Experience

UNIVERSITY OF NEW MEXICO, Albuquerque, New Mexico
Scientist (October 2009-)

Development of a stochastic simulation algorithm written in Matlab for exploring diffusion and reactions of signaling molecules on a cell surface, in particular, the IgE receptor, FcεRI. Created software for the contact analysis of proteins on the surface of a yeast cell, developing an appropriate co-localization methodology for projections onto a spherical surface. Established a methodology for fitting experimental biofilm diffusion curves based on a theoretical model, taking into account evaporation from the top of the biofilms. Developed a top-down hierarchical clustering algorithm to collapse clusters of observations of blinking fluorophores into single estimates of the true locations of the fluorophores for super-resolution imaging. This led to the creation of a Matlab class containing the above as well as a variety of simulation, statistical and clustering algorithms that work in both 2D and 3D. Also, wrote a parallelized glucan unmasking simulation to try to understand the underlying biological mechanism of immune recognition by Candida albicans, and built an optimized Zernike polynomial class for fitting super-resolution pupil functions during phase retrieval. Created a parallelization protocol for a Bayesian inference scheme for distinguishing overlapping multi-emitter super-resolution localizations. Finally, provided general mathematical and software support for a variety of other computational biologically related research endeavours. This work was performed under the auspices of the New Mexico Center for the Spatiotemporal Modeling of Cell Signaling (STMC).

Development of a small molecule protein folding code, written in C, Fortran 95 and Perl, in collaboration with Evangelos Coutsias, along with associated research in optimizing RMSD calculations and exploring certain constrained molecular conformational spaces.

UNIVERSITY OF NEW MEXICO HEALTH SCIENCES CENTER, Albuquerque, New Mexico
Scientific Coordinator for the Shared Biocomputing Core (July 2000-June 2007)

Coordinated the use of computational resources with diverse groups inside and outside the Medical School. Managed a variety of Unix based servers and a robotic backup system, installing hardware and software as well as networking the systems together and planning future purchases. Interacted with users on a variety of levels from providing them access to the Biocomputing facilities to educating them in the use of complex software. Also managed an assistant for a time who took care of the Microsoft based systems. Participated in the construction and teaching of a self-paced graduate level course on structure-based drug design. Suggested and co-organized the one-day Biocomputing @ UNM mini-conference every year starting in 2003. As the core transformed into a research division, took the lead in writing a grant for the Systematic Enumeration of Molecular Scaffolds, which funded a student to work on this project. Here, analyzed various cheminformatic databases for topological descriptors to compare against our theoretical structures.

MODULAR INTEGRATED TECHNOLOGIES, Albuquerque, New Mexico and Las Vegas, Nevada
Member (January 1998-February 2000)

Continuation of software development for PECOS on a variety of fronts, such as improving the graphical user interface, creating a generalized communications package, etc. Directly involved in systems installed in Albuquerque, Las Vegas and the Nevada Test Site.

SPECTRA RESEARCH INSTITUTE, Albuquerque, New Mexico
Member (July 1992-present)

Collaborated in developing software for PECOS (Process Equipment COntrol System), a unique PC-based, distributed, physical security system. Work involved improving the graphical user interface, adding audio capabilities, various network issues, and installation of systems at the Nevada Test Site, Rocky Flats and local sites.

AMPARO CORPORATION, Santa Fe, New Mexico
Scientist (February 1989-August 1989)

Collaborated in extending the 2D version of the HULL hydrocode (for dynamic modeling of solids subject to impulsive forces) to handle multiple Eulerian meshes, under an SBIR to Eglin AFB, Florida. Work involved making major structural changes to the code, improving existing numerical schemes and constructing a contour plotting package. Development was done on the Cray-2 (running CTSS) at the Air Force SuperComputer Center, Kirtland AFB, New Mexico.

CONSULTANT (1987-March 1993), as COTOPAXI (March 1993-present)

Have performed various short term tasks involving software analysis and development (Fiber-Chem, Inc.), Internet research (Medical Instrumentation & Diagnostics Corp.), networked Sun installations (Department of Physics and Astronomy of the University of New Mexico and Quetzal Computational Associates), telecommunications technology research (JNA Telecommunications Limited), development of 2D and 3D linked Eulerian/Lagrangian solid dynamics visualization schemes using AVS graphics (Quetzal Computational Associates), teaching usage of the USENET news network (Professional Engineering Development Workshop Programs at the University of New Mexico), symbolic tensor and linear algebra algorithm development (Macsyma Inc.), editing and adding new material to an educational hypertext computer algebra discussion (Department of Nuclear Sciences and Physical Engineering of the Czech Technical University), development of World Wide Web pages (Department of Physics and Astronomy of the University of New Mexico and the International Conferences on Applications of Computer Algebra), system administration of HP, SGI and FreeBSD [Unix] machines (Kenneth Ingham Consulting), treasurer (International Conferences on Applications of Computer Algebra), translating Maple functions to other computer algebra languages (Joel Cohen, University of Denver), editing and contributing to the book Computer Algebra Systems: A Practical Guide published by John Wiley & Sons, providing a user perspective on software and documentation inadequacies (Waterloo Maple Inc.), LaTeX editing (Bill Pletsch, Central New Mexico Community College), publication of a pair of cheminformatic papers (Division of Biocomputing, University of New Mexico Health Sciences Center), updating statistical Matlab routines for analyzing gold particle and quantum dot tracking (Signal Transduction Modeling Center, University of New Mexico Health Sciences Center), incorporating automatic differentiation for sensitivity studies within a large C and Fortran~95 parallel solid dynamics material point method code, improving the parallel performance of this code and running case studies on high performance systems at UNM, LLNL and Purdue, developing a Python GUI using VTK to simplify visualization setup in ParaView, writing an introduction to verification and validation (V&V) and uncertainly quantification (UQ) concepts (Purdue University and Deborah Sulsky, Department of Mathematics and Statistics at the University of New Mexico), developing mainly Matlab software for analyzing online student test tracking data for the WISE system (Vanessa Svihla, Department of Teacher Education at the University of New Mexico).

UNIVERSITY OF NEW MEXICO, Albuquerque, New Mexico
Research Assistant, Department of Mathematics and Statistics
(August 1985-May 1988)

Major person responsible for system administration of a networked system of Sun-3s and a Sun-2 operating a derivative of BSD4.2/3 UNIX. Performed hardware and software installations and upgrades, crash recovery, and system and applications maintenance. Organized Network File Systems to provide extensive software sharing. Gained much experience in network communications. Programmed in shell, C, FORTRAN, Lisp, LaTeX, and various UNIX utilities and symbolic mathematical languages. In addition, spent much time providing advice and support to staff and faculty, including interacting with members of other departments.

THE PROTEUS CORPORATION, Albuquerque, New Mexico
Member of the Technical Staff (October 1982-September 1984)

Continuation of HECTR development at Sandia National Laboratories. Besides program development, compared predictions to experimental data and used HECTR to parametrically study accident scenarios for commercial reactors awaiting licensing, the latter frequently requiring calculations on very short notice. Also, wrote reports, made presentations at various locales and developed a variety of software tools. Participated in organizing and conducting a 2-day workshop in Washington, D.C. on HECTR for Nuclear Regulatory Commission staff.

THE DIKEWOOD CORPORATION, Albuquerque, New Mexico
Research Associate (February 1981-September 1982)

As an on-site contractor at Sandia National Laboratories, worked on reactor safety issues for the Nuclear Regulatory Commission. Performed graphical analysis of data that helped to settle the unresolved issue ``Containment Emergency Sump Performance''. Collaborated in developing the HECTR (Hydrogen Event: Containment Transient Response) lumped volume computer code for analyzing nuclear reactor accidents involving hydrogen transport and combustion. This involved modeling atmospheric physics, heat transfer mechanisms and engineered safety features, as well as producing a user friendly interface and a subsidiary plotting package. Used VAX, Cray and CDC computers running VMS, COS, NOS and SCOPE.

MASSACHUSETTS INSTITUTE OF TECHNOLOGY, Cambridge, Massachusetts
Summer Sponsored Research Staff Member, The Mathlab Group
(June 1979-August 1979)

Participated in the development of MACSYMA, a large computer program written in Lisp, designed to do symbolic mathematics, and which is now distributed worldwide. Duties included making bug fixes, assisting users online, organizing user contributed software, and substantially modifying, reorganizing and expanding the tensor analysis package. Major items in the latter were developing a tensorial simplifier for reducing complicated expressions (the typical situation) and establishing the ability to be able to automatically convert tensor expressions from an implicit to a component representation. In addition, was involved in rewriting the description of the tensor package in the MACSYMA Reference Manual.

ARGONNE NATIONAL LABORATORY, Argonne, Illinois
Participant in the Undergraduate Research Program (June 1977-August 1977)

Early involvement in computer resource sharing, working with various computers on the ARPANET. Built and manipulated a weather data base on the Computer Corporation of America's Datacomputer, and investigated and documented for Argonne users the use of facilities at Brookhaven National Laboratory (CDC 6600s and a 7600 running INTERCOM and SCOPE) and on the MIT MACSYMA Consortium computer (a DEC KL10 running ITS). Also, designed an editor in APL for an IBM 5100 minicomputer.

UNIVERSITY OF NEW MEXICO, Albuquerque, New Mexico
NSF grant Math Aide (April 1976-May 1978)
Teaching Assistant, Department of Mathematics and Statistics
(August 1978-December 1979)
Computer Consultant, Department of Mathematics and Statistics
(January 1980-May 1980)
Consultant (June 1980-August 1980)

As an NSF grant Math Aide to Professor Cleve Moler, performed various programming tasks involving mainly numerical analysis work. Primary duties were testing routines later collected into LINPACK and developing a program for automating data type conversions on them. Also, created an electronic mail system to maintain communication on UNM's IBM 360 mainframe and made 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, taught various pre-calculus mathematics courses over three semesters. Duties included lecturing, making up exams, grading homework and exams, holding office hours and assigning final grades to the students.

As the Mathematics Department Computer Consultant, taught members how to use the University's new IBM 3032 mainframe (running MVS and the VSPC timesharing system), including helping them to convert programs to run in this new environment. Also, developed a program for entering and doing statistical calculations on student grades. During this time, served on the TA Selection Committee with purpose to choose new TAs for the fall from a list of applicants.

As a consultant to a pair of professors in the Mathematics and Neurology Departments, archived neurological data onto magnetic tape and extended FORTRAN routines graphically displaying this data on Tektronix terminals.

Michael Wester's Vita