EMBIO Welcome to Cambridge

Why we are here… Overall objectives: to advance understanding of the self-organization of biomolecules to advance understanding of the self-organization of biomolecules to analyse the dynamics of molecules that leads to formation of native molecular structures 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 investigate the ‘informational content’ of the dynamics of molecules to elucidate the connection between chemical composition and dynamics leading to self-organisation 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 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 obtain experimental data on biomolecules and use these data in simulations develop software that can be used for general-purpose complexity analysis 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 University of Cambridge Chemistry Department, Lensfield Road, Cambridge, CB2 1EW, UK Principal Investigator: Prof. Robert C. Glen Dr Dmitry Nerukh Dr Dmitry Nerukh Participant 2 Rijksuniversiteit Groningen Postbus 72, 9700 AB Groningen, The Netherlands Principal Investigator: Prof. Alan E. Mark Rijksuniversiteit Groningen Postbus 72, 9700 AB Groningen, The Netherlands Principal Investigator: Prof. Alan E. Mark Herman Berendsen Herman Berendsen Participant 3 Centro interdipartimentale per lo Studio delle Dinamiche Complesse (CSDC) FIRENZE Dipartimento di Fisica, Universita' di Firenze, Via G. Sansone, 1, Sesto Fiorentino (FI), Italy Principal Investigator: Dr Lapo Casetti Centro interdipartimentale per lo Studio delle Dinamiche Complesse (CSDC) FIRENZE Dipartimento di Fisica, Universita' di Firenze, Via G. Sansone, 1, 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, Goteborg, Sweden Principal Investigator: Prof Kristian Lindgren Chalmers/Goteborg University Department of Physical Resource Theory, School of Physics and Engineering Physics, Goteborg, Sweden Principal Investigator: Prof Kristian Lindgren Martin Nilsson, Olof Gornerup (PhD student, started 1 April), Anders Eriksson (post doc) 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, Austria Principal Investigator: Prof. Peter Schuster University of Vienna University of Vienna, Institut fur Theoretische Chemie und Molekulare Strukturbiologie, Wahringerstrasse 17, A-1090 Wien, Austria Principal Investigator: Prof. Peter Schuster Ivo Ludwig Hofacker, Christoph Flamm Ivo Ludwig Hofacker, Christoph Flamm Participant 6 University of Heidelberg The Computational Molecular Biophysics Group, IWR, Uni- Heidelberg, Im Neuenheimer Feld 368, Heidelberg, Germany Principal Investigator: Prof. Jeremy C. Smith University of Heidelberg The Computational Molecular Biophysics Group, IWR, Uni- Heidelberg, Im Neuenheimer Feld 368, Heidelberg, Germany Principal Investigator: Prof. Jeremy C. Smith Participant 7 University of Leipzig Lehrstuhl für Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstr. 7b, Leipzig, Germany Principal Investigator: Prof. Peter F Stadler University of Leipzig Lehrstuhl für Bioinformatik, Institut für Informatik, Universität Leipzig, Kreuzstr. 7b, Leipzig, Germany Principal Investigator: Prof. Peter F Stadler Prof. Martin Middendorf, Konstantin Klemm Prof. Martin Middendorf, Konstantin Klemm Participant 8 Friedrich-Schiller-Universität Jena Lehrstuhl für Bioinformatik, Institut für Informatik, Ernst-Abbe- Platz 2, Jena Principal Investigator: Prof. Rolf Backofen Friedrich-Schiller-Universität Jena Lehrstuhl für Bioinformatik, Institut für Informatik, Ernst-Abbe- Platz 2, Jena Principal Investigator: Prof. Rolf Backofen

Partners objectives….. Partners objectives (needs to be discussed/updated): Partners objectives (needs to be discussed/updated): Cambridge: Dynamic complexity, non-linear dynamics of molecular systems, chaos, information from the dynamics; 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 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 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 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 Vienna: topological, statistical and dynamic properties of generic potential energy and fitness surfaces of RNA Heidelberg: unfolded and native state globular protein simulations Heidelberg: unfolded and native state globular protein simulations Leipzig: complexity of the energy landscapes of proteins and RNA Leipzig: complexity of the energy landscapes of proteins and RNA Jena: energy landscapes: structure predictions of lattice models 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 start the collaboration properly with face to face meetings exchange old and new information on the research background/progress of each partner 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 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. update plans of cross party collaborations: visits between the partners, collaborative research topics etc. information on reporting, ideas for the web site information on reporting, ideas for the web site exchange details on financing and formal obligations exchange details on financing and formal obligations have fun have fun

It’s the EU, so reporting will be important… Reporting: August 2006 the first report August 2006 the first report September 2008, second report September 2008, second report + a final report at the end (within 45 days) + 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 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. publications: first one from Lapo – seemed to work ok – about two weeks.

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

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

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

and off we go…