Wolfram Computation Meets Knowledge

Wolfram Summer School


Ashutosh Gupta

Summer School

Class of 2007


Born and brought up in Jaipur (Pinkcity – the capital of Rajasthan, a state in western part of India), Ashutosh received his bachelor’s and master’s degrees in Physics at the Indian Institute of Technology Kharagpur. He is currently a fourth year physics graduate student at the University of Maryland, College Park. His present research interests are optics, cryogenics, and biophysics.

Project: Modelling Gene Regulatory Networks Using Multiway Systems

Proteins are the elementary functional units responsible for growth and motility of all ‘living organisms’. The code (genes) for constructing (and deconstructing) the proteins is stored in the DNA; from there it is transcribed into RNAs. Some of these RNAs (called messenger RNA or mRNA) are than translated to proteins. The number of mRNAs varies among different species. Humans are believed to have about 30,000 different types of mRNAs giving as many different proteins. The total number of mRNAs is estimated to be 10^5 following a Pareto distribution.

Different proteins carry out different tasks at various stages in the cell cycle. Some proteins are responsible for transcription of DNA; some translate mRNAs to make new proteins; some help in the tranport of various molecules & nutrients from one region of the cell to other; and some are responsible for repairing of damaged cells, some proteins help in destruction of harmful bacteria and viruses. The quantities of each of these proteins are regulated depending on need and hence the name “Gene Regulatory Network”. It is a complex and dynamic network which is continuously interacting with its environment.

I plan to study the growth of such networks using multiway systems. These systems grow rapidly with a variety of different entities (strings) in different quantities and are an obvious choice to study regulatory networks.

Favorite Outer Totalistic Three-Color Rule

Rule chosen: 30224

That’s rule 13723198. This rule seems to know perfectly what it is doing, and appears somewhat generous in transparently showing the internal steps of its computation. If an analogy were to be found, I would think of the computation performed by a very complicated, but purely mechanical (not electronic) system, with small balls bouncing and dropping and fragmenting in orderly ways.