CBSB11: From Computational Biophysics to Systems Biology
Workshop, 20-22 July 2011, Forschungszentrum Jülich, Germany
Scope
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
Proceedings
From Computational Biophysics to Systems Biology (CBSB11) Celebrating Harold Scheraga’s 90th Birthday - Proceedings
Paolo Carloni, Ulrich H. E. Hansmann, Thomas Lippert, Jan H. Meinke, Sandipan Mohanty, Walter Nadler, Olav Zimmermann (Editors)
20 – 22 July 2011, Jülich, Germany
ISBN 978-3-89336-748-1, https://hdl.handle.net/2128/4600
Schriften des Forschungszentrums Jülich, IAS Series 8, 2012,v, 255 pages
From Computational Biophysics to Systems Biology (CBSB11) - Proceedings (pdf, 29 MB)
Programme
Wednesday, 21 July 2011
| 07:30 | Pick up at hotels in Jülich |
| 08:00-08:45 | Registration |
Morning Session (Chair: Ulrich H.E. Hansmann) | |
| 08:45-08:55 | Welcome by Prof. Dr. Dr. Thomas Lippert |
| 08:55-09:00 | Introductory remarks and introduction into session |
| 09:00-09:20 | Laudatio (Jeff Skolnick) |
| 09:20-10:05 | Harold Scheraga (Cornell University, Ithaca, NY, USA): Advances in Protein Biophysics |
| 10:05-10:50 | Adam Liwo (University of Gdansk, Gdansk, Poland): From Atomistic Simulations to Network Description of Biological Systems |
| 10:50-11:15 | Coffee break |
| 11:15-12:00 | Andrzej Kolinski (University of Warsaw, Warsaw, Poland): Coarse-grained Protein Modeling: Dynamics, Folding Pathways and Mechanical Unfolding |
| 12:00-12:45 | Panel discussion: Force fields Participants: H. Scheraga, Ch. Brooks, A. Kolinski, E. Lindahl, A. Liwo, U. Röthlisberger |
| 12:45-14:00 | Lunch |
Afternoon Session (Chair: Olav Zimmermann) | |
| 14:00-14:05 | Introduction to session |
| 14:05-14:50 | Richard Lavery (CNRS, Lyon, France): From Macromolecular Mechanics to Function |
| 14:50-15:35 | Kim Sneppen (Copenhagen University, Copenhagen, Denmark): Modeling Nucleosome Mediated Epigenetics |
| 15:35-16:00 | Coffee break |
| 16:00-16:45 | Michael Lässig (University of Cologne, Köln, Germany): From Biophysics to Fitness of a Molecular Pathway |
| 16:45-17:15 | Award talk: Marco Matthies (University of Hamburg, Hamburg, Germany): Continuous-space Sequence Optimisation for RNA Secondary Structures |
| 17:15-18:00 | Panel discussion: Molecular systems biology Participants: R. Lavery, M. Lässig, J. Skolnick, K. Sneppen |
| 18:00 | Welcome Reception and Poster Session |
| 20:00 | Bus to Hotels in Jülich |
Thursday, 21 July 2011
| 08:00 | Pickup at Hotels in Jülich |
Morning Session (Chair: Sandipan Mohanty) | |
| 08:30-08:35 | Introduction to session |
| 08:35-09:20 | David Wales (Cambridge University, Cambridge, UK): Exploring Energy Landscapes: From Molecules to Nanodevices |
| 09:20-09:50 | Award talk: Emal M. Alekozai (University of Heidelberg and Oak Ridge National Laboratory, Heidelberg, Germany): Multilevel Enhanced Sampling of Cellulose-Cellulase Interaction |
| 09:50-10:15 | Coffee break |
| 10:15-11:00 | Erik Lindahl (KTH Royal Institute of Technology, Stockholm, Sweden): Dynamics and Function of Voltage- and Ligand-gated Ion Channels |
| 11:00-11:30 | Award talk: Bettina Keller (Freie Universität Berlin, Berlin, Germany): Markov State Models and Dynamical Fingerprints: Unraveling the Complexity of Molecular Kinetics |
| 11:30-12:15 | Panel discussion: Exploring/interpreting energy landscapes Participants: H. Scheraga, H. Grubmüller, A. Kolinski, R. Lavery, D. Wales |
| 12:15-12:30 | Group photo |
| 12:30-14:00 | Lunch |
Afternoon Session (Chair: Jan Meinke) | |
| 14:00-14:05 | Introduction to session |
| 14:05-14:50 | Jeffrey Skolnick (Georgia Tech, Atlanta, USA): Crowding and Hydrodynamic Interactions Likely Dominate in vivo Macromolecular Motion |
| 14:50-15:35 | Frank Jülicher (Max Planck Society, Dresden, Germany): The Role of Pulling Forces in Cell Division |
| 15:35-16:00 | Coffee break |
| 16:00-16:45 | Amos Maritan (University of Padua, Padua, Italy): An Unified Perspective on Proteins: A Physics Approach |
| 16:45-17:15 | Award talk: Nicoletta Ceres (Université Lyon1 / CNRS, Lyon, France): PaLaCe: Toward a Transferable Coarse-grain Model for Protein Mechanics and Dynamics |
| 17:15-18:00 | Panel discussion: Cellular environments Participants: F. Jülicher, A. Liwo, A. Maritan, J. Skolnick |
| 18:15 | Bus to dinner at Castle Obbendorf (Hambach) |
| 18:30 | Dinner |
| 22:00 | Bus to Hotels in Jülich |
Friday, 22 July 2011
| 8:00 | Pickup at Hotels in Jülich |
Morning Session (Chair: Paolo Carloni) | |
| 08:30-08:35 | Introduction to session |
| 08:35-09:20 | Helmut Grubmüller (Max Planck Society, Göttingen, Germany): Exploring Protein Dynamics Space: The Dynasome |
| 09:20-10:05 | Ursula Röthlisberger (Ecole Polytechnique Fédérale Lausanne, Lausanne, Switzerland): Structural Stability of Prion Protein and Amyloid Beta Peptides and their Interaction with Metal Ions |
| 10:05-10:35 | Award talk: Yinghao Wu (Columbia University, New York, USA): Multiscale Simulations of Cadherin-mediated Cell Adhesion |
| 10:35-11:00 | Coffee break |
| 11:00-11:45 | Charles Brooks (University of Michigan, Ann Arbor, USA): Multi-scale Studies of Viral Capsid Dynamics and Mechanics |
| 11:45-12:30 | Panel discussion: Multi-scale modelling Participants: H. Scheraga, Ch. Brooks, H. Grubmüller, E. Lindahl, U. Röthlisberger |
| 12:30-12:45 | Concluding remarks |
| 12:45-14:00 | Lunch |
| 14:00-15:00 | Jülich Supercomputing Centre, Guided Tour |
| 15:15 | Bus to Cologne Social Event: Visit of a Traditional Brewhouse (drinks and food on one’s own expense) |
| 19:30 | Bus to Jülich |
Group photo
