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EMBIO

EMBIO. Welcome to Cambridge. Why we are here…. Overall objectives: to advance understanding of the self-organization of biomolecules to analyse the dynamics of molecules that leads to formation of native molecular structures

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EMBIO

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  1. EMBIO Welcome to Cambridge

  2. Why we are here… Overall objectives: • to advance understanding of the self-organization of biomolecules • to analyse the dynamics of molecules that leads to formation of native molecular structures • to investigate the ‘informational content’ of the dynamics of molecules • to elucidate the connection between chemical composition and dynamics leading to self-organisation • to investigate the energy landscapes of self-organising systems and investigate how self-organising dynamics appears • obtain experimental data on biomolecules and use these data in simulations • develop software that can be used for general-purpose complexity analysis

  3. Who we are.…. Participant 1 • University of CambridgeChemistry Department, Lensfield Road, Cambridge, CB2 1EW, UKPrincipal Investigator: Prof. Robert C. Glen • Dr Dmitry Nerukh Participant 2 • Rijksuniversiteit GroningenPostbus 72, 9700 AB Groningen, The NetherlandsPrincipal Investigator: Prof. Alan E. Mark • Herman Berendsen Participant 3 • Centro interdipartimentale per lo Studio delle Dinamiche Complesse (CSDC) FIRENZEDipartimento di Fisica, Universita' di Firenze, Via G. Sansone, 1, 50019 Sesto Fiorentino (FI), ItalyPrincipal Investigator: Dr Lapo Casetti Participant 4 • Chalmers/Goteborg UniversityDepartment of Physical Resource Theory, School of Physics and Engineering Physics, 41296 Goteborg, SwedenPrincipal Investigator: Prof Kristian Lindgren • Martin Nilsson, Olof Gornerup (PhD student, started 1 April), Anders Eriksson (post doc)

  4. Who we are.…. Participant 5 • University of ViennaUniversity of Vienna, Institut fur Theoretische Chemie und Molekulare Strukturbiologie, Wahringerstrasse 17, A-1090 Wien, AustriaPrincipal Investigator: Prof. Peter Schuster • Ivo Ludwig Hofacker, Christoph Flamm Participant 6 • University of HeidelbergThe Computational Molecular Biophysics Group, IWR, Uni-Heidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, GermanyPrincipal Investigator: Prof. Jeremy C. Smith Participant 7 • University of Leipzig Lehrstuhl für Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstr. 7b, 04103 Leipzig, GermanyPrincipal Investigator: Prof. Peter F Stadler • Prof. Martin Middendorf, Konstantin Klemm Participant 8 • Friedrich-Schiller-Universität Jena Lehrstuhl für Bioinformatik, Institut für Informatik, Ernst-Abbe-Platz 2, 07743 JenaPrincipal Investigator: Prof. Rolf Backofen

  5. Partners objectives….. • Partners objectives (needs to be discussed/updated): • Cambridge: Dynamic complexity, non-linear dynamics of molecular systems, chaos, information from the dynamics; • Groningen: Simulation of protein folding and lipid membrane self-assembly in explicit water • Florence: free energy funnels for simplified protein-in-water dynamic models, “good” and “bad” folders, experimental mechanical stretching of giant single molecular proteins • Chalmers: dynamic hierarchies, emergence of the dynamic forms and information flow at different scales in the system • Vienna: topological, statistical and dynamic properties of generic potential energy and fitness surfaces of RNA • Heidelberg: unfolded and native state globular protein simulations • Leipzig: complexity of the energy landscapes of proteins and RNA • Jena: energy landscapes: structure predictions of lattice models

  6. Objectives for the meeting Have a stimulating exchange of ideas- • start the collaboration properly with face to face meetings • exchange old and new information on the research background/progress of each partner • discuss what’s been initiated/completed since the start of EMBIO on the 1st of April and the outlook for the next six months • update plans of cross party collaborations: visits between the partners, collaborative research topics etc. • information on reporting, ideas for the web site • exchange details on financing and formal obligations • have fun

  7. It’s the EU, so reporting will be important… Reporting: • August 2006 the first report • September 2008, second report • + a final report at the end (within 45 days) • to gradually accumulate information for the major reports, we would ask for regular monthly reports from the partners • publications: first one from Lapo – seemed to work ok – about two weeks.

  8. Agenda • Monday 25 July • 12:00 Robert Glen: Welcome and Introduction • 13:00 lunch • 14:00 Scientific presentations • 14:00 Cambridge • 15:00 Chalmers • 16:00 tea break • 16:30 Florence • 17:30-18:00 discussion • 19:00 dinner

  9. Agenda… • Tuesday 26 July • 9:00 Jena • 10:00 Vienna • 11:00 break • 11:30 Heidelberg • 12:30 discussion • 13:00 lunch • 14:00 Helen Atkinson, Louise Balshaw: information on finances/organisation • 15:00 Leipzig • 16:00 Cambridge tour/punting/free evening

  10. Agenda… Wednesday 27 July • Summary and planning • 9:00 Summary: creating a draft of the results achieved so far • 10:30 Planning: future work and collaborations • 12:00 telephone (web) conference call: Groningen • 12:30 lunch • 13:00 - 14.00 Discussion and finish

  11. and off we go…

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