Biological Diffusion and
Brownian Dynamics Brainstorm
BDBDB Workshop Program
26-29 March 2007
Monday - 26.03.2007
11:00 Registration
12:00 Lunch
Introductory session
13:30 Historical overview
13:45 Brownian dynamics algorithm
14:00 Brownian & Langevin Dynamics, diffusion equations, hydrodynamics
14:15 Poisson-Boltzmann equation, dielectrics
Software presentation session
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 Jrg Langowski(DKFZ (German Cancer Research Center))
corchy++ - A Brownian dynamics / Monte Carlo simulation package for flexible polymer chains
15:20 Coffee break
15:50 Gary Huber(Howard Hughes Medical Institute)
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)
17:00 End Software presentations
Session 1 - Experimental approaches
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
18:00 End
20:00 Dinner 1
22:00 Social events
Tuesday - 27.03.2006
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
10:15 Coffee break
10:45 Jrg Langowski(DKFZ (German Cancer Research Center))
Coarse-grained modelling of chromatin
11:30 Discussion
Session 2 - Hydrodynamics
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(Universit degli Studi di Padova)
A coarse-grained approach to solvation of nanoparticle colloidal suspensions
13:00 Lunch
14:00 Poster session + demo
15:15 Gianni De Fabritiis(Barcelona Biomedical Research Park (PRBB))
Extending the time resolution: high performance and multiscale molecular simulations
16:00 Discussion
Session 3 - Multiparticle models
16:15 Adrian Elcock(University of Iowa)
Brownian Dynamics of Macromolecular Assemblies
17:00 Coffee break
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
22:00 Social events
Wednesday - 28.03.2006
Session 4 - Coarse-grained models
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
10:15 Coffee break
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
13:00 Lunch
14:00 Poster session + demo
Session 5 - Computational approaches
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
16:45 Coffee break
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-Universitt Bochum)
Mesoscale kinetic simulation: from reactive spin lattice models to multipole reactive DPD
18:20 Discussion
18:35 End
20:00 Dinner 2
22:00 Social events
Thursday - 29.03.2006
Session 6 - Applications
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
10:15 Coffee break
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
14:00 Bye-bye
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