dynamics (DPD) and multiparticle collision dynamics (MPCD).

This seminar is addressed to master students of physics and related fields, with a strong interest in statistical mechanics and computer physics. We will meet Monday at 4.15 pm in seminar room 44 of the Bioquant (INF 267) on a weekly basis to discuss the suggested topics. The two lecturers will present overviews in the first meetings and distribute the different subjects for the student talks that will follow later in the semester.