Introduction - University of Cambridge

Welcome to Cambridge
Why we are here…
Overall objectives:
to advance understanding of the self-organization of
to analyse the dynamics of molecules that leads to formation of
native molecular structures
to investigate the ‘informational content’ of the dynamics of
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
develop software that can be used for general-purpose
complexity analysis
Who we are.….
Participant 1
 University of Cambridge
Chemistry Department, Lensfield Road, Cambridge, CB2 1EW, UK
Principal Investigator: Prof. Robert C. Glen
 Dr Dmitry Nerukh
Participant 2
 Rijksuniversiteit Groningen
Postbus 72, 9700 AB Groningen, The Netherlands
Principal Investigator: Prof. Alan E. Mark
 Herman Berendsen
Participant 3
 Centro interdipartimentale per lo Studio delle Dinamiche Complesse
Dipartimento di Fisica, Universita' di Firenze, Via G. Sansone, 1,
50019 Sesto Fiorentino (FI), Italy
Principal Investigator: Dr Lapo Casetti
Participant 4
 Chalmers/Goteborg University
Department of Physical Resource Theory, School of Physics and
Engineering Physics, 41296 Goteborg, Sweden
Principal Investigator: Prof Kristian Lindgren
 Martin Nilsson, Olof Gornerup (PhD student, started 1 April), Anders
Eriksson (post doc)
Who we are.….
Participant 5
 University of Vienna
University of Vienna, Institut fur Theoretische Chemie und
Molekulare Strukturbiologie, Wahringerstrasse 17, A-1090 Wien,
Principal Investigator: Prof. Peter Schuster
 Ivo Ludwig Hofacker, Christoph Flamm
Participant 6
 University of Heidelberg
The Computational Molecular Biophysics Group, IWR, UniHeidelberg, Im Neuenheimer Feld 368, 69120 Heidelberg, Germany
Principal Investigator: Prof. Jeremy C. Smith
Participant 7
 University of Leipzig
Lehrstuhl für Bioinformatik, Institut für Informatik, Universität
Leipzig, Kreuzstr. 7b, 04103 Leipzig, Germany
Principal Investigator: Prof. Peter F Stadler
 Prof. Martin Middendorf, Konstantin Klemm
Participant 8
 Friedrich-Schiller-Universität Jena
Lehrstuhl für Bioinformatik, Institut für Informatik, Ernst-AbbePlatz 2, 07743 Jena
Principal Investigator: Prof. Rolf Backofen
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 selfassembly 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
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
 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
It’s the EU, so reporting will be
 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.
Monday 25 July
13:00 lunch
14:00 Scientific presentations
12:00 Robert Glen: Welcome and Introduction
14:00 Cambridge
15:00 Chalmers
16:00 tea break
16:30 Florence
17:30-18:00 discussion
19:00 dinner
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
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
and off we go…