BioComp: Collaborative Research: P Systems: Theory and Applications to Modeling and Simulation of Cells

University Of California-Santa Barbara, Santa Barbara CA

Investigators

Abstract

Membrane computing, a relatively new branch of molecular computing, holds great promise for new paradigms for computation suggested by processes that occur in live cells. This area was recently selected by the Institute for Scientific Information (ISI) as a fast "Emerging Research Front" in Computer Science. The project has three major directions of research using tools and techniques from the membrane computing area. The first concerns the simulation of cells using concepts from P systems implemented in the E-cell package. To help the simulation of cells the second research area focuses on defining models of P systems that mimic the processes in the cell. The PIs have already, as a preliminary result, one such example of a model of P systems that has several features not found in any other previous P system models: binding of objects and genetic information. Another major novelty of the proposed model is that time is associated with each rule. The PIs plan to search for other suitable models, and also work on the more theoretical aspects of the P systems: developing efficient algorithms (e,g., considering reachability between system configurations), and investigating important and fundamental computational issues in the models considered. The third area complements the first two: research in the area of P systems simulators. While in the first area the interest is in simulating cells using, among other ideas, the models developed in the second area; the third research focus goes in the opposite direction - simulation of P systems rather than the simulation of cells. This area of research complements the first two, since such a simulator for a bio-relevant P system could answer practical questions raised from biology. An ambitious goal of the whole project is to capture in these mathematical models the way the cells self-configure and self-maintain and view it as computation. These investigations could yield new ideas and useful models for computation inspired by the extraordinary system that is a cell. The proposed project topic is new, with great promise to significantly impact several areas. In Biology the project will help explore, model and simulate differential gene expression during various biological processes and transcriptional and signaling networks on a larger scale than the current capabilities; in Computer Science the research could yield new paradigms and new computing techniques (as has happened in the discovery of genetic algorithms and neural networks). One of the major contributions of this project will be the applications of a good cell-simulator in many areas - such a software would be an invaluable tool for designing and testing new drugs; for predicting the behavior of a specific type of cell in a specific environment; and, lastly, for teaching and gaining more knowledge and insight about the extraordinary systems that we call "the cells".