Ant Colonies as a Model of Human Computation, Melanie Moses, Tatiana Flanagan, Kenneth Letendre and G. Matthew Fricke, Handbook of Human Computation, Springer, 2014. website
Journals
Persistence and Adaptation in Immunity: T Cells Balance the Extent and Thoroughness of Search. Fricke, G. Matthew, Kenneth A. Letendre, Melanie E. Moses, and Judy L. Cannon. PLoS Comput Biol 12.3 (2016): e1004818. PDF
Immune-inspired search strategies for robot swarms. G. Matthew Fricke, Joshua Hecker, Judy Cannon, and Melanie Moses. Robotica 34, no. 08 (2016): 1791-1810. Cambridge Press. PDF
Quantifying the Effect of Colony Size and Food Distribution on Harvester Ant Foraging, Tatiana P. Flanagan, Kenneth Letendre, William R. Burnside, G. Matthew Fricke, and Melanie E. Moses, PLoS ONE, 2012.
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, Oxford Journals
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. PDF
Conference Proceedings
A Distributed Deterministic Spiral Search Algorithm for Swarms. G. Matthew Fricke, Joshua P. Hecker, Antonio D. Griego, Linh T. Tran, and Melanie Moses. In 2016 IEEE/RSJ International Conference on Intelligent Robots and Systems, IEEE Press, 2016.
Distinguishing Adaptive Search From Random Search in Robots and T cells, G. M. Fricke, J. P. Hecker, S. R. Black, J. L. Cannon, M. E. Moses, in Proceedings of the Conference on Genetic and Evolutionary Computation, Association for Computing Machinery, 2015.
From Microbiology to Microcontrollers: Robot search patterns inspired by T cell movement, G. Matthew Fricke, Francois Asperti-Boursin, Joshua P. Hecker, Cannon Judy L., and Melanie E. Moses. Proceedings of the 12th European Conference on Artificial Life, The MIT Press, 2013.
How Ants Turn Information into Food, T. Paz Flanagan, K. Letendre, W. Burnside, G. M. Fricke, M. Moses, in IEEE SSCI 2011 - Symposium Series on Computational Intelligence - IEEE Symposium on Artificial Life (2011), pp. 178–185.
Emergent Representation in a Robot Control Architecture, Claiborne, Andy., Fricke, G. Matthew., Lopes, L., Lewis, Joseph., and Luger, George, UNM-NASA PURSUE Conference, (2000).
Ant Colony Algorithms (ACOs) are used in shortest-path problem domains such as chip design and network routing. We investigated 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. This information was compared to computational models of various foraging strategies.
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.
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.
My wife, Suzanne, and I have four boys: Henry, Leo, Owen, and Tristan. We live in
Albuquerque, New Mexico, USA. I was born and raised in Shrewsbury, UK, but have lived in Mount Airy, North Carolina and Albuquerque, New Mexico for most of my life. I have been interested in computers since playing with a Commodore 64 when I was ten years old.
Go Figure Software is my contracting company. Through Go Figure Software I have provided programming services to scientists
at the UNM Physics Department and Los Alamos National Labs.
Pogonomyrmex Rugosus
T-Cell Targeting Infected Cell
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