Optimization of Simple Reaction-Diffusion PDE Simulations on a 64-Opteron Linux Cluster

We use a simple message-passing (MPI) algorithm on a parallel cluster to reduce the simulation times in our study of spiral and scroll waves in 2D and 3D excitable media. However, the efficiency of such parallel simulations can vary significantly based on a multitude of factors. We undertook a thorough investigation to find optimal ways of using our on-site 64-processor Linux cluster. This investigation includes a detailed 2D and 3D speed-up analysis, and a comparison of alternative MPI implementations, MPI configuration files, and a variety of other approaches and options. Due to the generic nature of our parallelization algorithm, the results of this study can be interesting to a broad body of scientific cluster users

Ionic Determinants of Functional Reentry in a 2-D Model of Human Atrial Cells During Simulated Chronic Atrial Fibrillation

Recent studies suggest that atrial fibrillation (AF) is maintained by fibrillatory conduction emanating from a small number of high-frequency reentrant sources (rotors). Our goal was to study the ionic correlates of a rotor during simulated chronic AF conditions. We utilized a two-dimensional (2-D), homogeneous, isotropic sheet (5 × 5 cm(2)) of human atrial cells to create a chronic AF substrate, which was able to sustain a stable rotor (dominant frequency ∼5.7 Hz, rosette-like tip meander ∼2.6 cm). Doubling the magnitude of the inward rectifier K(+) current (I(K1)) increased rotor frequency (∼8.4 Hz), and reduced tip meander (∼1.7 cm). This rotor stabilization was due to a shortening of the action potential duration and an enhanced cardiac excitability. The latter was caused by a hyperpolarization of the diastolic membrane potential, which increased the availability of the Na(+) current (I(Na)). The rotor was terminated by reducing the maximum conductance (by 90%) of the atrial-specific ultrarapid delayed rectifier K(+) current (I(Kur)), or the transient outward K(+) current (I(to)), but not the fast or slow delayed rectifier K(+) currents (I(Kr)/I(Ks)). Importantly, blockade of I(Kur)/I(to) prolonged the atrial action potential at the plateau, but not at the terminal phase of repolarization, which led to random tip meander and wavebreak, resulting in rotor termination. Altering the rectification profile of I(K1) also slowed down or abolished reentrant activity. In combination, these simulation results provide novel insights into the ionic bases of a sustained rotor in a 2-D chronic AF substrate