DEPARTMENT OF COMPUTER SCIENCE
DOCTORAL DISSERTATION DEFENSE


Candidate: Pankaj Agarwal
Advisor: Jacob T. Schwartz

Cell-based Computer Models in Developmental Biology
10:00 a.m., Wednesday, September 8, 1993
12th floor conference room, 719 Broadway




Abstract

In developmental biology, modeling and simulation play an important role in understanding cellular behavior. We suggest a simple language, the Cell Programming Language (CPL), to write computer programs to describe this behavior. Using these programs, it is possible to simulate and visualize cell behavior.

A genome is the program for the development of an organism. The genome, in conjunction with the environment, determines the behavior of each cell of the organism. The program for each cell (written in CPL) plays the role of its genome. The program for an individual cell consists of a set of states. In each state, rules are specified which determine the cell properties (i.e. shape, motility, concentrations of various molecular species, etc.). Different states of the same cell signify different phases in the cell's life. Each cell has a tissue type associated with it. Cells of the same tissue type execute the same CPL program.

We use the discrete time simulation model. At every time step, each cell executes all the instructions in its present state sequentially. All cells are assumed to be executing in parallel, with synchronization performed after every time step.

The cells are two-dimensional. Each cell has a physical location comprising a collection of discrete connected points. This physical presence imparts to the cells the attributes of area, perimeter, and neighbors (other cells). The neighbor attribute forms the basis for all intercellular communication.

The language contains features for specifying:

We have employed CPL to model the following: aggregation in cellular slime mold in response to a chemotactic agent; the formation of skeletal elements in the vertebrate limb; and cellular segregation due to differential adhesion.