Fricke Home Website

Matthew Fricke

I am a PhD student at the University of New Mexico Computer Science Department. I received a Baccalaureate of Art from the Anthropology Department at Appalachian State University in North Carolina. My Master of Science in Computer Science is from UNM where I concentrated in Artificial Intelligence and Computational Biology. Résumé.

My wife, Suzanne, and I have four wonderful boys: Henry, Leo, Owen, and Tristan. We live in Albuquerque, New Mexico, USA.

Go Figure Software is a contracting company I started three years ago. Through Go Figure Software I have provided programming services to scientists at the UNM Physics Department and Los Alamos National Labs.

Current Research

Pogonomyrmex Rugosus

Ant Colony Algorithms (ACOs) are used in various shortest-path problem domains such as chip design and network routing. We are investigating how three species of the desert harvester ant (Pogonomyrmex Rugosus, Maricopa, and Desertorum) share information about their surroundings, especially with regard to the scaling of information sharing with colony size.

Previous Interests and Research

GetBonNie for building, analyzing, and sharing rule-based models
Bin Hu; G. Matthew Fricke; James R. Faeder; Richard G. Posner; William S. Hlavacek Bioinformatics 2009; doi: 10.1093/bioinformatics/btp173
published by Oxford Journals

BioNetGen: Biochemical reaction networks are central to understanding and influencing the operation of biological cells. GetBonNie (http://getbonnie.org) and BioNetGen (http://www.bionetgen.org) automate the development of reaction networks so that biologists can create and study detailed models of cellular biochemistry. Poster. Video.

You can download the software here: OS X, Windows. Be warned however that these distributions are of RuleBuilder 1.50 Beta bundled with BioNetGen 2.0.28, which are out of date. For the latest builds please go to the bionetgen website.

Receptor aggregation by intermembrane interactions: A Monte Carlo study
G. Matthew Fricke; James L. Thomas
Biophysical Chemistry Volume 119, Issue 2, 20 Jan 2006; Pages 205-211

T-Cell Targeting Infected Cell

CemPro: Macrophages and T-cells communicate with one another at the cell surface through ligands and receptors. The proteins that form the ligands and receptors cluster during signaling. The mechanism for this clustering is unknown.

We model proteins on the cell surface with a Metropolis Monte Carlo lattice and measure the conditions under which clustering occurs. We then bring two virtual cell membranes into contact and measure the cross membrane binding forces needed to cause protein phase separation. Paper in Biophysical Chemistry. PowerPoint Web Slideshow. PDF Slideshow.

KomPhy: Algorithms for reconstructing phylogenies from character sequences encounter enormous search spaces even for small numbers of taxa. Techniques are needed to speed up the exploration of these spaces so that larger problems can be approached. In the past neural networks have provided a framework for tackling complex problems very quickly. My thesis describes and tests a new neural network approach to phylogenetic reconstruction called KomPhy. Thesis. Slideshow. Software.

CultureAL: Semester project for David Ackley's Artificial Life course at UNM. CulturAL uses a very simple framework to explore the interaction of learned traits (directly and through peer emulation) and biological traits. Processes such as 'shielding' and the Baldwin Effect are explored. Learning in this model benefits the population as a whole through emulation but is counterproductive for the learner who is much better off copying others and procreating. The population as a whole evolved to minimize direct learning and maximize emulation of peers relying on the background mutation rate to produce enough 'learners' to feed the emulation strategy.. The most prevalent impact shared knowledge has on genetic evolution is shielding, which allows populations to survive that would otherwise die out and allows genetic mutation to explore the fitness landscape with more freedom. Presentation.

Madcat: Extension of the Copycat AI framework to a robotic path finding problem which formed the basis of Joseph Lewis' PhD. Starcat is Joseph's current research. Madcat NASA Student Conference Paper.

Photographs

Tikal, Guatemala