Detailed Simulation of the Cochlea: Recent Progress Using Large Shared Memory Parallel Computers

Abstract

We have developed and are refining a detailed three-dimensional computational model of the human cochlea. The model uses the immersed boundary method to calculate the fluid-structure interactions produced in response to incoming sound waves. An accurate cochlear geometry obtained from physical measurements is incorporated. The model includes a detailed and realistic description of the various elastic structures present. Initially, a macro-mechanical computational model was developed for execution on a CRAY T90 at the San Diego Supercomputing Center. This code was ported to the latest generation of shared memory high performance servers from Hewlett Packard. Using compiler generated threads and OpenMP directives, we have achieved a high degree of parallelism in the executable, which has made possible to run several large scale numerical simulation experiments to study the interesting features of the cochlear system. In this paper, we outline the methods, algorithms and software tools that were used to implement and fine tune the code, and discuss some of the simulation results.

A stochastic immersed boundary method for fluid-structure dynamics at microscopic length scales

“…The immersed boundary method of (64) has found wide use as an efficient numerical method for simulating such systems. Some examples include the study of blood flow around heart valves (65), wave propagation in the inner ear (32), and the generation of lift in insect flight (56). With experimental advances in molecular and cellular biology has come an increasing interest in developing methods to model qualitatively and quantitatively microscopic biological processes at the cellular and subcellular level (12; 27; 41).…”