Abstract

In this project, we aim at improving a model devised to simulate the generation and transmission of electrical impulses by cardiac cells. This model is used to study the mechanisms of initiation and sustainment of vortices of excitation waves which underlie cardiac tachyarrhythmias. In a subsequent phase, and if the model can realistically reproduce vortices of excitation, we will study how membrane functions can be altered to terminate such vortices. We have developed a parallel version of our code using MPI. Based on our performance tests, using 32 processors on the IBM SP, it will take 10 hours (wall clock) to obtain an episode of tachycardia; i.e. 1 sec of vortex-like activity, in a small piece of cardiac tissue of 2 cm x 2 cm. The same simulation requires a little more than 8 days on a SPARC 10 model 512. During the period of support, we will improve the matrix inversion procedure of the current version. We believe that it is possible to divide the computation time by a factor ranging between 3 and 5 by using a preconditioning procedure suitable for parallelization

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR004293-09
Application #
6309537
Study Section
Project Start
1999-12-01
Project End
2000-11-30
Budget Start
1998-10-01
Budget End
1999-09-30
Support Year
9
Fiscal Year
2000
Total Cost
$24,318
Indirect Cost

  Institution

Name
Cornell University
Department
Type
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850

  Publications

Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek et al. (2008) Size-restricted proton transfer within toluene-methanol cluster ions. J Phys Chem A 112:11559-65
Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2003) Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem 100:261-80
Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2002) Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem 23:715-23
Liwo, Adam; Arlukowicz, Piotr; Czaplewski, Cezary et al. (2002) A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A 99:1937-42
Scheraga, Harold A; Pillardy, Jaroslaw; Liwo, Adam et al. (2002) Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J Comput Chem 23:28-34
Scheraga, Harold A; Vila, Jorge A; Ripoll, Daniel R (2002) Helix-coil transitions re-visited. Biophys Chem 101-102:255-65
Pillardy, J; Arnautova, Y A; Czaplewski, C et al. (2001) Conformation-family Monte Carlo: a new method for crystal structure prediction. Proc Natl Acad Sci U S A 98:12351-6
Vila, J A; Ripoll, D R; Scheraga, H A (2001) Influence of lysine content and pH on the stability of alanine-based copolypeptides. Biopolymers 58:235-46
Pillardy, J; Czaplewski, C; Liwo, A et al. (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci U S A 98:2329-33
Vila, J A; Ripoll, D R; Scheraga, H A (2000) Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc Natl Acad Sci U S A 97:13075-9

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