Digital Commons Network^™

Self-Organization Of Scroll Waves In Excitable Media : Parallel Simulations On A 64-Opteron Linux Cluster, Igor Kaplun

Theses, Dissertations and Culminating Projects

Spiral waves have been observed and studied in a variety of biological, physical and chemical systems, known as excitable media. The most famous examples of excitable media include cardiac tissue, the Belousov-Zhabotinsky chemical reaction, and aggregation of starving slime mold amoeba.

It had been shown previously that spiral waves could self-organize into multi- armed spirals. A 3D analog of a 2D spiral wave is called a scroll wave. It rotates around a 1D imaginary tube known as a filament. A later study based on the so-called Puschino model has reported formation of multi-armed scroll waves in 3D. But a question …

Parallel Nonnegative Matrix Factorization Algorithms For Hyperspectral Images, Lukasz Grzegorz Maciak

Theses, Dissertations and Culminating Projects

Hyperspectral imaging is a branch of remote sensing which deals with creating and processing aerial or satellite pictures that capture wide range of wavelengths, most of which are invisible to the naked eye. Hyperspectral images are composed of many bands, each corresponding to certain light frequencies. Because of their complex nature, image processing tasks such as feature extraction can be resource and time consuming. There are many unsupervised extraction methods available. A recently investigated one is Nonnegative Matrix Factorization (NMF), a method that given positive linear matrix of positive sources, attempts to recover them. In this thesis we designed, implemented …

Adapting The Phylogenetic Program Fitch For Distributed Processing, Robert A. Dubin

Theses, Dissertations and Culminating Projects

The ability to reconstruct optimal phylogenies (evolutionary trees) based on objective criteria impacts directly on our understanding the relationships among organisms, including human evolution, as well as the spread of infectious disease. Numerous tree construction methods have been implemented for execution on single processors, however inferring large phylogenies using computationally intense algorithms can be beyond the practical capacity of a single processor. Distributed and parallel processing provides a means for overcoming this hurdle. FITCH is a freely available, single-processor implementation of a distance-based, tree-building algorithm commonly used by the biological community. Through an alternating least squares approach to branch length …