Employment
| Position | Duration |
|---|---|
| Panofsky Fellow SLAC National Accelerator Laboratory, Linac Coherent Light Source Principle Investigator: Franklin Fuller |
2017-Present |
| Ruth Kirschstein Postdoctoral Fellow Lawrence Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging Division Principle Investigator: Franklin Fuller Sponsor: Junko Yano |
2015-2017 |
| Chemistry Postdoctoral Fellow Lawrence Berkeley National Laboratory, Molecular Biophysics and Integrated Bioimaging Division Principle Investigator: Junko Yano & Vittal Yachandra |
2014-2015 |
| Graduate Student Research Assistant University of Michigan, Department of Biophysics Principle Investigator: Jennifer Ogilvie |
2009-2014 |
Technical Skills
| Skill | Examples |
|---|---|
| High Performance Parallel Computing | I have used DASK, mpi4py, and tensorflow.distribute along with queue systems like SLURM and LSF to write distributed analysis code to process X-ray data at XFEL facilities like LCLS and SACLA, using multiple (10s) CPUs and GPUs |
| Streaming Big Data Analysis | Rapid access to experimental data at XFEL facilities is available to sample data before it is written to intermediate disk storage. I used existing python-based infrastructure to monitor experimental data as it was being collected and designed a variational model specifically to update signal estimates from streamed data. |
| Implementation of Machine Learning Algorithms | I have written and customized Gaussian Process libraries and Neural Network libraries to process X-ray spectroscopic data using mainly pytorch and Tensorflow. I keep a close eye on the literature relating to variational models for continuous, high dimensional data. |
| Non-linear parametric optimization | In matlab, julia, and python I have made extensive use of gradient based non-linear fitting with gradients supplied by automatic differentiation or hand-built to recover useful parameters in physically inspired models, such as time decay analysis, fitting of geometry parameters in calibration, and small scale maximum likelihood signal estimation. |
| Simuation | I calibrate expectations and diagnoise model deficiencies by training models I intend to employ on real data by first studying them on detailed physical simulations of the problem domain. |
| Data Munging | I work mainly with sensor (float or integer valued) data, but these come in a variety of formats and datasets need to be filtered according to experimental condition as well as be stripped of outliers detected via a variety of disparate beam and acclerator diagnostics |
| Statistical Modeling | I mainly use variational approximations to estimate the marginal likelihood of the data via minimization of the evidence lower bound. This is a class of model useful to provide uncertain quantification for intermediate to large scale datasets. |
Leadership Experience
| Skill | Examples |
|---|---|
| Postdoctoral Researcher Mentorship | I have mentored two researchers (Anton Loukianov and Chantal Mustoe), teaching both mathematical underpinnings for Machine Learning methods as well as working with them to develop software implementations for these methods so they can be applied to experimental data. Both have used these experiences to go into Data Science careers now. |
| Undergradaute Mentorship | Through the Linac Coherent Light Source summer internship program, I mentored two undergraduate researchers, which involved planning an 10 week project to train them in applied data analysis, teaching both python-based analysis (mainly using numpy and pytorch) as well as mathematical modeling. |
| Collaborative Mentorship | I maintain close ties with my former group at Lawrence Berkeley National Laboratory, providing training to new postdoctoral researchers and graduate students on the instrumention I developed there and guidance in developing related instrumentation. |
| Proposal reviews commitees | I have served on research proposal review committees for SLAC, National Institue of Health, and the Department of Energy, where my role was to assess the quality of the proposed research plans. |
Education
| Degree | Completion Date |
|---|---|
| PhD Biophysics University of Michigan, Department of Biophysics Dissertation: Observations of Coherence in Oxygenic Photosynthesis Advisor: Jennifer Ogilvie |
August 2014 |
| BS Physics University of Minnesota, Department of Physics |
May 2008 |
| BA Mathematics University of Minnesota, Department of Mathematics Thesis: Reaction Diffusion in Protein Expression and Actin Polymerization Advisor: Richard Moeckel |
May 2008 |
Select Publications
Resonant X-ray Emission spectroscopy from broadband stochastic pulses at an X-ray free electron laser Fuller, F. D., Loukianov, A., et al. Communications Chemistry 2021; 4 (84)
Observation of Seeded Mn K beta Stimulated X-Ray Emission Using Two-Color X-Ray Free-Electron Laser Pulses Kroll, T., Weninger, C., Fuller, F. D., et al. PHYSICAL REVIEW LETTERS 2020; 125 (3)
Untangling the sequence of events during the S2 S3 transition in photosystem II and implications for the water oxidation mechanism. Ibrahim, M., Fransson, T., Chatterjee, R., Cheah, M. H., Hussein, R., Lassalle, L., Sutherlin, K. D., Young, I. D., Fuller, F. D., Gul, S., et al. PNAS 2020
Structures of the intermediates of Kok’s photosynthetic water oxidation clock. Kern, J., Chatterjee, R., Young, I. D., Fuller, F. D., et al. Nature 2018
X-ray Emission Spectroscopy as an in Situ Diagnostic Tool for X-ray Crystallography of Metalloproteins Using an X-ray Free-Electron Laser. Fransson, T., Chatterjee, R., Fuller, F. D., et al. Biochemistry 2018
Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Franklin D. Fuller, Sheraz Gul, et al. Nature Methods 2017; v 14.4, pp 443-449.
Structure of photosystem II and substrate binding at room temperature Young, I. D., Ibrahim, M., Chatterjee, R., Gul, S., Fuller, F. D., et al. Nature 2016; 540 (7633): 453
Concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem II Sierra, R. G., Gati, C., Laksmono, H., Dao, E. H., Gul, S., Fuller, F., et al. Nature Methods 2016; 13 (1)
Experimental Implementations of Two-Dimensional Fourier Transform Electronic Spectroscopy Fuller, F. D., Ogilvie, J. P. ANNUAL REVIEW OF PHYSICAL CHEMISTRY 2015; 66: 667–90
Vibronic coherence in oxygenic photosynthesis Fuller, F. D., Pan, J., et al. Nature Chemistry 2014; 6 (8): 706–11
Pulse shaping based two-dimensional electronic spectroscopy in a background free geometry Fuller, F. D., Wilcox, D. E., Ogilvie, J. P. OPTICS EXPRESS 2014; 22 (1): 1018–27
Conformational dynamics of single pre-mRNA molecules during in vitro splicing Abelson, J., Blanco, M., Ditzler, M. A., Fuller, F., et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY 2010; 17 (4): 504–U156