NCRR Resources at the Biophysical Society Meeting
From BTRR
The 2009 Biophysical Society Meeting is held in Boston, MA, on Feb 28 to Mar 4, 2009.
NBCR and RVBI are coordinating the joint project booth for selected NCRR Resource Centers. The schedule is available at BPS 2009 or NBCR at BPS 2009 for Booth #631. The final
Presentations from NBCR
Sunday, 4 to 5 pm,
Stuart Campbell*, Andrew McCulloch
Effects of Myocyte Heterogeneity on Ventricular Function: A Multi-Scale Modeling Study using Continuity 6 Cardiac muscle cells isolated from the left-ventricular (LV) wall exhibit region-dependent behavior. Those isolated from the outer third of the wall (epicardium) contract and relax more rapidly than myocytes found in the inner region of the wall (endocardium). These differences in contraction dynamics have unknown effects on the regional and global function of the LV. Using the Continuity environment, we have created a three-dimensional, multi-scale model of LV function which simultaneously solves equations describing electrical propagation, finite tissue deformation, muscle contraction, and ventricular loading. This model enabled prediction of LV pump function and regional strains under two conditions: 1) with cell-level parameters assigned in a physiologic manner, spatially arranged in layers through the LV wall (BASELINE), and 2) with cell-level parameters assigned in a randomized fashion (RANDOM). The two simulations produced identical stroke volumes and peak LV pressures. Strains at end-ejection were also nearly identical in the two simulations. The greatest differences were evident during early ejection, where BASELINE produced a larger range of fiber strains as measured across the LV wall in comparison with the RANDOM simulation. We conclude that the principal effect of myocyte heterogeneity in the LV is on fiber strains during early systole. We also conclude that global LV pump function is not sensitive to the observed spatial patterns of myocyte behavior.
Monday, 12 to 1 pm
Yuhui Cheng, Zeyun Yu*, Anushka Michailova
Multi-scale Meshing and Numerical Approaches for Modeling Ca2+ Signaling in Cardiac Muscle Cells
A tight coupling between cell structures, ionic fluxes and intracellular Ca2+ transients underlies the regulation of cardiac cell function. We have used multi-scale meshing and numerical approaches and tools (GAMer, FETK, MCell) to investigate these complex interactions at nanometer (dyadic cleft) and micrometer (single t-tubule) scales in rat ventricular myocytes. The realistic model geometries have been extracted from both light and electron microscopy images. Preliminary results suggest that cardiac cell function is tightly regulated by the localization of Ca2+-handling proteins and strongly relies on the presence of mobile and stationary Ca2+ buffers and cell geometry.
Tuesday, 12 to 1 pm
Vision based workflow management for computer aided drug discovery application services
Luca Clementi, Jane Ren, Guillaume Vareille, Sriram Krishnan, Michel Sanner, Peter Arzberger, Wilfred Li* Computer aided drug discovery (CADD) involves complex multiscale simulation setups, and lengthy pre-, post-analysis steps that require workflow management tools and customized workflow modules based upon specific usage scenarios. In addition, transparent access to distributed resources (grid, cloud computing) beyond a user’s desktop/laptop is required for scalability and on demand computing. Using the Vision workflow environment, and the Opal 2 web service toolkit for scientific applications, we have built a flexible and scalable service oriented architecture for CADD. It currently supports the Relaxed Complex Scheme (RCS) using molecular dynamics programs such as NAMD, and docking programs such as AutoDock and AutoDockTools. The workflow modules are freely available through the NBCR workflow repository, and may be adapted easily to provide a GUI based workflow environment for other command line based applications. Training is available at the annual NBCR Summer Institute.
Tuesday, 2 to 3 pm
Opal 2.0 for Scientific Applications in the Software as a Service (SaaS) environment
Luca Clementi, Jane Ren, Sriram Krishnan, Wilfred Li*
With the advent of Cloud computing, the concepts of Software as a Service (SaaS), where vendors provide key software products as services over the internet that can be accessed by users to perform complex tasks, and Service as Software (SaS), where customizable and repeatable services are packaged as software products that dynamically meet the demands of individual users, have become increasingly popular. Both SaaS and SaS models are highly applicable to scientific software and users alike. Opal2 is a toolkit for wrapping scientific applications as Web services on Grid and cloud computing resources, which provides a mechanism for scientific application developers to expose the functionality of their codes via simple Web services APIs, abstracting out the details of the back-end infrastructure. Complex services may be combined via customized workflows for specific research areas and enables the packaging of complete work environment to be distributed as virtual machine images. The new plug-in architecture for Opal2 will be demonstrated, with available plug-ins for CSF4, Globus-GRAM, DRMAA and fork.
