The July 9-12, 2012 workshop "Towards in silico biological cells: Bridging experiments and simulations" in Lausanne, Switzerland will bring together researchers from two basic and complementary approaches for simulating the dynamics of cellular processes within the cytoplasm of bacterial cells: particle-based Brownian dynamics algorithms that have been used to describe the diffusive transport in crowded environments and reaction-diffusion master equations that have been used to describe stochastic kinetics of gene expression, genetic switches and biochemical pathways functioning in modeled biological cells. This Workshop will provide the opportunity to bring researchers from the scientific fields of molecular simulations and system biology together with experimentalists who are labeling and imaging cellular components. We envision that this cross fertilization will lead to significant scientific advances in the computational modeling of an entire cell, its components, cell division and the coupling of universal processes of transcription and translation to the response of the cell's metabolic network.
The travel award for the CECAM/NSF sponsored workshop on "Towards in Silico Biological Cells: Bridging Experiments and Simulations" brought together theoretical/computational biological physicists from the scientific fields of molecular and cellular simulations and system biology together with experimentalists who are labeling and imaging cellular components. The exchange of information and approaches among the 17 speakers and students during the poster session is already leading to significant scientific advances in the computational modeling of an entire cell, its components, cell division and the coupling of universal processes of transcription and translation to the response of the cell’s metabolic network. The novelty of this workshop was in its interdisciplinary character. The meeting was held at the CECAM Headquarters, Building Batochime, EPFL, Lausanne, Switzerland and had 33 participants July 9, 2012 Monday – 8:50 – 12:15 Visualizing and Simulating Cellular Processes 1 8:50 – 9:00 Welcoming by Organizers: Luthey-Schulten & Elcock 9:00 – 9:45 W.E. Moerner (Stanford)– "Exploring Protein Superstructures in Bacteria Using Two- and Three-Dimensional Super-Resolution Imaging" 9:45 – 10:00 Discussion 10:00 – 10:15 Coffee break 10:15 – 11:00 Zan Luthey-Schulten (UIUC) – "Stochastic Simulations of Cellular Processes in Bacteria" 11:00 – 11:15 Discussion 11:15 – 12:00 James Weisshaar (U. Wisconsin) – "Superresolution Imaging of Ribosomes and RNA Polymerase in Live E. coli." 12:00 – 12:15 Discussion Monday – 12:15 – 14:00 pm – Lunch Break Monday – 14:00 – 17:30 Visualizing and Simulating Cellular Processes 2 14:00 – 14:45 Jie Xiao (Johns Hopkins U.) – "Direct In-vivo Visualization of DNA Looping Mediated by Bacteriophage Lambda Repressor CI" 14:45 – 15:00 Discussion 15:00 – 15:15 Coffee break 15:15 – 16:00 Adrian Elcock (U. Iowa)– "Molecular Simulation Methods for Modeling Macromolecular Behavior in vivo" 16:00 – 16:15 Discussion 16:15 – 17:00 Terry Hwa (UCSD) – "Growth Laws, Proteome Partition, and Metabolic Coordination" 17:00 – 17:15 Discussion 17:15 – 18:15 Poster Session July 10 Tuesday – 9:00 – 12:15 Visualizing and Simulating Cellular Components 1 9:00 – 9:45 E. Villa (Max-Planck Institute)– "Opening windows into the cell: structural proteomics with cryo-electron tomography" 9:45 – 10:00 Discussion 10:00 – 10:15 Coffee break 10:15 – 11:00 K. Schulten (UIUC) – "Towards Cell Scale Molecular Dynamics" 11:00 – 11:15 Discussion 11:15 – 12:00 J. Skolnick (Georgia Tech) – "On the Importance of Hydrodynamic Interactions in Lipid Membrane Formation" 12:00 – 12:15 Discussion Tuesday – 12:00 – 14:00 – Lunch Break Tuesday – 14:00 – 17:30 Visualizing and Simulating Cellular Components 2 14:00 – 14:45 Ido Golding (Baylor) – "A Quantitative Narrative for the Living Cell: From Precise Measurements to General Principles" 14:45 – 15:00 Discussion 15:00 – 15:15 Coffee break 15:15 – 16:00 T. Geyer – "Bridging the Scales: From Microscopic Simulations to Macroscopic Experiments --- and Back" 16:00 – 16:15 Discussion 16:15 – 17:00 Rebecca Wade (Heidelberg) – "Brownian Dynamics Simulation of Protein Diffusion in Crowded Environments." 17:00 – 17:15 Discussion 19:00 Conference Dinner at Port de Pully Restaurant July 11 Wednesday – 9:00 – 12:00 Visualizing and Simulating Reaction Networks in the Cells 1 9:00 – 9:45 A. Feist (UCSD) – "The E. coli Network Reconstruction: The History, Applications, and What's Next" 9:40 – 10:00 Discussion 10:00 – 10:15 Coffee break 10:15 – 11:00 Elijah Roberts (UIUC/John Hopkins) – "Extrinsic Noise Modifies Decision Making and Growth in Modeled E. coli Populations " 11:00 – 11:15 Discussion 11:15 – 12:00 G. Tauriello, (for) P. Koumoutsakos, ETHZ – "Accelerated, Multi-Resolution Stochastic Simulation Algorithms" 12:00 – 12:15 Discussion Wednesday – 12:00 – 14:00 – Lunch Break Wednesday –14:00 – 17:30 Visualizing and Simulating Reaction Networks in the Cells 2 14:00 – 14:45 Horst Vogel (EPFL) – "Imaging and Manipulating Cellular Biochemical Networks: From Single Cells to Single Molecules" 14:45 – 15:00 Discussion 15:00 – 15:15 Coffee break 15:15 – 16:00 J. Alberts (U. Washington) – "The Evolution of Actomyosin Contractions: Filament Reorganization and Other Motor Behaviors from an in silico Model" 16:00 – 16:15 Discussion 16:15 – 17:00 Contributed Talks - Halatek and Reichl - Best Posters 17:00 – 17:30 Round Table Discussion - New Directions for Visualizing and Simulating Cellular Processes.
