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Program "New trends in simulating biological systems and soft matter"

Download program (PDF, 1,1 MB) [1]. Download schedule (PDF, 237,3 KB) [2].

 

Please put up your poster before the poster session - on wednesday at 6:15 pm.

Wednesday, February 22
Registration and Lunch (12:00 – 1:45 pm)
 
Dr. Wilhelm Krull (Volkswagen Foundation, Hannover)
Opening remarks
 

Session 1 (2:00 pm – 3:45 pm): Simulations of biomolecular systems

 
2:00 – 2:45 Charles L. Brooks (University of Michigan, Ann Arbor)
Multi-scale explorations of virus maturation dynamics and mechanics
 
2:45 – 3:05 Markus Miettinen (Universität Potsdam)
Kinetic stabilities of suggested polyglutamine aggregation initiating conformers
 
3:05 – 3:25 Ilpo Vattulainen (Tampere University of Technology)
Cholesteryl ester transfer protein interacting with lipoproteins and anacetrapib
 
3:25 – 3:45 Christoph Globisch/Venky Krishnamani
(Max-Planck-Institut für Polymerforschung, Mainz/Carnegie Mellon University, Pittsburgh)
Atomistic and coarse grained simulations of viral capsids
 
Coffee break
 

Session 2 (4:15 pm – 6:00 pm): Simulations of soft matter I

4:15 – 5:00 Ard Louis (Oxford University)
Coarse-grained model for self-assembling DNA
 
5:00 – 5:20 Ernst-Walter Knapp (Freie Universität Berlin)
Influence of Spacer-Receptor Interactions on the Stability of Bivalent Ligand-Receptor Complexes
 
5:20 – 5:40 Agur Sevink (Universiteit Leiden)
A hybrid method for efficiently modeling lipid membranes with molecular resolution
 
5:40 – 6:00 Jonathan James Ward (European Molecular Biology Laboratory, Heidelberg)
Physical principals underlying the morphogenesis of the fission yeast spindle
 
Buffet and Poster Session (6:15 pm -late)
Thursday, February 23
Breakfast
 
Session 3 (9:00 am – 10:25 am): Modeling of active systems I
 
9:00 – 9:45 Lev Tsimring (University of California, San Diego)
Ordering and instabilities in dense bacterial populations
 
9:45 – 10:05 Johannes Baumgart (Max-Planck-Institute for the Physics of Complex Systems, Dresden)
Modeling the Fluid-Structure Interaction of the Hair Bundle
 
10:05 – 10:25 Wolfgang Alt (Universität Bonn)
Coupling of cytoplasm flow dynamics and membrane protein kinetics
drives adhesive cell locomotion and interaction
 
Coffee break
 
Session 4 (11:00 am – 12:45 pm): Modeling of active systems II
 
11:00 – 11:45 Martin Falcke (Max-Delbrück-Center for Molecular Medicine, Berlin)
Actin filament elasticity and retrograde flow shape the force-velocity relation of motile cells
 
11:45 – 12:05 Roland G. Winkler (Forschungszentrum Jülich)
Swimming of Bacteria: Synchronization and Bundling of Flagella
 
12:05 – 12:25 Holger Stark, Reinhard Vogel (Technische Universität Berlin)
Modeling the Motor-Driven Bacterial Flagellum
 
Lunch
 
Session 5 (2:00 pm – 3:25 pm): Transport through nanopores and in confined geometries
 
2:00 – 2:45 Murugappan Muthukumar (University of Massachusetts, Amherst)
How DNA worms through protein channels and nanopores
 
2:45 – 3:05 Steffen Martens (Humboldt-Universität Berlin)
Biased and flow driven Brownian motion in periodic channels
 
3:05 – 3:25 Gerhard Schmid (Universität Augsburg)
Entropic Splitter
 
Coffee break
 
Session 6 (3:55 pm – 6:15 pm): Modeling of enzymatic reactions and QM/MM
 
3:55 – 4:40 Rich A. Friesner (Columbia University, New York)
DFT-LOC methods applied to metal-containing system
 
4:40 – 5:00 Biswaroop Mukherjee / Nikos Doltsinis
(Max Planck Institut für Polymerforschung, Mainz / Universität Münster)
Multiscale modelling of photoactive liquid crystals: from quantum to coarse grained
 
5:00 – 5:20 Bernd Engels (Universität Würzburg)
New approaches for efficient simulation of complex soft matter
 
Coffee break
 
5:35 – 5:55 Christian Ochsenfeld (Ludwig-Maximilians-Universität München)
Efficient Quantum-Chemical Schemes for Scanning Potential Energy Landscapes in Complex Systems
 
5:55 – 6:15 Walter Thiel (Max-Planck-Institut für Kohlenforschung, Mülheim)
Semiempirical QM/MM excited-state dynamics
 
6:20 pm: Bus departure to Krongut Bornstedt, Conference Dinner
Friday, February 24
Breakfast
 

Session 7 (9:00 am – 10:45 am): Simulations of soft matter II

9:00 – 9:45 Sabine Klapp (Technische Universität Berlin)
Dynamics of ferrofluids in external fields: Chaining, layering, and anomalous diffusion
 
9:45 – 10:05 Ulf D. Schiller (Forschungszentrum Jülich)
Modeling red blood cells as a liquid crystalline elastic membrane:
insights into equilibrium shape and remaining elastic strains
 
10:05 – 10:25 Jasna Zelko (Max Planck Institut fuer Polymerforschung, Mainz)
Towards a New Algorithm for Multiphase Lattice Boltzmann Simulations
 
10:25 – 10:45 Owen A. Hickey (Universität Stuttgart)
Implicit method for the electrohydrodynamics of polyelectrolytes using Lattice-Boltzmann
 
Coffee break (12:00 – 1:45 pm)
 

Session 8 (11:15 am – 13:00 pm): Biomatter in nonequilibrium

 
11:15 – 12:00 Stefan Klumpp (Max Planck Institut für Kolloid und Grenzflächenforschung, Potsdam)
Tug-of-war: Mechanical coordination of biomolecular motors
 
12:00 – 12:45 Roland Netz (Freie Universität Berlin)
Simulation approaches to friction in biomatter
 
12:45 – 13:00 Closing remarks
 
Lunch (Lunch packages are available) and Departure

Poster Session

Please prepare your poster in upright format.

Wednesday, February 22, starts 6:15 pm - late
 
C. Seitz, K. Kopp, I. Antes (Technische Universität München)
Efficient sampling of conformational changes in proteins induced by peptide binding
 
Michele Campisi (Universität Augsburg)
Quantum Fluctuation Relations
 
Cristiano L. Dias, Hue Sun Chan (University of Toronto)
Pressure dependence of hydrophobic interactions
 
Denis Flaig, Matthias Beer, Christian Ochsenfeld (Ludwig-Maximilians-Universität München)
Describing Dynamic Molecular Systems by Nuclei-Selected NMR Shieldings within Linear- and Sublinear-Scaling QM and M/MM Approaches
 
Nikos Doltsinis, Marcus Böckmann, Dominik Marx, Biswaroop Mukherjee, Luigi Delle Site, Christine Peter, Kurt Kremer (Universität Münster)
Multiscale modelling of photoactive liquid crystals I: from quantum to classical
 
Stephan Gekle (Technische Universität München)
Dielectric spectrum of interfacial water
 
Jan Philipp Götze, Mario Silva-Junior, Walter Thiel (MPI für Kohlenforschung, Mülheim an der Ruhr)
The N5•••H excited state decay channel of 1-deaza-flavin depends on rotational orientation of the donor water molecule
 
Z. Jurek, R. Thiele, B. Ziaja, R. Santra (Deutsches Elektronen-Synchrotron, Hamburg)
Effect of two-particle correlations on x-ray coherent diffractive imaging studies performed with continuum models
 
Stefan Kesselheim, Christian Holm (Universität Stuttgart)
Lattice Boltzmann Simulations of Electrokinetic Phenomena with explicit Ions
 
Rong-Zhen Liao, Walter Thiel (MPI für Kohlenforschung, Mülheim an der Ruhr)
Comparison of QM-only and QM/MM Models for the Mechanism of Tungsten-Dependent Acetylene hydratase
 
P. K. Ghosh, P. Hänggi, F. Marchesoni, Steffen Martens, F. Nori, L. Schimansky-Geier, G. Schmid
(Humbold Universität Berlin)
Driven Brownian transport through arrays of symmetric obstacles
 
Tim Meyer, Ernst Walter Knapp (Freie Universität Berlin)
Database of multivalent receptors (MVR-DB) deduced from the database of protein structures
 
Markus Miettinen, Volker Knecht, Luca Monticelli and Zoya Ignatova (Universität Potsdam)
Kinetic stabilities of suggested polyglutamine aggregation initiating conformers
 
Biswaroop Mukherjee, Luigi Delle Site, Christine Peter, Kurt Kremer, Marcus Böckmann, Dominik Marx, Nikos Doltsinis (Max Planck Institut für Polymerforschung, Mainz)
Multiscale modelling of photoactive liquid crystals II: from atomistic to coarse grained
 
Jorge Numata, Alok Juneja, Ernst-Walter Knapp (Freie Universität Berlin)
Balanced and bias-free computation of conformational entropy differences for molecular trajectories
 
Iakov Polyak, Manfred T. Reetz, Walter Thiel (MPI für Kohlenforschung, Mülheim an der Ruhr)
QM/MM Study on the Mechanism of the Enzymatic Baeyer-Villiger Reaction
 
Shervin Raafatnia (Universität Stuttgart)
Colloidal electrophoretic mobility in the presence of multivalent salt
 
Ilkay Sakalli, Elankumaran. K, Joachim-Schöberl, Ernst-Walter Knapp (Freie Universität Berlin)
Calculation of pKa values and solving the Poisson equation using the Finite Element Method
 
Kakali Sen, Walter Thiel (MPI für Kohlenforschung, Mülheim an der Ruhr)
Investigation of Molecular Oxygen Activation in P450eryF using hybrid QM/MM methodology
 
Jiajia Zhou, Aleksey V. Belyaev, Olga I. Vinogradova, Friederike Schmid
(Johannes Gutenberg-Universität Mainz)
Pressure-driven flow through a channel with symmetric striped-pattern
 
Manuela Mura, Andrei V Zvelindovsky (University of Central Lancashire, Preston)
Modelling of aurein 2.3 in a biomembrane
 
 
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