Öffentliche Seminare

Gastgeber: Joseph Rudzinski

Improving accuracy of systematic coarse-grained simulations

Billion atom simulations are just now becoming possible in molecular simulation for nanoseconds. We've also crossed the millisecond barrier for simulating biomacromolecules. What's left? Unfortunately, a typical cell contains 100 trillion atoms. Even simulating something like a polymer nanoparticle (~100 million atoms) has timescales of interest far beyond nanoseconds. One way around the length-scale limitation is coarse-grained simulation. Coarse-graining requires two ingredients: (i) a mapping that determines how to group atoms into coarse beads and (ii) a force field that describes these interactions. In this talk, I will describe our recent progress on determining mapping operators, which has previously been an arcane topic with little rigor. We've developed novel theory, shown what role symmetry plays, and developed ML models that find mappings for arbitrary molecular systems. Finding the force field of a coarse-grained model is a rich field with a long history. Typically, it is broken into two types: top-down, where we choose the force field to reproduce an observed phonemenon in experiment; and bottom-up, where we draw upon the observed forces in a molecular simulation. I will describe our recent work on combining these approaches to create hybrid top-down/bottom-up models via the principle of maximum entropy. [mehr]

Development of a coarse-grained model for liquid-like protein assemblies

In this talk, I will describe ongoing efforts in my group aimed at developing an accurate simulation model to study the thermodynamics and kinetics of multiprotein assembly. We use a "top-down" approach for constructing a Cα-based (one interaction site per amino acid) protein model. Development of the proposed model involves comparisons with experimental data available from the recent literature as well as comparisons with atomistic simulations of a single protein chain. The usefulness of our approach will be demonstrated by discussing results on multiple biological systems of interest. Of particular interest to us is the formation of liquid-like assemblies of disordered proteins that have been found to be important for the physiological function of membraneless compartments in living cells including the nucleolus and ribonucleoprotein (RNP) granules as well as many organelles in prokaryotic cells. [mehr]
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