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An Exhibition of Applications: Molecular Computing

An Exhibition of Applications: Molecular Computing. Dr. Chrisantha Fernando Systems Biology Centre Birmingham University. Don’t think we can escape from chemotaxis just yet…. http://flash.uchicago.edu/~emonet/biology/agentcell/. Stochastic Modeling.

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An Exhibition of Applications: Molecular Computing

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

  2. Don’t think we can escape from chemotaxis just yet… http://flash.uchicago.edu/~emonet/biology/agentcell/

  3. Stochastic 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.

  4. BioNetS Easy to use

  5. Here is a paper written using the tool…

  6. Lets start with some simple chemical networks…

  7. R RCheZ Rm CheZ Example of a Saturated Enzyme (CheZ) acting to methylate R

  8. Applications • Development and Cellular Differentiation • A Molecular Machine: Bacteriorhodopsin • Molecular Self-Assembly • Liquid State Machines in Cellular Networks?

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

  10. T1 T2 acron T3 head A1 A2 thorax A3 abdomen A4 A5 telson A6 A7 A8 http://www.bio.unc.edu/courses/2006Spring/Biol052-006/April%2010%20-%20Drosophila%20A-P%20polarity.ppt Fly Development anterior T dorsal A posterior “stripy” expression epithelium of segmentation gene (6,000 cells) fushi tarazu (ftz) egg blastoderm fate map larva (cuticle)

  11. A diffusion gradient is set up by maternally expressed genes bcd mRNA Bcd protein anterior posterior

  12. The Reaction Diffusion Principle cells source of morphogen Gradient threshold blue threshold white cells

  13. The Fly ‘French Flag’ colors are made like this… bcd protein binds differentially to enhancers of target (gap) genes low affinity high affinity target genes are zygotically expressed gap genes

  14. maternally expressed genes > protein gradients caudal bicoid zygotically expressed genes Krüppel bicoid (gap gene) > distinct protein expr. domain even-skipped bicoid (pair-rule gene) > 7 stripes of protein expr.

  15. From Bio to Techno • Can we make self-assembling, self-organizing machines that utilize the robust mechanisms displayed by multicellular development?

  16. The French Flag Problem http://www.elec.york.ac.uk/intsys/users/jfm7/gecco2004.pdf

  17. MIT Amorphous Computing Lab • 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 binding Spatial constraints = Allostery and diffusion constraints Adaptable topology = Individual differences between cells/organs Code 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

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

  19. Archaebacteria Halobacteria Salinarium absorbs green light Bacteriorhodipsin • protons are pumped one at a time from the inside of the cell to the outside • Photons react with a bound retinal group causing conformational change in BR 1. Retinal changes form when absorbing a photon www.chembio.uoguelph.ca/educmat/chm455/bacterio.ppt

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

  21. Agent Based Models of ‘Molecular’ Self-Assembly

  22. Molecular Dynamics computer simulation is useful in designing molecular self-assembling systems http://www.iupac.org/publications/pac/2003/pdf/7505x0609.pdf

  23. 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.

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