Kyle Sunden

Madison, WI

(269) 615-0174

contact@ksunden.space

Education

University of Wisconsin–Madison

2016-present

In pursuit of a PhD in Analytical Chemistry

GPA: 3.83 transcript

Kalamazoo College

2010-2016

BA in Chemistry (ACS Approved Curriculum)

BA in Computer Science

Minor in Mathematics

F.W. Heyl Scholar Full-ride academic scholarship awarded for excellence in mathematics and sciences

Enrolled concurrent with High School as a Dual Enrollment student from 2010-2012.

Magna Cum Laude

Honors in Chemistry

Honors in Computer Science

GPA: 3.90 transcript

Gull Lake High School

2008-2012

Kalamazoo Area Mathematics and Science Center

2008-2012

Experience

Graduate Research Assistant: Spectroscopy

2016-Present Madison, WI

John C. Wright Group

  • Maintained software infrastructure for data acquisition, representation, manipulation, and simulation
  • All software work is open source and available on GitHub or GitLab

Undergraduate Researcher: Computational Chemistry

2014-2016 Kalamazoo, MI

Laura Lowe Furge Group

  • Performed computational analysis of human Cytochrome P450 2D6, a drug metabolizing enzyme
  • Used the AMBER 14 molecular dynamics suite with Pytraj and CAVER 3.0 to analyze results
  • Completed a Senior Individualized Project, investigating polymorphic variants and their interactions with bufuralol, a substrate of CYP2D6
  • Published analysis of mechanism based inactivation in PLoS ONE (DOI: 10.1371/journal.pone.0108607)
  • Presented findings to the Great Lakes Drug Metabolism & Disposition Group, May 2015

Teaching Assistant: Computer Science

2013-2016 Kalamazoo, MI

Kalamazoo College Computer Science Department

  • Departmental Student Advisor, chosen by the department to serve as peer resource to underclassmen as they explore academic options
  • Aid in-class activities for Introduction to Computer Science, Pictures and Sounds, Introduction to Programming, Data Structures, Mobile Computing, and Building the Internet
  • Hold regular office hours to assist and teach students in all classes in the department

Laboratory Teaching Assistant: Chemistry

2014-2015 Kalamazoo, MI

Kalamazoo College Chemistry Department

  • Selected by Dr. Stevens-Truss to share knowledge of computational methods for medicinal chemistry laboratory, including visualizing protein structure and docking substrates with Autodock Vina
  • Oversaw laboratory experiments for introductory chemistry

Open Source Contributions

Wright Group Projects

  • WrightTools

    • Primary maintainer
    • HDF5 based library for representing and manipulating multidimensional datasets
    • Read data from commercial manufacturers and custom instruments into a standardized format
    • Tools for combining, splitting, and adjusting multidimensional datasets
    • Provide easy plotting for rapid data quality assessment and for publication quality figures

  • attune

    • Primary maintainer, original author
    • Represent tuning curves for Optical Parametric Amplifiers
    • Record a history of changes to the tuning curves

  • yaqc-cmds

    • Primary maintainer
    • Custom GUI program to perform multidimensional spectroscopy acquisitions
    • Provides a queue of acquisitions
    • Allows for acquisition queue manipulation including adding new acquisitions and reordering
    • Provides live plots for rapid feedback as data is collected
    • Records data into the WrightTools “wt5” format

  • bluesky-cmds

    • Primary maintainer, original author
    • forked from yaqc-cmds, modified to use bluesky-queueserver
    • Allows for acquisition queue manipulation including adding new acquisitions and reordering
    • Provides live plots for rapid feedback as data is collected
    • Is decoupled from the acquisition/recording process, and thus can be closed without consequence

  • WrightSim

    • Original author
    • Simulate experiments performed by the Wright Group
    • Used algorithmic improvements to gain an order of magnitude improvement over previous implementation
    • (Optional) CUDA implementation to provide an additional order of magnitude performance
    • Recognized as one of the top three projects in the Fall 2017 University of Wisconsin High Performance Computing class

yaq

Bluesky Collaboration Projects

  • yaqc-bluesky

    • Maintainer
    • Implement a Bluesky device wrapping a yaq daemon
    • Map yaq concepts into the Bluesky abstraction

  • wright-plans

    • Maintainer and Original Author
    • Bluesky plans to perform tasks required by the Wright Group
    • Enhanced Unit support for many default Bluesky plans
    • Added capability to set additional hardware to track linear combinations of other hardware
    • Implement specialized plans for tuning Optical Parametric Amplifiers

  • bluesky-hwproxy

    • Maintainer and Original Author
    • Provide TCP based access to bluesky device information

  • bluesky

    • Contributor
    • Wrote the PEP 544 compliant Protocol classes to allow duck typing with static type checks for common bluesky device behavior

  • bluesky-queueserver

    • Early adopter/tester

  • bluesky-in-a-box

    • Collection of docker containers to run the services required for bluesky-queueserver
    • Uses Docker Compose to coordinate dependencies
    • Includes running Mongo and Redis servers
    • Includes custom data writer to the WrightTools “wt5” data format

Scientific Python Ecosystem

  • pyqtgraph

    • Maintainer, Release Manager
    • Focus on easing maintenance burden of the code base
      • Use static analysis tools to find unused or broken code
    • Use automation to ease release procedure
    • Rework CI to use Github Actions
    • Relieve PR backlog through code review and resolving merge conflicts

  • matplotlib

    • Contributor
    • Test pre-release code against my libraries to catch bugs/deprecations early
    • Track and fix bugs when found

  • numpy

    • Contributor
    • Fixed 128-bit float printing on ARM architecture

  • JOSS Reviewer

  • Conda Forge Packaging

    • Update Conda Forge packages for most of the projects I maintain

  • Many smaller bug fixes/documentation fixes

Publications

  1. 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)

    DOI: 10.21105/joss.01141

    Github: WrightTools

    BibTeX Citation

    @article{Thompson_2019,
 author = {Thompson, Blaise and Sunden, Kyle and Morrow, Darien and Kohler, Daniel and Wright, John},
 title = {WrightTools: a Python package for multidimensional spectroscopy},
 journal = {Journal of Open Source Software},
 publisher = {The Open Journal},
 year = {2019},
 month = {jan},
 number = {33},
 volume = {4},
 pages = {1141},
 url = {https://doi.org/10.21105%2Fjoss.01141},
 doi = {10.21105/joss.01141}
}

  2. 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)

    DOI: 10.1021/acs.jpca.8b07678

    OSF: https://osf.io/x4w2p

    BibTeX Citation

    @article{Handali_2018c,
 author = {Handali, Jonathan D. and Sunden, Kyle F. and Thompson, Blaise J. and Neff-Mallon, Nathan A. and Kaufman, Emily M. and Brunold, Thomas C. and Wright, John C.},
 title = {Three Dimensional Triply Resonant Sum Frequency Spectroscopy Revealing Vibronic Coupling in Cobalamins: Toward a Probe of Reaction Coordinates},
 journal = {The Journal of Physical Chemistry A},
 publisher = {American Chemical Society (ACS)},
 year = {2018},
 month = {oct},
 number = {46},
 volume = {122},
 pages = {9031--9042},
 url = {https://doi.org/10.1021%2Facs.jpca.8b07678},
 doi = {10.1021/acs.jpca.8b07678}
}

  3. Interference and phase mismatch effects in coherent triple sum frequency spectroscopy

    Handali, J. D.; Sunden, K. F.; Kaufman, E. M.; and Wright, J. C.

    Chemical Physics (2018)

    DOI: 10.1016/j.chemphys.2018.05.023

    OSF: https://osf.io/m9ycr

    BibTeX Citation

    @article{Handali_2018,
 author = {Handali, Jonathan D. and Sunden, Kyle F. and Kaufman, Emily M. and Wright, John C.},
 title = {Interference and phase mismatch effects in coherent triple sum frequency spectroscopy},
 journal = {Chemical Physics},
 publisher = {Elsevier BV},
 year = {2018},
 month = {aug},
 volume = {512},
 pages = {13--19},
 url = {https://doi.org/10.1016%2Fj.chemphys.2018.05.023},
 doi = {10.1016/j.chemphys.2018.05.023}
}

  4. 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)

    DOI: 10.25080/Majora-4af1f417-00c

    Github: WrightSim

    BibTeX Citation

    @inproceedings{Sunden_2018,
 author = {Sunden, Kyle and Thompson, Blaise and Wright, John},
 title = {WrightSim: Using PyCUDA to Simulate Multidimensional Spectra},
 publisher = {SciPy},
 year = {2018},
 url = {https://doi.org/10.25080%2Fmajora-4af1f417-00c},
 doi = {10.25080/majora-4af1f417-00c},
 booktitle = {Proceedings of the 17th Python in Science Conference}
}

  5. Molecular Dynamics of Human Cytochrome P450 2D6 to Investigate Effects of Polymorphic Variation on Metabolism of Bufuralol

    Sunden, K. F.; and Furge, L. L.

    Senior Individualized Project at Kalamazoo College (2015)

    BibTeX Citation

    @misc{sunden_2015,
 author = {Sunden, Kyle F. and Furge, Laura Lowe},
 title = {Molecular Dynamics of Human Cytochrome P450 2D6 to Investigate Effects of Polymorphic Variation on Metabolism of Bufuralol},
 institution = {Kalamazoo College},
 year = {2015},
 url = {http://hdl.handle.net/10920/30372}
}

  6. Molecular Dynamics of CYP2D6 Polymorphisms in the Absence and Presence of a Mechanism-Based Inactivator Reveals Changes in Local Flexibility and Dominant Substrate Access Channels

    de Waal, P. W.; Sunden, K. F.; and Furge, L. L.

    PLoS One (2014)

    DOI: 10.1371/journal.pone.0108607

    BibTeX Citation

    @article{de_Waal_2014,
 author = {de Waal, Parker W. and Sunden, Kyle F. and Furge, Laura Lowe},
 title = {Molecular Dynamics of CYP2D6 Polymorphisms in the Absence and Presence of a Mechanism-Based Inactivator Reveals Changes in Local Flexibility and Dominant Substrate Access Channels},
 journal = {PLoS ONE},
 publisher = {Public Library of Science (PLoS)},
 year = {2014},
 month = {oct},
 number = {10},
 volume = {9},
 pages = {e108607},
 url = {http://dx.doi.org/10.1371/journal.pone.0108607},
 doi = {10.1371/journal.pone.0108607},
 editor = {Papaleo, Elena}
}

Presentations

  1. Yet Another Acquisition: The Yaq Daemon Interface for Heterogeneous Instrumentation

    Sunden, K. F.; Thompson, B. J.; Wright, J. C.

    ‘Poster’ Presentation

    19th Science in Python Conference (2020)

    Held Virtually

  2. Birds of a Feather Driving Hardware for Instrumentation

    Sunden, K. F.; Thompson, B. J.

    Panel Discussion Video

    19th Science in Python Conference (2020)

    Held Virtually

  3. pyqtgraph project update

    Sunden, K. F.

    Presentation Video

    19th Science in Python Conference (2020)

    Held Virtually

  4. WrightSim: Using PyCUDA to Simulate Multidimensional Spectra

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

    _Poster_

    17th Science in Python Conference (2018)

    Austin, TX, USA

  5. Molecular Dynamics of Human CYP2D6 Provides Insights Into Structure, Function, and Susceptibility to Inactivation of Polymorphic Variants of CYP2D6

    Sunden, K. F.

    Oral Presentation

    Great Lakes Drug Metabolism and Disposition Group (2015)

    Ann Arbor, MI, USA

(Last modified on April 14, 2022)