| BDBDB Workshop Program |
| 26-29 March 2007 |
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| Monday - 26.03.2007 |
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| 11:00 |
Registration |
| 12:00 |
Lunch |
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| Introductory session |
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| 13:30 |
Historical overview |
| 13:45 |
Brownian dynamics algorithm |
| 14:00 |
Brownian & Langevin Dynamics, diffusion equations, hydrodynamics |
| 14:15 |
Poisson-Boltzmann equation, dielectrics |
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| Software presentation session |
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| 14:30 |
• Jose Garcia de la Torre (University of Murcia, Department of Physical Chemistry)
• The HYDRO Suite of Computer Programs for Macromolecular Hydrodynamics in
Dilute Solutions. |
| 15:00 |
• Jörg Langowski (DKFZ (German Cancer Research Center))
• corchy++ - A Brownian dynamics / Monte Carlo simulation package for flexible polymer chains |
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| 15:20 |
Coffee break |
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| 15:50 |
• Gary Huber (Howard Hughes Medical Institute)
• UHBD / SMOL |
| 16:20 |
• Razif Gabdoulline (BIOMS (Center for Modeling and Simulation in the Biosciences))
• SDA - Simulation of diffusional association of proteins |
| 16:40 |
• Kathryn Thomasson (University of North Dakota)
• MACRODOX |
| 17:00 |
End Software presentations |
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| Session 1 - Experimental approaches |
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| 17:05 |
Welcome |
| 17:15 |
• Jan Ellenberg (European Molecular Biology Laboratory)
• Dissecting the contribution of diffusion, interactions and molecular crowding to the mobility of nuclear proteins in living cells |
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| 18:00 |
End |
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| 20:00 |
Dinner 1 |
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| 22:00 |
Social events |
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| Tuesday - 27.03.2006 |
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| 9:00 |
• G. V. Shivashankar (National Center for Biological Sciences, TIFR-Bangalore)
• Spatio-temporal organization of chromatin assembly and function within single living cells |
| 9:45 |
• Dimitar Pachov (Brandeis University / Martin Fisher School of Physics)
• Adenylate Kinases (ADKs) at Pressures - Characterization of the Conformational Transition Energy Landscape by MD, TMD and NMR Experiments |
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| 10:15 |
Coffee break |
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| 10:45 |
• Jörg Langowski (DKFZ (German Cancer Research Center))
• Coarse-grained modelling of chromatin |
| 11:30 |
Discussion |
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| Session 2 - Hydrodynamics |
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| 11:45 |
• Jose Garcia de la Torre (University of Murcia, Department of Physical Chemistry)
• Hydrodynamics and Brownian Dynamics of Rigid and Flexible Bioparticles in
Solution: Theoretical and Computational Aspects |
| 12:30 |
• Silvia Carlotto (Universitā degli Studi di Padova)
• A coarse-grained approach to solvation of nanoparticle colloidal suspensions |
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| 13:00 |
Lunch |
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| 14:00 |
Poster session + demo |
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| 15:15 |
• Gianni De Fabritiis (Barcelona Biomedical Research Park (PRBB))
• Extending the time resolution: high performance and multiscale molecular simulations |
| 16:00 |
Discussion |
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| Session 3 - Multiparticle models |
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| 16:15 |
• Adrian Elcock (University of Iowa)
• Brownian Dynamics of Macromolecular Assemblies |
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| 17:00 |
Coffee break |
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| 17:20 |
• Razif Gabdoulline (BIOMS (Center for Modeling and Simulation in the Biosciences))
• Reduced protein models for multiparticle simulations |
| 17:50 |
• Martin Zacharias (International University Bremen)
• Approximate inclusion of flexibility during Brownian dynamics and docking of proteins |
| 18:35 |
Discussion |
| 18:50 |
End |
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| 22:00 |
Social events |
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| Wednesday - 28.03.2006 |
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| Session 4 - Coarse-grained models |
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| 9:00 |
• Joanna Trylska (ICM Warsaw University)
• Binding pathways of ligands to HIV-1 protease |
| 9:45 |
• David Sept (Washington University)
• Multiscale Modeling of Actin Filament Dynamics |
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| 10:15 |
Coffee break |
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| 10:45 |
• Matthias Weiss (German Cancer Research Center)
• Probing the size-dependent diffusion of membrane inclusions and nonequilibrium fluctuations of lipid bilayers with mesoscopic simulations |
| 11:30 |
• Dirk Lebiedz (IWR)
• Modeling subdiffusion using reaction diffusion systems |
| 12:00 |
• Karel Jelinek (Polymer Research, BASF Aktiengesellschaft)
• Simulation of Polymer Chain Collapse and Swelling Process |
| 12:30 |
Discussion |
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| 13:00 |
Lunch |
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| 14:00 |
Poster session + demo |
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| Session 5 - Computational approaches |
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| 15:15 |
• Dieter W. Heermann (Institute of Theoretical Physics)
• Lattice and Off-Lattice Simulation Methods for Diffusive Systems |
| 16:00 |
• Gary Huber (Howard Hughes Medical Institute)
• Generic Software Engineering Techniques for Simulations |
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| 16:45 |
Coffee break |
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| 17:05 |
• Yaakov (Koby) Levy (Weizmann Institute of Science)
• Energy landscape of protein self-assembly: Lessons from native topology-based models |
| 17:35 |
• John McCaskill (Ruhr-Universität Bochum)
• Mesoscale kinetic simulation: from reactive spin lattice models to multipole reactive DPD |
| 18:20 |
Discussion |
| 18:35 |
End |
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| 20:00 |
Dinner 2 |
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| 22:00 |
Social events |
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| Thursday - 29.03.2006 |
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| Session 6 - Applications |
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| 9:00 |
• Volkhard Helms (Saarland University)
• Diffusional Encounter of Barnase and Barstar |
| 9:45 |
• Michal Harel (Weizmann Institute of Science)
• On the dynamic nature of the transition state for protein-protein association as determined by double-mutant cycle analysis and computer simulation |
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| 10:15 |
Coffee break |
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| 10:45 |
• Kathryn Thomasson (University of North Dakota)
• Brownian Dynamics Simulations of Glycolytic Enzyme/Actin Interactions |
| 11:30 |
• Domantas Motiejunas (EML Research gGmbH)
• Following protein-protein association towards the bound complex |
| 12:00 |
• Jan Antosiewicz (Department of Physics, Warsaw University)
• Binding of mRNA cap analogues to eIF4E protein: Simulations using SDA package. |
| 12:45 |
Closing discussion |
| 13:00 |
Lunch |
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| 14:00 |
Bye-bye |
