Exascale Computational Crystallographer Project Scientist

Discover your future at Berkeley Lab!

Berkeley Lab’s Molecular Biophysics & Integrated Bioimaging Division has an opening for an Exascale Computational Crystallographer Project Scientist. The Project Scientist, with a strong interest in high-performance computing and an intuitive feel for experimental data, will be affiliated with the Exascale Computing Project, specifically Nick Sauter’s Data Analytics for X-ray Free Electron Lasers (XFELs) group focusing on scientific software for X-ray crystallography.  The next decade of structural biology at the Linac Coherent Light Source (LCLS) will include groundbreaking advances in time-domain crystallography, performed at room temperature to preserve biologically relevant dynamic mechanisms.  Considering the anticipated scale of these datasets, we have an ambitious collaboration between SLAC, LANL, and LBNL to utilize national supercomputer facilities for near real-time analysis, in close collaboration with scientists at NERSC (also located in Berkeley). The Project Scientist will be positioned to launch into HPC careers at light sources or other experimental facilities.

The group’s projects will include:

1. Photosystem II, discovering the sequence of redox events leading to the release of molecular oxygen, using a combination of time-resolved crystallography and X-ray emission spectroscopy.  http://dx.doi.org/10.1038/s41586-018-0681-2

2. Examining the electronic environment of metalloenzyme catalytic metals, with detection based on anomalous scattering. http://dx.doi.org/10.1107/S2059798320000418

What You Will Do:

• Take the lead on developing and testing software for X-ray free-electron laser (XFEL) crystallography, using our previously developed packages (DIALS and cctbx.xfel) as a starting point.

• Develop a deep understanding of the hardware available for Exascale computing (including Perlmutter, Aurora, and Frontier), along with GPU accelerators.

• Work at the interface between supercomputer design teams, computer science groups, LCLS beamline scientists, and X-ray crystallography user groups. 

• Derive new algorithms to adapt to heterogeneous experimental designs.

• Deliver new features on time and in support of structural biology.

• Deliver DOE-mandated software development milestones on time, including tested code checked in to repositories, accompanied by written reports. 

• Write one first-author paper per year in scientific publications.

• Present work at conferences, and continuously communicate results to several collaborating groups.

• Support scheduled beam time data collections at remote global facilities.

What Is Required:

• Ph.D. in Biophysics, Bioinformatics, Mathematics, Computer Science, Engineering or Physical Sciences preferred, with at least 3 years of professional experience, or an equivalent combination of education and experience.

• We are looking for a practicing crystallographer or someone with bioimaging experience.

• Demonstrated ability to analyze complex problems with only broad supervision, develop strategies to solve specific problems, while running appropriate controls to validate the correct results.

• Experience in Python & C++

• Excellent oral and written communication skills.

• Proven ability to work effectively in an R&D environment as part of a cross-disciplinary coding team. O-O, version control and Agile are a plus.

Additional Desired Qualifications:

• Proven excellence in signal processing, image processing, and multivariate statistics.

• TensorFlow, PyTorch, machine learning, Linux, GPU (CUDA or OpenCL) 

 The posting shall remain open until the position is filled.

Notes: 

• This is a full time, 2 year, term appointment that may be renewed to a maximum of five years.

• Exempt (monthly paid) from overtime pay.

• Salary is commensurate with experience.

• This position may be subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.

• Work will be primarily performed at Lawrence Berkeley National Lab, 1 Cyclotron Road, Berkeley, CA.

Learn about us:

Molecular Biophysics & Integrated Bioimaging’s mission is to generate a mechanistic and predictive understanding of biological processes, by developing and applying molecular- and meso-scale visualization and advanced spectroscopies, enabling the control, manipulation and generation of biological function.

Berkeley Lab (LBNL) addresses the world’s most urgent scientific challenges by advancing sustainable energy, protecting human health, creating new materials, and revealing the origin and fate of the universe. Founded in 1931, Berkeley Lab’s scientific expertise has been recognized with 13 Nobel prizes. The University of California manages Berkeley Lab for the U.S. Department of Energy’s Office of Science.

Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision under 41 CFR 60-1.4.  Click here to view the poster and supplement: "Equal Employment Opportunity is the Law."