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Blaise J Thompson


University of Wisconsin-Madison 2011-2018

PhD, Analytical Chemistry
GPA: 3.82/4.00 - transcript - completion letter

Bates College 2007-2011

BS: Chemistry
Minor: Philosophy
Concentration: Applying Mathematical Methods
GPA: 3.19/4.00 - transcript

City High School 2002-2007

GPA: 3.69/4.00 - transcript


Instrumentation Scientist 2018-present

University of Wisconsin-Madison
  • Manage an instrumental "makerspace" for the Chemistry department.
  • Maintain an inventory of over 1000 types of small electronic components.
  • Serve as a mentor to graduate students and undergrads who undertake instrumental design projects.
  • Create custom scientific instrumentation for researchers and educators throughout the department.

Graduate Research Assistant 2011-2018

John C. Wright Group
  • Used ultrafast spectroscopy to research semiconductor systems, with a focus on solar energy candidates.
  • Designed and constructed software tools to collect and process multidmensional spectra.
  • Designed and constructed optomechanical and optoelectronic hardware.
  • Developed novel algorithms to streamline optical paramteric amplifier tuning procedures.
  • Maintained and conducted experiments on a custom ultrafast laser system.
  • Contributed to general-purpose multidimensional spectra modeling software.
  • Taught fellow students how to use instruments.
For more information, see my dissertation: Development of Frequency Domain Multidimensional Spectroscopy with Applications in Semiconductor Photophysics

Undergraduate Researcher (Plasmonics) 2009-2011

Matthew J. Cote Group
  • Designed and constructed a combined total internal reflection / atomic force microscope.
  • Coordinated work with my advisor and other staff and faculty.
For more information, see my thesis: Investigating Plasmons with Total Internal Reflection Microscopy

Undergraduate Researcher (Neuroscience) 2008

Michael Dailey Group
  • Dissected and prepared mouse brain samples for in-vivo microgial imaging studies.
  • Trained to utilize confocal microscopy setup

High School Researcher (Epigenetics) 2007

Peter L. Nagy Group
  • Designed and created plasmid, taught myself techniques from reference materials.
  • Inserted plasmid into yeast.


  1. The yaq project: Standardized software enabling flexible instrumentation

    Sunden, K. F.; Kohler, D. K.; Meyer, K. A.; Cruz Parrilla, P. L.; Wright, J. C.; and Thompson, B. J.
    Review of Scientific Instruments (2023)
    • Invented a new, standardized way of communicating with hardware peripherals.
    • Software is highly modular, configurable.
    • Used by multiple research groups from different fields.
    • Collaborated with others around the world to "build bridges" between adjacent software projects.
    • Project continues to grow after publication, with documentation at
  2. The Wisconsin Oscillator: A Low-Cost Circuit for Powering Ion Guides, Funnels, and Traps

    Kregel, S. J.; Thompson, B. J.; Nathanson, G. M.; and Bertram, T. H.;
    Journal of the American Society for Mass Spectrometry (2021)
    • Designed and constructed low-cost high voltage MHz oscillator based on a resonant LC circuit.
    • Design is appropriate for a variety of simple ion guides in mass spectrometry and adjacent specialties.
    • Scientists previously used expensive and hard-to-repair commercial devices to drive ion guides.
    • Circuit is also low power, suitable for battery powered or field operations.
    • All fabrication files publicly avaliable on GitHub.
  3. Versatile Open-Source Photoreactor Architecture for Photocatalysis Across the Visible Spectrum

    Lampkin, P. P.; Thompson, B. J.; and Gellman, S. H.;
    Organic Letters (2021)
    • Designed and constructed low-cost 3D-printed photoreactor.
    • Optimized for customization: choice of wavelength, reaction vessel and incorporation of other sensors.
    • Made many reactors for researchers and educators throughout the Chemistry Department.
    • Taught graduate students how to make their own reactors.
    • Made all design files publicly avaliable on github.
  4. Multichannel gas-uptake/evolution reactor for monitoring liquid-phase chemical reactions

    Salazar, C. A.; Thompson, B. J.; Knapp, S. M. M.; and Stahl, S. S.;
    Review of Scientific Instruments (2021)
    • Designed and constructed novel chemical reactor.
    • Incorporated pressure transducers and appropriate ADCs for high sensitivity to small headspace pressure changes.
    • Designed integrated reaction cell and heating block with integrated temperature control.
    • Built custom software with graphical user interface for control and data recording.
    • Reactor is used heavily by organic chemists from multiple research groups.
    • Made all design files publicly avaliable on github.
  5. The XyloTron: Flexible, Open-Source, Image-Based Macroscopic Field Identification of Wood Products

    Ravindran, P.; Thompson, B. J.; Soares, R. K.; and Wiedenhoeft, A. C.;
    Frontiers in Plant Science (2020)
    • Designed and constructed an all-in-one digital imaging device: the XyloScope.
    • Designed a custom internal illumination system with visible and ultraviolet options.
    • Lighting system can be moved along a set of rails that also supply power.
    • When combined with machine learning tools developed by coauthors, the XyloScope forms a complete automated wood identification system.
    • Code and hardware designs freely available and open source.
    • Hardware designed using 3D printed pieces and off-the-shelf components for facile reproduction.
  6. WrightTools: a Python package for multidimensional spectroscopy

    Thompson, B. J.; Sunden, K. F.; Morrow, D. J.; Kohler, D. D.; and
    Wright, J. C.;

    The Journal of Open Source Software (2019)
    • Designed a python-based toolkit for multidimensional spectroscopy.
    • Single processing toolkit for wide variety of instrumental data, built to be extensible as more data-types become relevant.
    • Offers specialized interactions, such as transformations, that are particularly suited to multidmensional spectroscopy.
    • Prior to JOSS publication, WrightTools directly enabled no fewer than eleven publications.
    • Fully open source project, with continuing development on GitHub.
    • Central package used as a data management pipeline by other packages simulating and acquiring multidimensional spectra.
    • Complete, "living" documentation at
  7. Three Dimensional Triply Resonant Sum Frequency Spectroscopy Revealing Vibronic Coupling in Cobalamins: Toward a Probe of Reaction Coordinates

    Handali, J. D.; Sunden, K. F.; Thompson, B. J.; Neff-Mallon, N. A.;
    Kaufman, E. M.; Brunold, T. C.; and Wright, J. C.;

    The Journal of Physical Chemistry A (2018)
    • For the first time, achieved true three-dimensional frequency TRSF spectroscopy.
    • Analyzed results carefully in context of prior spectroscopic work on Cobalamins.
    • Raw data and code freely available on the open science framework.
  8. Resonant Third-Order Susceptibility of PbSe Quantum Dots Determined by Standard Dilution and Transient Grating Spectroscopy

    Kohler D. D.; Thompson, B. J.; and Wright, J. C.;
    The Journal of Physical Chemistry C (2018)
    • Extracted the quantitative third-order susceptibility of PbSe quantum dots through a method of standard dilution.
    • After accounting for differences in pulse width and experimental geometry, we found agreement between our measured susceptibility and prior measurements.
    • Our internal standard methodology should be generally applicable to nonlinear spectroscopy.
    • Raw data and code freely available on the open science framework.
  9. WrightSim: Using PyCUDA to Simulate Multidimensional Spectra

    Sunden, K. F.; Thompson, B. J.; and Wright, J. C.;
    Proceedings of the 17th Python in Science Conference (2018)
    • Developed unique Python package to simulate multidimensional spectra.
    • First openly licensed package of its kind.
  10. Exploring Electronic Structure and Order in Polymers via Single-Particle Microresonantor Spectroscopy

    Horak, E. H.; Rea, M. T.; Heylman, K. D.; Gelbwaser-Klimovsky, D.; Saikin, S. K.; Thompson, B. J.; Kohler, D. D.; Knapper, K. A.; Wei, W.; Pan, F.; Gopalan, P.; Wright, J. C.; Aspuru-Guzik, A.; and Goldsmith, Randall H.
    Nano Letters (2018)
    • Performed three-pulse photon echo experiments on a conductive polymer.
    • Developed model and performed lineshape analysis to interrogate ultrafast processes in the material.
    • Raw data and code freely available on the open science framework.
  11. Frequency-domain coherent multidimensional spectroscopy when dephasing rivals pulsewidth: Disentangling material and instrument response

    Kohler, D. D.; Thompson, B. J.; and Wright, J. C.
    The Journal of Chemical Physics (2017)
    • Applied numerical model to simple system to explore artifacts of mixed-domain nonlinear spectroscopy
    • Defined new strategies to extract desired information despite these artifacts.
    • Raw data and code freely avaliable on the open science framework.
  12. Measurement of Ultrafast Excitonic Dynamics of Few-Layer MoS2 Using State-Selective Coherent Multidimensional Spectroscopy

    Czech, K. J.; Thompson, B. J.; Kain, S.; Ding, Q.; Shearer, M.; Hamers, R. J.; Jin, S.; and Wright, J. C.
    ACS Nano (2015)
    • Analyzed three-dimensional frequency-frequency-delay transient grating data.
  13. Solution Growth of Single Crystal Methylammonium Lead Halide Perovskite Nanostructures for Optoelectronic and Photovoltaic Applications

    Fu, J.; Meng, F.; Rowley, M. B.; Thompson, B. J.; Shearer, M. J.; Ma, D.; Hamers, R. J.; Wright, J. C.; and Jin, S.
    Journal of the Americal Chemical Society (2015)
    • Performed transient reflectance spectroscopy.
  14. Ionization of High-Density Deep Donor Defect States Explains the Low Photovoltage of Iron Pyrite Single Crystals

    Caban-Acevedo, M.; Kaiser, N. S.; English, C. R.; Liang, D.; Thompson, B. J.; Chen, H.-E.; Czech, K. C.; Wright, J. C.; Hamers, R. J.; and Jin, S.
    Journal of the Americal Chemical Society (2014)
    • Performed transient reflectance spectroscopy.


  1. Scientific Software Development: A Pragmatic Approach

    Invited Speaker
    University of Colorado Boulder Department of Chemistry (2020)
    Boulder, CO USA
  2. Nonlinear Multidimensional Spectroscopy

    Chaos and Complexity Seminar (2017)
    Madison, WI USA
  3. A Robust, Fully Automated Algorithm to Collect High Quality OPA Tuning Curves

    Conference for Coherent Multidimensional Spectroscopy (2016)
    Groningen, the Netherlands
  4. Utilizing Coherent Multidimensional Spectroscopy to Investigate Nanomaterials for Solar Energy Generation

    Midwest Universities Analytical Chemistry Conference (2012)
    Madison, WI USA
  5. Spectroscopic Investigation of Plasmonic Nanoparticles

    Bates College Mount David Summit (2011)
    Lewiston, ME USA


Graduate Chemical Instrumentation:
Design & Control
2017, 2019-2020

Teaching assistant, 1 semester. Lab manager, 2 semesters.
  • Led laboratory section of course.
  • Introduced graduate students to basic electronics skills such as breadboarding, oscilliscope usage, component choice, and circuit analysis.
  • Assisted students during extended independent instrument design and construction.
  • Assisted in course design and improvement.

Fundamentals of Analytical Science
(Quantitative Analysis)

Teaching assistant, 1 semester.
  • Led laboratory and discussion sections for honors section.
  • Prepared worksheets and homework keys.
  • Contributed to staff notes for future teaching assistants.

Graduate Instrumental Analysis 2012, 2015

Teaching assistant, 2 semesters.
  • Led laboratory section of course.
  • Prepared homework assignments and led homework review sessions.
  • Lectured in professor's absence.
  • Switched course from mathcad to Python using Jupyter notebooks, introducing first-year graduate students to script-based programming.

Undergraduate Research Mentor 2012-2013, 2015-2017

6 semesters.
  • Designed appropriate experiments that were complementary to my own research.
  • Introduced undergraduates to spectroscopy, programming, and instrument design.
  • Advised students in coursework and future directions.

General Chemistry II 2011-2012

Teaching assistant, 2 semesters.
  • Coordinated two sections: total of ~50 students in each semester.
  • Led laboratory section of course.
  • Designed and led weekly discussion sections.

General Chemistry I 2010-2011

Peer science leader, 2 semesters.
  • Designed and led class-wide review sessions.
  • Assisted in first trials of new peer leadership program at Bates College.
  • Attended regular meetings to share teaching strategies with other peer leaders.


SciPy Conference 2020


Science Olympiad 2019-2020

  • Lead "mechatronics" section of region-wide science and engineering competition for middle- and high-school students (2019).
  • Coached "detector building" team of high-school students (2020).
  • Designed and administered exam testing microcontroller programming and basic circuit design and construction.
  • Created and curated real electronic hardware for use during test.
  • See

PEOPLE Program 2017, 2019

  • "Pre-college Enrichment Opportunity Program for Learning Excellence"
  • Program for low-income, first generation prospective college students.
  • Taught high school students about electronics, science, and what it is like to be an analytical chemist.
  • Designed and created circuit boards for students to fill with components and take home.

Science Bowl 2017, 2019

Scientific Judge & Moderator
  • Judged middle school students in statewide science-knowledge competition.
  • Winning team proceeded to national competition.

Plasma Group Python Introduction 2017

  • Helped introduce a group of faculty and gradute students to Python for data analysis.
  • Created lesson sections and chose topics.
  • Group was switching to Python from IDL.
  • Introduction consisted of weekly meetings across several months.

McElvain Committee 2013-2014

  • Graduate student committee to choose seminar speakers.

OutFront 2009-2010

  • Held weekly meetings, organized social and political events.
  • For the first time, organized and executed collaborative events with other local LGBTQ groups in Lewiston ME.

Freewill Folk Society 2008-2011

  • Contradance club, offering alcohol-free community-engaging social activity to college students.
  • Reorganized club structure, recruited other students to new club positions.
  • Organized monthly folk dances, bringing in bands and callers.
  • See publication in Lewiston Sun Journal: "Dancing to a different beat"


GSFLC Mentor Award 2022, 2023

Awarded by Graduate Students at the University of Wisconsin-Madison for outstanding mentorship of young researchers. Won twice: 2022 and 2023.

Nominated: Letters & Science Early Career Award 2020

Nominated by Chemistry Department faculty, graduate students, and postdocs for outstanding performance, promise of future contributions, and a high degree of professionalism. See letter from the Dean of Letters & Sciences.

Roger Carlson Award 2017

Awarded by the University of Wisconsin Chemistry department for excellence in research.

James W. Taylor Excellence in Teaching Award 2016

Selected by University of Wisconsin Chemistry students and faculty as one of the most outstanding teaching assistants of the 2015-2016 school year.

Rodney F. Johonnot Graduate Award 2011

Selected by Bates College faculty as most deserving of aid in furthering his or her studies in professonal or postgraduate work.

Bates College Key 2011

Awarded by Bates College faculty and staff to 20 students in each graduating class based on academic standing, character, campus and community service, leadership, and future promise.

President's Excellence Award 2007

Awarded for high achievement in High School academics.

Science National Honor Society 2007

Awarded for high achievement in science within High School.

National Honor Society 2007

Awarded for scholarship, leadership, service and character during High School.