Multiscale Molecular Simulations and Stochastic Feedback

The workshop will be held at Palazzo Giovannelli, 22 Nov/5 Dec 2004   

PURPOSE
Multiscale molecular simulation  
This workshop will focus on molecular dynamics and self-assembly simulation methods at different time- and length- scales. The format will include both presentations and 'hands-on classes'. The hands-on classes consist of experts guiding students through the implementation of their simulations (mostly open source/publicly available software) on the participant's laptops and helping them use these simulations. Who the experts and students are will change depending on the specific type of simulation. Tasks include:
• Multiscale representation of oil/water droplets, micelles and emulsions, membrane systems using MD, DPD, MD lattice gas, lattice Boltzmann, LGA, CA, Navier Stokes, Ginzburg Landau and related methods.
• Introduction of chemical reactions into the self-assembly process, e.g., (i) template (e.g. PNA, RNA) or metabolic aggregate interactions with oil/water interfaces or amphiphilic aggregates; (ii) template melting in different phases and environments; (iii) reaction diffusion kinetics, e.g. Gray-Scott.
• Presentation and development of methods to 'glue' together the different time- and length-scale simulations. • Review how to apply the presented methods to key PACE molecular systems and problems in future collaborative projects with both PACE participants and external experts.  
• Design interfaces of simulation tools for communities both inside and outside PACE: brainstorm with TILS (Telecom Italia Learning Services).

Statistical experimental design and stochastic control  
This workshop will focus on the following issues:
• Ion dynamics, and the problem of electrophoretic control of ion dynamics with pulses on electrodes. Goals: Establish a model that can predict properties of flow control realized in micro-reactors. Design of experimental sequences to provide data for model validation.
• Inclusion of reaction and diffusion into the experimental model. Develop PRESS model (from BioMIP group) for integration into modeling. Connect with TCIL for standardization of interface using SBML (Systems Biology Markup Language cf. http://sbml.org).
• Statistical experimental design. Use time scales of flow, reaction, diffusion, observational noise levels, to design data gathering protocols for a micro-reactor array. Goal: Take the first steps of designing the framework, without details of chemical reaction rates, etc. This latter phase will be followed up in subsequent workshops with specific involvement of chemists.
• Other questions to be addressed: How can spatially extended data be used to increase resolution of chemo- fluidic dynamics? How may experimental perturbations (addition of noise) be designed to increase resolution of chemo-fluidic dynamics?


PROGRAM


PACE participants:
1. Venezia University Ca’ Foscari:  Irene Poli, Claudio Agostinelli, Roberto Serra, Mario Romanazzi
2. Venezia ProtoLife: Norman Packard, Mark Bedau, Rob Shaw, Andy Buchanan, Pietro Speroni
3. ITPA (Lituania): Arvydas Tamulis
4. Chalmers: Kristian Lindgren, Martin Nilsson, Anders Eriksson
5. U Zurich: Ralph Peifer, Lukas Lichtensteiger
6. U Pumpeu Fabra (Barcelona): Ricard Sole
7. U Copenhagen, USD (Denmark): Steen Rasmussen, Goran Goranovitz, Ole Mouritzen, Ask Jacobsen, Morten Jensen
8. U Bochum: John McCaskill , Rudolf Fuechslin , Uwe Tangen, Thomas Maeke  
9. Telecom Italia (TILS): Richard Walker, Giuliano Stillo
10. Dublin (DCU): Barry McMullin

External participants (ECLT invitees):
Reinhard Lipowsky, Max Planck Inst., Berlin, Germany (interfaces, membranes and polymers)
Dietrich Stauffer, U. Koln, Germany (Monte Carlo simulations of molecular systems - and almost everything else)
Reinhard Strey, U Koln, Germany (lipid phases)
Peter Stadler’s student, U Leipzig (reaction kinetics & theory)
Peter Coveney, University College London, England (meso scale molecular simulations)
Doran Lancet, Israel, or perhaps his postdoc Extremely interested in collaboration.  Reaction kinetics mostly.  
Kuni Kuneko, U. Tokyo, Japan (already in Italy as part of the Torino workshop)
Takashi Ikegami, U. Tokyo, Japan (already in Italy as part of the Torino workshop)

External participants (visitors from Los Alamos):
Yi Jiang, LANL, US (MD & G-L simulations: membranes & proteins)
Bryan Travis, LANL, US (LGA & Lattice Boltzmann: micron scale flows in channels with bacteria)
Stirling Colgate and Hans Ziock, LANL, thermodynamic landscape of the self-assembly processes.
 
2. Participants and talks  
 
Participants outside the PACE partnership are indicated with an asterisk *.
 
Overviews
 
Norman Packard
John McCaskill
Steen Rasmussen
 
 
Interaction between experiment and simulation
 
Statistics for experimental design: questions for the chemistry
Irene Poli
Roberto Serra
Mario Romanazzi
 
Microfluidic fluid dynamic phenomenology
Goran Goranovic
 
Framework for interactions between simulator and experiment
Uwe Tangen
Thomas Maeke
 
Simulator approaches
Claudio Agostinelli
 
Evolutionary Statistical Methods  
Irene Poli
Roberto Serra
Tommaso Minerva
 
Information flow in spatial chemical systems
Kristian Lindgren
 
 
Presentation of simulations and results
 
Simulation presentations
Richard Walker
Stefano Cancedda
Giuliano Stillo
 
 
Lipid structure and chemistry
 
DPD simulations of lipid structures
Ask Jacobson
 
Lipid structures and simple chemistry in DPD
Mark Bedau
Andy Buchanan
 
Toward chemistry in DPD
Ruedi Fuchslin
 
 
Lipid assembly in MD lattice gases
Martin Nilsson
 
Monte Carlo (MC) simulations of single- and multicomponent fluid vesicles & MC Simulations of fluid vesicles with solid domains.
Thomas Gruhn *
 
Templating molecules and chemistry
 
Quantum Mechanical MD Modelling of Sensitizers of Artificial Living Organisms
Arvydas Tamulis
Jelena Tamuliene  
 
MD methods for hybridization simulations
Thomas Hedegaard *
 
Origins and properties of the genetic code  
Peter Wills *
 
 
Chemical reaction networks
 
Simulation of lipid structure with chemistry  
Barak Shenhav *
 
Artificial chemistry getting realistic
Gil Benkoe *
 
Organizations in chemical reaction networks
Pietro Speroni
 
 
Other topics
 
Breve  
Jon Klein
 
Molecular gaming
Anders Eriksson
 
Asymmetric Diffusion
Rob Shaw*