Department of Physics and Astronomy
I have been interested in applied mathematics and computing ever since I started college. This has led me to explore a variety of subjects and become involved in many different areas of mathematical (and also non-mathematical) programming. Some of these are computer algebra (tensor analysis, linear algebra, etc.), simulations and visualizations of physical and biological phenomena (hydrogen transport and combustion in nuclear reactor containments, dynamic modeling of solids subject to impulsive forces, antigens clustering on the surface of a cell, etc.), development of helpful utilities (for TeX, Fortran 90, etc.), development of networking and graphical user interface software (for a unique PC-based, distributed, physical security system), creation of World Wide Web pages (for various groups), system administration of networked Sun workstations (also for various groups), mathematical analysis of atonal music compositions, and examination of logs of student activity in online learning scenarios.
Since 2000, I have been extensively involved with computational biology, including drug related applications (protein folding/conformer generation, molecular scaffold topological classification, cheminformatics), and spatiotemporal modeling and analysis (reaction/diffusion stochastic simulations of cell signaling, clustering of proteins as well as super-resolution observations of blinking fluorophores, collapsing the latter into estimates of their true locations, contact analysis of proteins on the surface of yeast cells, simulations of glucan unmasking on the surface of Candida albicans, fitting super-resolution pupil functions during phase retrieval with Zernike polynomials).
I attended the University of New Mexico and received from there the degrees Bachelor of Science (physics and mathematics), Master of Arts (applied mathematics) and Doctor of Philosophy (computer algebra: my advisor was Stanly Steinberg). My first job was as an aide to Cleve Moler where I performed various programming tasks involving mainly numerical analysis work, including testing routines later collected into LINPACK and making a variety of plots, some of which were later incorporated into the textbook Computer Methods for Mathematical Computations (Forsythe, Malcolm and Moler). As a teaching assistant, I taught various pre-calculus courses for the Department of Mathematics and Statistics. Later, I was employed as a research assistant, acting as a system administrator for the department. I spent one summer working at Argonne National Laboratory working with computer resource sharing on the ARPANET, and another at the Massachusetts Institute of Technology where I participated on the MACSYMA project.
Outside the university, I spent 4 years as an on-site contractor at Sandia National Laboratories working on nuclear reactor safety issues, and more recently at Spectra Research Institute developing a variety of software components for a PC-based physical security system which has been installed at the Nevada Test Site, Rocky Flats and local sites. I also operate as a consultant (under the name Cotopaxi), which has allowed me to become involved in many different activities. Besides the ones mentioned above, these include teaching people how to use various Internet facilities, editing and adding new material to an educational hypertext computer algebra discussion for the Czech Technical University, and co-conducting computer algebra workshops at 3 different locales in the United States and Sweden.
Since 2007, I have been a member of the associated faculty of the Cancer Research and Treatment Center Shared Resource for Bioinformatics and Computational Biology at the Center for High Performance Computing, and Research Assistant Professor in the Department of Mathematics and Statistics, both at the University of New Mexico. I have co-advised one Ph.D. student.
I have edited two books and published 62 articles, co-edited 8 journal special issues, and given 22 invited talks on four continents. I am an editor of the SIGSAM Bulletin and the (Spanish) Sociedad `Puig Adam' de Profesores de Matemáticas. I have been the primary author of one grant proposal, which was funded for $23,300. I co-organized (with Stanly Steinberg) the 1st International Conference on Applications of Computer Algebra (ACA) at the University of New Mexico, Albuquerque, New Mexico, May 16-19, 1995. 93 attendees from 16 countries participated. Since then, I have been involved in ACA conference organization as general chair (1997, 2021), program co-chair (2000, 2002, 2006, 2009-2010, 2016, 2019) treasurer (1998, 2000-2003), exhibition chair (2004), member of the organizing committee (1998-2003, 2006), advisory committee member (2012-2018, 2022), session organizer (1996-1997, 2000-2003, 2005-2019, 2021-2022), and co-chair of the ACA working group (2016--2017). I also co-organized the one-day mini-conference Biocomputing @ UNM 2003-2007.
Scaffold topologies. 1. Exhaustive enumeration up to eight rings.
Journal of chemical information and modeling Jul, 2008 | Pubmed ID: 18605680
Scaffold topologies. 2. Analysis of chemical databases.
Journal of chemical information and modeling Jul, 2008 | Pubmed ID: 18605681
Insights into cell membrane microdomain organization from live cell single particle tracking of the IgE high affinity receptor FcϵRI of mast cells.
Bulletin of mathematical biology Aug, 2012 | Pubmed ID: 22733211
A new tool to quantify receptor recruitment to cell contact sites during host-pathogen interaction.
PLoS computational biology May, 2014 | Pubmed ID: 24874253
Super-resolution imaging of C-type lectin spatial rearrangement within the dendritic cell plasma membrane at fungal microbe contact sites.
Frontiers in physics Aug, 2014 | Pubmed ID: 25506589
Exhaustive Conformational Sampling of Complex Fused Ring Macrocycles Using Inverse Kinematics.
Journal of chemical theory and computation Sep, 2016 | Pubmed ID: 27447193
A computational model for regulation of nanoscale glucan exposure in Candida albicans.
PloS one , 2017 | Pubmed ID: 29232689
Mechanism of Stx17 recruitment to autophagosomes via IRGM and mammalian Atg8 proteins.
The Journal of cell biology 03, 2018 | Pubmed ID: 29420192
Mechanisms of inside-out signaling of the high-affinity IgG receptor FcγRI.
Science signaling 07, 2018 | Pubmed ID: 30042128
Mannan Molecular Substructures Control Nanoscale Glucan Exposure in Candida.
Cell reports 08, 2018 | Pubmed ID: 30157435
RMSD and Symmetry.
Journal of computational chemistry 06, 2019 | Pubmed ID: 30828834
γ9δ2T cell diversity and the receptor interface with tumor cells.
The Journal of clinical investigation 09, 2020 | Pubmed ID: 32484803
Comparing lifeact and phalloidin for super-resolution imaging of actin in fixed cells.
PloS one , 2021 | Pubmed ID: 33508018
Robust, fiducial-free drift correction for super-resolution imaging.
Scientific reports 12, 2021 | Pubmed ID: 34880301
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