Working Group 1: Filament Dynamics and Simulation (FDS)

Working Group 1: Filament Dynamics and Simulation (FDS) 

Working Group Leads: Victor Barocas,, Roger Kamm,

Goals and Objectives:

Our goal is to develop and implement models of filament-filament and filament-fluid interactions in biological systems so as to increase our understanding of biology and to identify new approach to medical diagnosis and treatment.


Working Group 1 Participants

Victor Barocas (co-lead)

James Brasseur

Mohammad Kaazempur-Mofrad

Roger Kamm (co-lead)

George Karniadakis

Anthony Ladd

Jay Schieber


Thursday July 23, 2009 4-5pm EDT - Roger D. Kamm, TaeYoon Kim, Wonmuk Hwang, MIT


TITLE: A computational model for cytoskeletal mechanics -- comparisons with cell and gel experiments
ABSTRACT - Spanning a period of a few decades, there have been several models proposed for the elasticity or viscoelasticity of the cytoskeleton. In addition, there have been numerous experiments using cells and reconstituted actin gels, with or without cross-linkers, designed to characterize the rheology of actin networks under various conditions. Still, debates continue regarding the contributions of various potential mechanisms (filament bending stiffness, thermal fluctuations, filament extensional stiffness, cross-linker stiffness, cross-link binding and unbinding) to cell viscoelasticity, and which model (semiflexible polymer network, tensegrity network, cellular solids) is best able to capture the measured characteristics. Here, we use a computational model of a thermally-active cross-linked network to probe the important factors and discuss these in the context of the different models. We conclude that thermal fluctuations are not important in the cytoskeleton, in contrast to the semiflexible polymer network theory. But both the cellular solids and tensegrity models fail to capture some of the salient mechanical features. For cross-linked networks under prestress, the tensegrity model appears to be the most consistent with the results of our simulations. However, currently no single model satisfactorily captures viscoelastic behaviors of actin networks over a wide range of conditions. Our simulation scheme provides a basis for delineating multiple mechanisms involved in this complex system.

Thursday September 18, 2008 2pm EDT - Victor Barocas

The discussion focused on the problem of predicting flow through dilute fiber networks. It began with a brief review of the problems of interest and of the existing solutions, which are primarily for regular and/or isotropic networks. Recent finite-element simulations of flow through model networks with different degrees of anisotropy will then be presented, along with comparison to different approaches to predict the permeability of the network without requiring direct simulation of the flow field. The followup discussion brought out some open issues, particularly the issue of flow through inhomogeneous networks.


Monthly Reports

July, 2006 Report

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