High School Researcher (Epigenetics) 2007

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

PUBLICATIONS

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 yaq.fyi.

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 wright.tools.

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.

PRESENTATIONS

1. Scientific Software Development: A Pragmatic Approach

   Invited Speaker
   University of Colorado Boulder Department of Chemistry (2020)
   Boulder, CO USA

2. Nonlinear Multidimensional Spectroscopy

   Presentation
   Chaos and Complexity Seminar (2017)
   Madison, WI USA

3. A Robust, Fully Automated Algorithm to Collect High Quality OPA Tuning Curves

   Poster
   Conference for Coherent Multidimensional Spectroscopy (2016)
   Groningen, the Netherlands

4. Utilizing Coherent Multidimensional Spectroscopy to Investigate Nanomaterials for Solar Energy Generation

   Poster
   Midwest Universities Analytical Chemistry Conference (2012)
   Madison, WI USA

5. Spectroscopic Investigation of Plasmonic Nanoparticles

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

TEACHING EXPERIENCE