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International Conference on Mathematical Biology and

Annual Meeting of The Society for Mathematical Biology,

July 27-30, 2009

University of British Columbia, Vancouver

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Program

MSB1d
Steven Andrews
Lawrence Berkeley National Laboratory
Title New particle-based simulation algorithms for molecule-membrane interactions enable a yeast signaling model
Abstract Particle-based simulation is a method for computationally modeling biochemical reaction networks with both spatial and stochastic detail. In it, a simulator represents molecules of interest with individual point-like particles that diffuse, react, and interact with surfaces, all in continuous space. I will present several molecule-surface interaction algorithms. These simulate adsorption, desorption, and transmission through permeable membranes. While technically inexact, these algorithms are nevertheless quite accurate; they are exact in the limit of short simulation time steps, yield correct concentrations at steady-state, are simple to implement, and are computationally efficient. The adsorption algorithm uses a fixed adsorption probability for molecules that diffuse into a surface, the desorption algorithm uses an error-function distributed initial separation between the surface and the desorbed molecules, and the partial transmission algorithm combines these approaches. I implemented and verified these algorithms in the Smoldyn simulator.

These new algorithms, along with others, enable a simple model of signal transmission between yeast cells. By investigating the distribution of pheromone molecules that bind to yeast cell receptors, it shows that cells are best able to find the direction to potential mates when approximately half of the receptors are bound to pheromone. It also shows, somewhat paradoxically, that this direction sensing improves substantially when yeast cells secrete a pheromone-degrading protease which destroys some of the pheromone signal before it can be received. This occurs because the protease amplifies the local pheromone concentration gradient.
LocationWoodward 1