The thirteenth Pacific Symposium on Biocomputing (PSB), will be held January 4-8, 2008 at the Fairmont Orchid on the Big Island of Hawaii. PSB will bring together top researchers from North America, the Asian Pacific nations, Europe and around the world to exchange research results and address open issues in all aspects of computational biology. The session is organized jointly by researchers from Simbios (http://simbios.stanford.edu/) and NCBR (http://nbcr.sdsc.edu/).

Developing tools, techniques, algorithms, and mathematical theory to integrate modeling and simulation from the micro to the macro-scale is important in biocomputing. This session aims to foster the interactive environment for researchers working on different scales of biological problems, so that more collaborations and activities to bridge multi-scales will be initiated. Specifically, two aspects are emphasized in this session: physics-based modeling and simulation at individual different scales, as well as modeling and simulation for problems across scales. The topics will cover scales of molecules, cells, tissues, organs, up to organisms.

Session schedule

 
Keynote speaker: Dr. Roger D. Kamm, MIT

Friday, January 4, 2008
9:00 - 9:50	Session Tutorial: Multiscale Modeling and Simulation: from Molecules to Cells to Organisms Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anushka Michailova, Peter Arzberger		Salon 2 & 3
Saturday, January 5, 2008
8:40 - 10:50	MULTISCALE MODELING AND SIMULATION: FROM MOLECULES TO CELLS TO ORGANISMS Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anushka Michailova, Peter Arzberger		Salon 2 & 3
	8:40 - 8:50	Session Introduction Jung-Chi Liao, Jeff Reinbolt, Roy Kerckhoffs, Anushka Michailova, Peter Arzberger
	8:50 - 9:10	Combining Molecular Dynamics and Machine Learning to Improve Protein Function Recognition Dariya S. Glazer, Randall J. Radmer, Russ B. Altman
	9:10 - 9:30	Predicting the Structure of G-Protein Coupled Receptors and of Bound Ligands with Applications for Drug Design Youyong Li, William A. Goddard III
	9:30 - 9:50	Markov Chain Models of Coupled Intracellular Calcium Channels: Kronecker Structured Representations and Benchmark Stationary Distribution Calculations Hillary DeRemigio, Peter Kemper, M. Drew Lamar, Gregory D. Smith
	9:50 - 10:10	Spatially-Compressed Cardiac Myofilament Models Generate Hysteresis that Is Not Found in Real Muscle John Jeremy Rice, Yuhai Tu, Corrado Poggesi, Pieter P. De Tombe
	10:10 - 10:30	Modeling Ventricular Interaction: A Multiscale Approach from Sarcomere Mechanics to Cardiovascular Systems Hemodynamics Joost Lumens, Tammo Delhaas, Borut Kirn, Theo Arts
	10:30 - 10:50	Sub-Micrometer Anatomical Models of the Sarcolemma of Cardiac Myocytes Based on Confocal Imaging Frank B. Sachse, Eleonora Savio-Galimberti, Joshua I. Goldhaber, John H. B. Bridge
11:30 - 12:30	Conference Keynote Lecture		Salon 2 & 3
		Introduction Russ Altman
		Systems Biology and Multi-Scale Modeling of the Heart Andrew McCulloch
6:30 - 9:00	Social Event for Multiscale Modeling and Simulation Organized by Simbios		Ocean Bar
Sunday, January 6, 2008
3:30 - 4:30	Discussion Session		Salon 2 & 3
	3:30 - 4:00	Keynote Lecture: Modeling force transmission at the sub-cellular scale and its role in intracellular signaling R. D. Kamm, T. Kim, W. Hwang, H. Lee, P. Honarmandi, P. Bransford, S. Lee J. Ferrer, M. J. Lang Abstract It has become increasingly apparent that “mechanical signaling” plays an important role in regulating biological function in health and disease. In order to understand the underlying processes, it is essential to appreciate how forces are transmitted through the various load-bearing structures within the cell and how these forces act to create conformational change in critical signaling proteins or protein complexes. This needs to be done in a hierarchical manner, considering the transmission of stresses from the extracellular environment, across the cell membrane, and through the intracellular milieu. Prediction of these stress distributions and their consequences draws upon methods of simulation ranging from molecular dynamics, to Brownian dynamics to finite element methods. In this presentation, we use as an example, models that focus on forces acting through the focal adhesion complex and transmitted throughout the actin cytoskeleton. A specific focus is on the activation of talin and the recruitment of vinculin to a focal adhesion. Experimental data will be presented as needed as either input or validation of the computational models, including single molecule experiments on actin cross-linking proteins and measurements of cytoskeletal rheology.
	4:00 - 4:30	Discussion

Session topics

We cordially invite submissions of papers or abstracts that will address modeling activities focused on a particular system level (such as proteins, cells, tissues, organs, up to organisms) or encompassing multiple levels (across the length scale from nanometers for molecules to meters for human bodies, as well as across time scale from nano-seconds for molecular interactions to minutes, hours and years for human life). In order to better understand human physiology and to allow for predictive capabilities of disease prevention and treatment it is crucial to develop simulation systems that can operate at these scales. The session is organized jointly by researchers from Simbios (http://simbios.stanford.edu/) and NCBR (http://nbcr.sdsc.edu/). Submission topics can include, but not limited to:

Physics-based simulations at all scales

   Multiscale

• Methods for making the connection between continuum macroscale models (e.g., fluid) and discrete molecular phenomena (e.g., molecular behavior)

• Model reduction and systems identification for multiscale dynamical systems

• Algorithmic tools for multi-scale modeling systems using optimization and simulation in time and space

• Mesoscale methods to bridge microscales and macroscales

• Multiscale simulation of biochemical networks 

• Finite-element method for molecules, cells, tissues, and organs

• Functional coupling within a scale

   Molecular

• Protein dynamics and conformational changes

• Coarse-grained model for biomolecules

• Molecular biology of ion channels and transporters

• Protein-protein interaction networks

• Molecular mechanism of disease

   Cellular

• Excitation-contraction coupling and mechanoelectric feedback in normal and diseased cells

• Metabolic and neurohumoral regulation of excitation-contraction coupling

• Cellular force transmission

• Motility and cytoskeletal dynamics

   Tissue, organ, organisms

• Tissue mechanics

• Cardiovascular systems modeling

• Dynamic simulation of neuromuscular systems

• Patient-specific modeling

• Cardiac resynchronization therapy

Session chairs

Jung-Chi Liao

National Center for Physics-based Simulation of Biological Structures (Simbios)

Stanford University

liaojc@stanford.edu

Peter Arzberger

National Biomedical Computation Resource (NBCR)

parzberg@sdsc.edu

Roy Kerckhoffs

University of California San Diego

roy@bioeng.ucsd.edu

Anushka Michailova

University of California San Diego

amihaylo@bioeng.ucsd.edu

Jeff Reinbolt

National Center for Physics-based Simulation of Biological Structures (Simbios)

Stanford University

reinbolt@stanford.edu 

Papers and abstracts

The core of the conference consists of rigorously peer-reviewed full-length papers reporting on original work. Accepted papers will be published in a hard-bound archival proceedings. Researchers wishing to present their research without official publication are encouraged to submit a one page abstract by November 9, 2007.

Important dates

Paper submissions due: July 16, 2007
Notification of paper acceptance: September 5, 2007
Final paper deadline: September 24, 2007 at midnight PDT
Abstract deadline: November 9, 2007 at noon PST
Meeting: January 4-8, 2008

Paper format

All papers and abstracts must be submitted to psb-submit @ helix.stanford.edu in electronic format with PSB in the subject line. The file formats we accept are: postscript (*.ps) and Adobe Acrobat (*.pdf). Attached files should be named with the last name of the first author (e.g. altman.ps or altman.pdf). Hardcopy submissions or unprocessed TEX or LATEX files will be rejected without review.

Each paper must be accompanied by a cover letter. The cover letter must state the following:

• The email address of the corresponding author.
• The specific PSB session that should review the paper or abstract.
• The submitted paper contains original, unpublished results, and is not currently under consideration elsewhere.
• All co-authors concur with the contents of the paper.

Submitted papers are limited to twelve (12) pages in our publication format. Please format your paper according to instructions found at http://psb.stanford.edu/psb-online/psb-submit/. If figures can not be easily resized and placed precisely in the text, then it should be clear that with appropriate modifications, the total manuscript length would be within the page limit.

Color pictures can be printed at the expense of the authors. The fee is $500 per page of color pictures, payable at the time of camera ready submission.

Contact Russ Altman (psb-submit@helix.stanford.edu) for additional information about paper submission requirements.