Biological and Chemical problems for the

computer scientist: an overview

Outline• Motivation

• General obstacles in studying chemical and biological systems

• Select problems

• Summary and Q&A

Motivation• Technological and algorithmic advances =

computation as a useful tool

• Novel biological and chemical problems

• Growing need for ‘us’ to understand the problems

• Lack of undergraduate interdisciplinary focus

General obstacles

• Complex systems = numerous variables (signal transduction)

• Vast amounts of data (DNA, microarrays)

• Inherent redundancy in nature

• Conversion of microscale models to macroscale models (interactions between molecules)

Signal Transduction

Some applications• Drug design

• Epidemiology (interaction of genes & environment)

• Evolutionary trends (phylogenetic trees)

• Environmental trends (acid rain, global warming)

• Chemical engineering (polymers, aerospace, automobiles)

Outline

Abstract and motivation • Sequencing of human genome = 3 billion

nucleotides!• How does the code translate into structure

and function?• What parts of the code are switched “on”

or “off” and when?• Microarrays = information describing gene

expression• Algorithms try to interpret the information

Metabonomics • Problem with genomics and proteomics?

• Older approach

• Screen for metabolites per phenotype

• Familiar problem?

Environmental• Computational Modeling of Nitric Oxide Formation in Biomass

Combustion (Torleif Weydahl, Mette Bugge, Inge R. Gran, and Ivar S. Ertesvåg)

• NOx = main contributor to acid rain, smog, ozone degradation

• Develop a quantitative model for prediction of NOx formation from nitrogen-containing fuels

Describing Equilibria• dG = -RTln(K), (thermodynamics) aA + bB <-> cC + dD, K = ([C]^c[D]^d) / ([A]^a[B]^b) • Questions -Macro and Micro? -Predicting dG for a rxn• Applications: Industry, Drug design

Concluding points• Growing number of computationally

complex problems

• Requires novel algorithms => requires understanding of background

• Largest problems: communication and collaboration, personal who have fulfilled the I requirement!