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Interdisciplinary Seminar on Mathematical & Computational Modeling: "A Micro-Macro Framework for Analyzing Steric and Hydrodynamic Interactions in Gliding Assays"

Dr. Steve Cook, CS & Engineering, UC Riverside

Monday, March 13, 2017
  12:10–1:10 p.m.


Location: Surge Building 268
  Parking Information

Category: Seminar

Description:

Macroscopic flows of filament-motor mixtures, driven by the hydrolysis of ATP, are important to many cellular processes such as cytoplasmic streaming in Drosophila oocytes and cortical flow in the first cell division of C.~elegans. Gliding assays, reduced in vitro model systems where motor proteins adsorbed onto a planar substrate bind to and move filaments, recreate large-scale dynamic patterns like coherent swarming motion and density waves. These systems are sensitive to the microscopic behavior such as the motor protein binding and unbinding dynamics, which take place on a faster timescale than the direct and fluid-mediated filament interactions. In this work, we present a multiscale modeling and simulation framework for gliding assays that allows detailed microscopic motor modeling as well as both steric and hydrodynamic interactions between filaments. Our model is based on continuum kinetic theory, and our implementation utilizes CPU and GPU parallelism to track the sparse but high-dimensional state space arising from the microscopic motor protein configurations. We find that steric interactions play a role in the formation of spatiotemporally coherent flow structures, and qualitatively reproduce experimentally observed behaviors including filament crossover and alignment, and clump formation, merging, and splitting.



Additional Information: ISMCM

Open to: General Public
Admission: Free
Sponsor: Mathematics

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