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PICS Colloquium: Unraveling Internal Friction in a Coarse-Grained Protein Model with Pep Español

February 21 @ 2:00 PM3:00 PM

Abstract: Understanding the dynamic behavior of complex biomolecules requires simplified models that not only make computations feasible but also reveal fundamental mechanisms. Coarse-graining (CG) achieves this by grouping atoms into beads, whose stochastic dynamics can be derived using the Mori-Zwanzig formalism, capturing both reversible and irreversible interactions. In liquid, the dissipative bead-bead interactions have so far been restricted to hydrodynamic couplings. However, friction does not only arises from the solvent but notably, from the internal degrees of freedom missing in the CG beads. This leads to an additional “internal friction” whose relevance is studied in this contribution. By comparing with all-atom molecular dynamics (MD), we neatly show that in order to accurately reproduce the dynamics of a globular protein in water using a coarse-grained (CG) model, not only a precise determination of elastic couplings and the Stokesian self-friction of each bead is required. Critically, the inclusion of internal friction between beads is also necessary for a faithful representation of protein dynamics. We propose to optimize the parameters of the CG model through a self-averaging method that integrates the CG dynamics with an evolution equation for the CG parameters. This approach ensures that selected quantities, such as the radial distribution function and the time correlation of bead velocities, match the corresponding MD values.

Bio:
Pep Español is a theoretical physicist with a strong background in computer simulation methods. His research interests include soft matter, complex fluids, and dynamic descriptions of complex molecular structures. He is an expert in particle simulation methods applied to the hydrodynamics of simple and complex fluids. He has contributed substantially to the development of the dissipative particle dynamics method, a very popular approach for simulating coarse-grained models of complex fluids. Additionally, he has advanced the fundamental understanding of the inclusion of thermal fluctuations in computational (discrete) hydrodynamics, both in Lagrangian descriptions (through the invention of the Smoothed Dissipative Particle Dynamics Method) and Eulerian formulations. More recently, he has directed efforts toward understanding the microscopic origin of boundary conditions. He is particularly interested in the theoretical foundations and thermodynamic consistency of new coarse-graining-based simulation methods and is currently writing a book on the theory of coarse-graining. A very recent advancement generalizes the venerable Euler equations for a free body to incorporate dissipation and fluctuations in a thermodynamically consistent manner.

After earning his PhD in Physics in 1992 at the Universidad Nacional de Educación a Distancia in Madrid, he completed a postdoctoral fellowship at the University of Cambridge as a Marie Curie Fellowship holder during 1993–1994, where he joined the Group of Polymer and Colloids at the Cavendish Laboratory, led by Sir Sam Edwards. He served as an Assistant Professor (Profesor Titular) from 1998 to 2010 at UNED and took a sabbatical leave in 2009 as a Senior Fellow at the Freiburg Institute for Advanced Studies. Since 2010, he has been a Full Professor of Applied Physics (Catedrático de Universidad) at the Department of Fundamental Physics of the Universidad Nacional de Educación a Distancia in Madrid.

Details

Date:
February 21
Time:
2:00 PM – 3:00 PM
Event Category:

Organizer

Delaney Parks
Phone
7034701288
Email
dkparks@seas.upenn.edu

Venue

PICS Large Conference Room – 534
3401 Walnut Street, 5A
Philadelphia, PA 19104 United States
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