EMBIO

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

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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

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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 whats 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

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Its 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.

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Agenda

• Monday 25 July
• 1200 Robert Glen Welcome and Introduction
• 1300 lunch
• 1400 Scientific presentations
• 1400 Cambridge
• 1500 Chalmers
• 1600 tea break
• 1630 Florence
• 1730-1800 discussion
• 1900 dinner

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Agenda

• Tuesday 26 July
• 900 Jena
• 1000 Vienna
• 1100 break
• 1130 Heidelberg
• 1230 discussion
• 1300 lunch
• 1400 Helen Atkinson, Louise Balshaw
  information on finances/organisation
• 1500 Leipzig
• 1600 Cambridge tour/punting/free evening

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Agenda

• Wednesday 27 July
• Summary and planning
• 900 Summary creating a draft of the results
  achieved so far
• 1030 Planning future work and collaborations
• 1200 telephone (web) conference call Groningen
• 1230 lunch
• 1300 - 14.00 Discussion and finish

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and off we go