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From Computational Biophysics to Systems Biology

July 20 - 22 2011, Jülich, Germany



This workshop was dedicated to Harold Scheraga. Dr. Scheraga pioneered the use of computers in chemistry and biology. His work inspired many of the research areas that are the topic of this meeting, ranging from biophysics to systems biology. In the spirit of Harold Scheraga's work, we aimed at bringing together researchers from physics, chemistry, biology, and computer science to acquaint each other with current trends in computational biophysics and systems biology, to explore avenues of cooperation, and to establish together a detailed understanding of cells at a molecular level.

That meeting was the fifth in a series of workshops of the same name organized in both Germany and the USA. Its main focus was on:

  • Protein folding and aggregations
  • Multi-protein complexes and supramolecular assemblies
  • Cellular environments and interaction networks
  • Models, Algorithms and Computers



Wednesday 20.07.2011

07:30Pick up at hotels in Jülich

Morning Session (Chair: Ulrich H.E. Hansmann)

08:45-08:55Welcome by Prof. Dr. Dr. Thomas Lippert
08:55-09:00Introductory remarks and introduction into session
09:00-09:20Laudatio (Jeff Skolnick)
09:20-10:05Harold Scheraga (Cornell University, Ithaca, NY, USA):
Advances in Protein Biophysics
10:05-10:50Adam Liwo (University of Gdansk, Gdansk, Poland):
From Atomistic Simulations to Network Description of Biological Systems
10:50-11:15Coffee break
11:15-12:00Andrzej Kolinski (University of Warsaw, Warsaw, Poland):
Coarse-grained Protein Modeling: Dynamics, Folding Pathways and Mechanical Unfolding
12:00-12:45Panel discussion: Force fields
Participants: H. Scheraga, Ch. Brooks, A. Kolinski, E. Lindahl, A. Liwo, U. Röthlisberger

Afternoon Session (Chair: Olav Zimmermann)

14:00-14:05Introduction to session
14:05-14:50Richard Lavery (CNRS, Lyon, France):
From Macromolecular Mechanics to Function
14:50-15:35Kim Sneppen (Copenhagen University, Copenhagen, Denmark):
Modeling Nucleosome Mediated Epigenetics
15:35-16:00Coffee break
16:00-16:45Michael Lässig (University of Cologne, Köln, Germany):
From Biophysics to Fitness of a Molecular Pathway
16:45-17:15Award talk: Marco Matthies (University of Hamburg, Hamburg, Germany):
Continuous-space Sequence Optimisation for RNA Secondary Structures
17:15-18:00Panel discussion: Molecular systems biology
Participants: R. Lavery, M. Lässig, J. Skolnick, K. Sneppen
18:00Welcome Reception and Poster Session
20:00Bus to Hotels in Jülich

Thursday 21.07.2011

08:00Pickup at Hotels in Jülich

Morning Session (Chair: Sandipan Mohanty)

08:30-08:35Introduction to session
08:35-09:20David Wales (Cambridge University, Cambridge, UK):
Exploring Energy Landscapes: From Molecules to Nanodevices
09:20-09:50Award talk: Emal M. Alekozai (University of Heidelberg and Oak Ridge National Laboratory, Heidelberg, Germany):
Multilevel Enhanced Sampling of Cellulose-Cellulase Interaction
09:50-10:15Coffee break
10:15-11:00Erik Lindahl (KTH Royal Institute of Technology, Stockholm, Sweden):
Dynamics and Function of Voltage- and Ligand-gated Ion Channels
11:00-11:30Award talk: Bettina Keller (Freie Universität Berlin, Berlin, Germany):
Markov State Models and Dynamical Fingerprints: Unraveling the Complexity of Molecular Kinetics
11:30-12:15Panel discussion: Exploring/interpreting energy landscapes
Participants: H. Scheraga, H. Grubmüller, A. Kolinski, R. Lavery, D. Wales
12:15-12:30Group photo

Afternoon Session (Chair: Jan Meinke)

14:00-14:05Introduction to session
14:05-14:50Jeffrey Skolnick (Georgia Tech, Atlanta, USA):
Crowding and Hydrodynamic Interactions Likely Dominate in vivo Macromolecular Motion
14:50-15:35Frank Jülicher (Max Planck Society, Dresden, Germany):
The Role of Pulling Forces in Cell Division
15:35-16:00Coffee break
16:00-16:45Amos Maritan (University of Padua, Padua, Italy):
An Unified Perspective on Proteins: A Physics Approach
16:45-17:15Award talk: Nicoletta Ceres (Université Lyon1 / CNRS, Lyon, France):
PaLaCe: Toward a Transferable Coarse-grain Model for Protein Mechanics and Dynamics
17:15-18:00Panel discussion: Cellular environments
Participants: F. Jülicher, A. Liwo, A. Maritan, J. Skolnick
18:15Bus to dinner at Castle Obbendorf (Hambach)
22:00Bus to Hotels in Jülich

Friday 22.07.2011

8:00Pickup at Hotels in Jülich

Morning Session (Chair: Paolo Carloni)

08:30-08:35Introduction to session
08:35-09:20Helmut Grubmüller (Max Planck Society, Göttingen, Germany):
Exploring Protein Dynamics Space: The Dynasome
09:20-10:05Ursula Röthlisberger (Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland):
Structural Stability of Prion Protein and Amyloid Beta Peptides and their Interaction with Metal Ions
10:05-10:35Award talk: Yinghao Wu (Columbia University, New York, USA):
Multiscale Simulations of Cadherin-mediated Cell Adhesion
10:35-11:00Coffee break
11:00-11:45Charles Brooks (University of Michigan, Ann Arbor, USA):
Multi-scale Studies of Viral Capsid Dynamics and Mechanics
11:45-12:30Panel discussion: Multi-scale modelling
Participants: H. Scheraga, Ch. Brooks, H. Grubmüller, E. Lindahl, U. Röthlisberger
12:30-12:45Concluding remarks
14:00-15:00Jülich Supercomputing Centre, Guided Tour
15:15Bus to Cologne
Social Event: Visit of a Traditional Brewhouse (drinks and food on one’s own expense)
19:30Bus to Jülich

CBSB11 group photo