CBCComputing with Biology & Chemistry

MSc Natural ComputationDepartment of Computer ScienceUniversiy of York

Module description

To give a foundation in computational systems that are inspired by biological and chemical systems,

or that are themselves bio-chemical systems, or that include a bio-chemical part as an essential

constituent.

This goes from well-understood areas like DNA computing to less mature areas like reaction-diffusion computers, P-systems, H-systems…Unifying theme is their differences from conventional computational systems, both in the approach taken to the computation and to the physical substrate used for the computation.

Who is it aimed at?

Basic computer science experience of algorithms and complexity will be assumedNo biological/chemical background will be necessary – but we will cover some genetics and chemistry very quickly, so be prepared to read a lot!

Level of mathematics required

Ability to follow formal definitions of machines But this is not essential for very much

of the module

Basic complexity theorySome statistics/probability

Content 1: DNA Computing

Starting point is the use of biological macromolecules for computing

How do we represent data?

How do we manipulate it?

Is it efficient?

Image from

http://www.blc.arizona.edu/Molecular_Graphics/DNA_Structure/DNA_Tutorial.HTML

C A T A T A G G C A A T A T C C G T A G

V1,left V1,right V2,left V2,right

Ex,left =Vc1,right Ex,right= Vc2,left

V1,left V1,right

Representing data structures

Each node represented by a 20-mer strandEach possible edge represented by a complementary 20-mer

Content 2: Complex systems

GRN

Content 3: RD systems

Complex chemical reactions don’t always behave as expected…

Chemical logic gates: 3 input OR gate

Controlled inputs are xyz1-input (“clock”) is required to get output in the 000 case (shown)Graph shows response to three patterns (000, 111 and 010). In the latter two cases, there is a single intensity peak in the output.Gradually increasing response is due to “ageing” of the systemMuch more complicated functions can be implemented…

Practical elements

As yet, no lab work with DAN or chemical systemsThere will be seminars Discussions on topics from the module based

around a specified piece of reading

Other possibilities include Simulation of DNA systems Analysis of complex dynamic systems (GRNs) Use of P-system simulators

Assessment

The assessment for the module is openThe assessment will consist of some or all of the following: Demonstration of understanding of lecture

material Selection and application of algorithms to

given datasets Analysis of the output of specific algorithms Review of the literature on a particular topic.