Kick-off meeting

Cambridge, 25-27 July 2005

The meeting was devoted to the review of the previous work and planning. A summary of the meeting can be found here.


2006 EMBIO meeting

Vienna, 21-24 May 2006

participantsThe summary of the research since the kick-off meeting has been presented by the participants. Very fruitful discussions took place between the groups that resulted in new links.

Monday, 22 May

  • Robert Glen, Cambridge opened the meeting as the coordinator of the Consortium
  • Dmitry Nerukh discussed various organisational issues
  • Cambridge presentations:
    • Dmitry Nerukh: the overall research in Cambridge within EMBIO; some results on the complexities of water dynamics
    • Christian Jensen: Simulating protein folding - some ideas; Calculate transition probabilities from molecular dynamics simulations; Clustering done in various ways; Use Wang - Landau simulations to calculate density of states for a transition in a protein
  • Cosma Shalizi talk First lecture by Cosma Shalizi on computational mechanics
  • Roberto Livi talk First lecture by Roberto Livi on non-linear dynamics and statistical mechanics
  • Groningen presentations:
    • Alan Mark: simulations of the folding and aggregation of peptides, proteins and lipids; overview of MD simulations done; list of the peptides that are shown experimentally to fold and that are possible to simulate (1 ns); remark: course grain models are not good, since they are too simple
    • Aldo Rampioni: amyloid fibris; forms in various cases in nature (Alzheimer, BSE, Parkinson, Type II diabetes); MD are used to do simulations; Forces system into correct conformation by using improper dihedrals
  • Heidelberg presentations:

Tuesday, 23 May

  • Florence presentations:
    • Francesca Sbrana: probing the free energy landscape of a folding protein by means of AFM stretching experiments (Titin)
    • Lorenzo Mazzoni: curvature of the energy landscape of folding proteins; curvature fluctuation as geometrical marker of folding are used to destinguish between good and bad folders
    • Roberto Livi: folding and unfolding simulations of hPhil WW domain and MyBPC C5 domain; a graph theoretic approach (Transition matrix)
  • Freiburg presentations:
    • Rolf Backofen, Martin Mann, Sebastian Will(internal access only): constriant-based approach to protein structure prediction; lattice proteins (HP-model); energy function describes hydrophobic forces; the method is based on precompution "cores" that can be used in other simulations; this makes these simulations significantly faster
  • Second lecture by Cosma Shalizi on computational mechanics
  • Second lecture by Roberto Livi on non-linear dynamics and statistical mechanics
  • Vienna presentations:
    • ?: folding dynamics of RNA secondary structures and lattice proteins; description (course graining) in terms of secondary structures
    • Michael Wolfinger: estimating low energy refolding paths; visualisation of lattice proteins; HP-model; transition rates and transition matrix; a visualisation tool
  • Leipzig presentations:

Wednesday, 24 May

  • Chalmers presentations:
    • Martin Nilsson Jacobi, Anders Eriksson, Johan Nystrom, Olof Gornerup: methods for simulating self-organising molecular systems; mapping from microvariables into macrovaribles; probably possible to write equation for macrovariables evolution; self-assembly of micro-particles using dissipative particle dynamics; similar to Langevin dynamics; clustering as a mechanism for repulsion between particles in DPD simulation; phase space partitioning in the context of simple dynamical systems; generating partitioning - good; Markov partitioning - better; neither - bad
  • Summary and conclusions resulted in the list of things todo

Summary reports

Thing to do after the Vienna meeting (internal access only)

Brief summaries about the meeting and new links established(internal access only):

2007 EMBIO meeting

Leipzig, 17-19 May 2007

Thursday, May 17

  • Robert Glen, Cambridge opened the meeting
  • Dmitry Nerukh: organisational issues
  • Cambridge presentations:
    • Dmitry Nerukh: Complex temporal patterns in molecular dynamics: a direct measure of the phase space exploration by the trajectory at macroscopic time scales
    • Christian Jensen: Markov Models of Protein Folding - Application to Molecular Dynamics Simulations
  • Groningen presentation:
    • Aldo Rampioni: Behaviour of velocities in protein folding events
  • Invited lecture by Roumen Dimitrov
  • Goteborg presentations:
    • ...
  • Heidelberg presentations:

Friday, May 18

  • Invited lecture by Nihat Ay
  • Florence presentation:
    • Stefano Luccioli: Reconstructing the free energy landscape of a mechanically unfolded model protein
  • Freiburg presentation:
    • Martin Mann: Optimal Structure Prediction and Application
  • Invited lecture by Wolfhard Janke
  • Vienna presentation:
  • Leipzig presentations:

Saturday, 19 May

  • Summary and conclusions

Summary reports

Brief summaries about the meeting and new links established(internal access only):

2008 EMBIO meeting

Venice, 12-15 May 2008
European Center for Living Technology (ECLT)

Monday, May 12

  • Robert Glen, Cambridge opened the meeting
  • Cambridge presentations:
    • Dmitry Nerukh: Computational Mechanics reveals nanosecond time correlations in liquids and dynamical frustration of protein's environment
    • Christian Jensen: How to accelerate protein folding
  • Goteborg presentations:

Tuesday, May 13

  • Florence presentation:
  • Leipzig presentations:
  • Vienna presentation:

Wednesday, 14 May

  • Heidelberg presentations:
  • Freiburg presentation:
  • Groningen presentation:
  • notes on finishing EMBIO

Thursday, 15 May

  • Discussion
  • Summary and conclusions

15 Oct 2008
Dmitry Nerukh []