Difference between revisions of "CometWiki"

This wiki describes the set up and usage of `comet', an actin-based bead motility simulator.

Introduction

Cell Movement

Cells in our body use actin to move. Unlike the actin-myosin interaction that produces muscle movement, this kind of movement is on a much smaller scale---the scale of individual cells---and allows, for example, neurons to migrate and wire up to the right part of the brain, and cells in our immune system to track down and engulf bacteria. To achieve this movement, cells lay down actin polymer networks that produce force.

Bead Motility

One popular way to study how our cells use actin networks to produce force and move is using a simplified system---actin-based bead motility---which recreates motility in vitro. To do this, we coat a bead with proteins that normally tell the cell to polymerize actin, then put the bead a solution similar to that inside of the cell, which causes an actin network to build around the bead. Surprisingly, even when the bead is spherically symmetric, rather than just building a symmetric shell that gets bigger and bigger, the bead moves off in 'comet tail' of actin.

The Comet Bead-Motility Simulator

This bead motility simulator (named 'Comet') helps us understand how this process works, by recreating the process in silico. It's a top-down model, based on idea that the large-scale elastic behavior of the network is the key to motility, rather than small-scale filament effects. Because it's able, by simulating the elastic behavior alone, not only to reproduce the experimental observations, but also to make new predictions that turn out to hold in the experimental system, it shows how the elastic behavior of the actin network works to produce motility.

Essential Information

Video Tutorials

How to run the comet program on OS X How to make 3D isosurfaces.

How the program works

• Description of the Model
• Overview of Program Flow

Installing the program

comet runs on any unix-like operating system, including OS X, Linux or Windows (under cygwin).

• Instructions for downloading and installing comet

Running the program

The program is called from the command line. The command line parameters tell the program what to do (calculate a new run, re-process existing data, interactive 3D view etc.). A cometparams.ini file in the working directory tells the program detailed information about the model parameters to use for calculation and display.

• Command line parameters for the comet program
• Model settings in the cometparams.ini file
• Display settings in the cometparams.ini file
• Running comet on a cluster

Simulator Output

Example Results

• Symmetry Breaking and Motility
• Forces during Symmetry Breaking
• Circumferential and Radial measurements
• Ellipsoid and Capsule symmetry breaking

Model Robustness

• The effect of changing the main parameters

In Vitro

• 3D Reconstructions of in vitro Constrained Shells
• 3D Reconstructions of in vitro Unconstrained Shells

In Depth Information

Inner workings of the code

• Detailed Program Flow
• Implementation in C++

Making Measurments

• Tracking network movement and making measurements
• Radial Force Movies