An Exhibition of Applications: Molecular Computing Dr. Chrisantha Fernando Systems Biology Centre...

An Exhibition of Applications: Molecular Computing

An Exhibition of Applications: Molecular Computing

Dr. Chrisantha Fernando

Systems Biology Centre

Birmingham University

Dr. Chrisantha Fernando

Systems Biology Centre

Birmingham University

Don’t think we can escape from chemotaxis just yet…

Don’t think we can escape from chemotaxis just yet…

http://flash.uchicago.edu/~emonet/biology/agentcell/

QuickTime™ and aCinepak decompressor

are needed to see this picture.

Stochastic ModelingStochastic Modeling

So far we have been doing deterministic modeling. Stochastic models consider individual molecules,

undergoing discrete reaction events, i.e. chemical (autonomous) agents.

These models diverge from deterministic models when particle numbers are low, but also they allow “emergent” reactions…

To get a feel for stochastic modeling, try BioNetS.

So far we have been doing deterministic modeling. Stochastic models consider individual molecules,

undergoing discrete reaction events, i.e. chemical (autonomous) agents.

These models diverge from deterministic models when particle numbers are low, but also they allow “emergent” reactions…

To get a feel for stochastic modeling, try BioNetS.

BioNetSBioNetS

QuickTime™ and aTIFF (LZW) decompressor


Easy to use

Here is a paper written using the tool…

Here is a paper written using the tool…



Lets start with some simple chemical networks…

Lets start with some simple chemical networks…






are needed to see this picture.CheZ

RCheZQuickTime™ and aTIFF (LZW) decompressor


R



Rm

Example of a Saturated Enzyme (CheZ) acting to methylate R

ApplicationsApplications

Development and Cellular Differentiation A Molecular Machine: Bacteriorhodopsin Molecular Self-Assembly Liquid State Machines in Cellular

Networks?

Development and Cellular Differentiation A Molecular Machine: Bacteriorhodopsin Molecular Self-Assembly Liquid State Machines in Cellular

Networks?

DevelopmentDevelopment

QuickTime™ and aTIFF (Uncompressed) decompressor


http://www.cogs.susx.ac.uk/users/inmanh/easy/alife06/Lecture%206/lec06.pdf





egg blastoderm fate map larva

T

A

Fly Development

acron

head

thorax

abdomen

telson

T1

T2

T3A1A2A3

A4

A5

A6

A7

A8

(cuticle)

“stripy” expressionof segmentation gene

fushi tarazu (ftz)

anterior

posterior

dorsal

epithelium(6,000 cells)

http://www.bio.unc.edu/courses/2006Spring/Biol052-006/April%2010%20-%20Drosophila%20A-P%20polarity.ppt

A diffusion gradient is set up by maternally expressed genes

A diffusion gradient is set up by maternally expressed genes

bcd mRNA

Bcd proteinanterior posterior

The Reaction Diffusion PrincipleThe Reaction Diffusion Principle

source ofmorphogen

threshold blue

threshold white

Gradient

Gradient

cells

cells

The Fly ‘French Flag’ colors are made like this…

The Fly ‘French Flag’ colors are made like this…

bcd protein binds differentially to enhancers of target (gap) genes

target genes are zygotically expressed gap genes

low affinity

high affinity

bicoid

bicoid

Krüppel

even-skipped

(gap gene)

(pair-rule gene)

bicoid

maternally expressed genes

caudal

> protein gradients

> 7 stripes of protein expr.

> distinct protein expr. domain

zygotically expressed genes

From Bio to TechnoFrom Bio to Techno

Can we make self-assembling, self-organizing machines that utilize the robust mechanisms displayed by multicellular development?

Can we make self-assembling, self-organizing machines that utilize the robust mechanisms displayed by multicellular development?

The French Flag Problem

http://www.elec.york.ac.uk/intsys/users/jfm7/gecco2004.pdf





MIT Amorphous Computing LabMIT Amorphous Computing Lab

Printable computers http://www-swiss.ai.mit.edu/projects/amorphous/papers/butera-phd.pdf

Printable computers http://www-swiss.ai.mit.edu/projects/amorphous/papers/butera-phd.pdf



Asynchrony = Stochastic noise in/between cells Fault tolerance = Protein misfolding/non-specific bindingSpatial constraints = Allostery and diffusion constraintsAdaptable topology = Individual differences between cells/organsCode compactness = Slow protein conformation changes

"A programming model employing a self-organizing ecology of mobile process fragments supports a variety of useful applications on a paintable computer”

Inspired by biological development

http://chaos.c.u-tokyo.ac.jp/study/papers1.html



BacteriorhodipsinBacteriorhodipsin

Archaebacteria Halobacteria Salinarium absorbs greenlight

www.chembio.uoguelph.ca/educmat/chm455/bacterio.ppt

protons are pumped one at a time from the

inside of the cell to the outsidePhotons react with a bound retinal group

causing conformational change in BR

1. Retinal changes form when absorbing a photon





http://www.ks.uiuc.edu/Services/Class/BIOPHYS490M/04-bR-retinal.pdf

Agent Based Models of ‘Molecular’ Self-Assembly

Agent Based Models of ‘Molecular’ Self-Assembly











http://www.iupac.org/publications/pac/2003/pdf/7505x0609.pdf



Molecular Dynamicscomputer simulation is useful in designing molecular self-assembling systems

Now for a special guest… Now for a special guest…

Ben Jones (PhD student), will talk about our recent paper that we will present in Hawaii this weekend.

We model the gene transcription network of E.Coli, and ask if it works like a bucket of water.

Ben Jones (PhD student), will talk about our recent paper that we will present in Hawaii this weekend.

We model the gene transcription network of E.Coli, and ask if it works like a bucket of water.

An Exhibition of Applications: Molecular Computing Dr. Chrisantha Fernando Systems Biology Centre...

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