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From Computational Biophysics to Systems Biology

May 2 - 4 2007, Jülich, Germany



During the last two decades computer simulations have become an invaluable tool for researching biological systems reaching from single macromolecules to entire organisms. Examples range from folding and structural transitions in isolated proteins, the interaction between the various biomolecules, to their regulation in the cell. Future challenges will include the integration of these simulation - situated at a molecular level - into a functioning model of cells, a task that will require both new hardware and new techniques.

The workshop was organized by the John von Neumann Institute for Computing (NIC) at the Forschungszentrum Jülich, Jülich, Germany, which celebrated in 2007 its 20th anniversary. The goal of the workshop was to bring together expertise from physics, biology, and computer science to discuss current trends in computational biophysics and systems biology. In brief, the workshop concerned the following general areas:

  • Protein folding (both structure prediction and mechanics)
  • Interaction between proteins and other molecules
  • Assembly of nano-structures, multi-protein, protein-DNA/RNA complexes
  • Cellular systems at the molecular level



Wednesday 02.05.2007

07:40Pick up at Hotels in Jülich
09:00-09:20Welcome by Prof. Dr. A. Bachem (CEO, FZ Jülich)
09:20-09:30Introductory Remarks (Prof. U. H. E. Hansmann, NIC-CBB)

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

09:30-10:15Harold Scheraga (Cornell University, Ithaca, USA):
Evolution of Protein Simulation
10:15-11:00Robert B. Russell (EMBL, Heidelberg, Germany):
Pushing Details into the Interactome
11:00-11:30Coffee break
11:30-12:15Koichi Takahashi (tMSI, Berkeley, USA):
The E-Cell Project and Challenges in Computational Systems Biology

Afternoon Session (Chair: Jan H. Meinke)

14:00-14:45Adrian Roitberg (University of Florida, Gainesville, USA):
Mixed Quantum Mechanics/Classical Mechanics Methods for the Study of Enzymatic Reactions
14:45-15:30Marek Cieplak (Polish Academy of Sciences, Warsaw, Poland):
Stretching to Understand Proteins
15:30-16:00Coffee break
16:00-16:30Bernd Berg (FSU, Tallahassee, USA):
Residual Entropy of Ice I from Multicanonical Simulations
16:30-17:00Abhinav Verma (FZK, Karlsruhe, Germany):
All-Atom Protein Folding and Structure Prediction in a Transferable Universal Free-Energy Force-Field
17:00-17:30Walter Nadler (MTU, Houghton, USA):
Channel Transport and Molecular Motors without Brownian Ratchets
17:30-18:00Inta Liepina (Latvian Institute of Organic Synthesis, Riga, Latvia):
Multiple Beta-Sheet Molecular Dynamics of Two Abl-SH3 Domain Peptides
18:00Welcome Reception and Poster Session
20:00Open Discussion: Supercomputing and the Physics of Cells
20:00/21:30Bus to Hotels in Jülich

Thursday 03.05.2007

08:10Pickup at Hotels in Jülich

Morning Session (Chair: Olav Zimmermann)

09:00-09:45Jeffrey Skolnick (Georgia Institute of Technology, Atlanta, USA):
Prediction of Protein Structure, Function and Druggability on a Proteomic Scale
09:45-10:30Christodoulos Floudas (Princeton University, Princeton, USA):
Advances In De Novo Protein Design
10:30-11:00Coffee break
11:00-11:30Mai Suan Li (Polish Academy of Sciences, Warsaw, Poland):
Mechanism of Fibril Formation of Short Peptides
11:30-12:00Velia Minicozzi (University of Rome "Tor Vergata", Rome, Italy):
The Role of Metals in Misfolding and Aggregation Processes X-ray Spectroscopy and Numerical Simulations
12:00-12:30Wolfhard Janke (University of Leipzig, Leipzig, Germany):
Microcanonical Analyses of Peptide Aggregation Processes

Afternoon Session (Chair: Tatjana Eitrich)

14:00-14:45Rebecca Wade (EML, Heidelberg, Germany):
Bridging from Molecular Simulation to Biochemical Networks
14:45-15:30Adam Liwo (University of Gdansk, Gdansk, Poland):
Mesoscopic Dynamics with the UNRES Force Field - a Tool for Studying the Kinetics and Thermodynamics of Protein Folding
15:30-16:00Coffee break
16:00-16:30Peter Virnau (Johannes Gutenberg-Universität, Mainz, Germany):
Knots in Proteins, DNA and Polymers: Statistics, Function and Evolution
16:30-17:00Siegfried Höfinger (MTU, Houghton, USA):
Comparing Semi-Empirical versus Classic Charge Assignments in BioMolecules and their Effect on Electrostatic Potentials
17:00-17:30Klaas Hellingwerf (University of Amsterdam, Amsterdam, NL):
Photosensory Proteins as Vehicles to Bridge Computational Biophysics and Systems Biology to Initiate the Field of Synthetic Biology
17:30-18:00Léo Degrève (Universidade de São Paulo, Ribeirao Preto, Brazil):
A Molecular Dynamics Study of the Basic Fibroblast Growth Factor - Fibroblast Growth Factor Receptor Complex
18:15Bus to Castle Obbendorf (Hambach) for Dinner
18:30Dinner in Celebration of 20 Years of NIC (sponsored by IBM)
Commemorative Speech by Prof. Dr. Dr. Thomas Lippert, Director of NIC and ZAM
22:00Bus to Hotels in Jülich

Friday 04.05.2007

8:10Pickup at Hotels in Jülich

Morning Session (Chair: Sandipan Mohanty)

09:00-09:45Dave Thirumalai (University of Maryland, College Park, USA):
Measuring Energy Landscape Parameters of Biomolecules and their Complexes
09:45-10:30Bogdan Lesyng (Warsaw University, Warsaw, Poland):
Causality and Correlation Analyses of Molecular Dynamics Simulation Data
10:30-11:00Coffee break
11:00-11:30Nikolay Korolev (Nanyang Technological University, Singapore):
DNA Packaging and Electrostatic Interactions
11:30-12:00Georgios Papadopoulos (University of Thessaly, Larisa, Hellas):
The Zinc-Finger Motif of T.thermophilus Ribosomal Protein S14 and the Functionality of E.coli Ribosome
12:00-12:30Giovanni La Penna (National Research Council, Florence, Italy):
Anisotropic Internucleosome Interactions and Geometrical Constraints Favour the Two-Start Helical Structure of Chromatin

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

13:30-14:15José Onuchic (UCSD, La Jolla, USA):
Mechanisms of Protein Assembly and Folding: Lessons from Minimalist Models
14:15-15:00Jörg Langowski (Deutsches Krebsforschungszentrum, Heidelberg, Germany):
Chromatin Dynamics in Silicio
15:00-15:05Concluding Remarks (Prof. Ulrich H. E. Hansmann, NIC-CBB)
afterwardsBus to Cologne
Social Event: Guided Tour Cologne Cathedral and Treasure Chamber, Visit of a Traditional Brewhouse
21:30Bus to Jülich