Postdoctoral Research Associate: Computational Crystallography (SSRL)

Postdoctoral Research Associate Position in Computational Crystallography

The SSRL (Stanford Synchrotron Radiation Lightsource) Directorate at SLAC National

Accelerator Laboratory invites applications for a Postdoctoral Research Associate to join a DOE-

funded project titled PECS: Protein Ensemble Compound Screening for Biothreat Response and

Drug Discovery.

This project seeks to expand the capabilities of the Macromolecular Crystallography Group at

SSRL, enabling users to routinely capture, extract, and apply protein ensemble information from

X-ray diffraction data using novel machine learning (ML), advanced simulation, and high-

performance computing (HPC) techniques.

The successful candidate will specifically lead the Dynamics Optimized High Throughput

Workflows component of the PECS project. This involves developing automated, real-time

pipelines and advanced algorithms to autonomously steer and optimize time-resolved, compound

screening, and/or other high throughput crystallography experiments.

This role offers a unique opportunity to gain expertise in the intersecting disciplines of structural

biology, macromolecular crystallography, data science and high-performance computing at a

DOE light source user facility.

Key responsibilities of this role are focused on software architecture, algorithm development,

and data analysis:

• Algorithmic Steering: Develop and benchmark advanced algorithms for automatic

experiment steering, using real-time feedback from supervised ML models to optimize

beamtime and maximize the targeted detection of structural intermediates.

• Forward Simulations: Adapt existing forward diffraction simulation pipelines to

produce model training data for various experimental scenarios.

• HPC Implementation: Implement and optimize GPU-accelerated diffraction data

reduction and analysis algorithms to achieve ultra-fast processing times, further enabling

real-time decision-making during experiments.

• Software Integration: Design and implement the software architecture required to

integrate laboratory automation systems and beamline control with the real-time data

analysis and experiment steering routines.

• Scientific Validation & Collaboration: Collect, analyze, and publish time-resolved

compound screening data in collaboration with beamline staff and key beamline users.

• Dissemination: Write a high-impact paper promoting the new SSRL resource, publish

key results, and present research at a common crystallography conference.

Required qualifications

• Ph.D. in a relevant computational or experimental field (e.g., Physics, Computational

Chemistry, Computer Science, Bioinformatics, Structural Biology, or a related discipline)

completed within the last three years, or confirmation of Ph.D. requirements completion

prior to the start date.

• Strong foundation in structural biology, macromolecular crystallography, or a related

discipline, as demonstrated through publication history.

• Extensive experience with Python and professional software development practices

(including test-driven code development and version control).

• Familiarity with computational methods and concepts in optimization and machine

learning.

• Excellent data processing, analysis, organization, and interpersonal skills, with the ability

to work effectively in a large, multi-disciplinary team.

• Proficiency working in a Unix shell environment

Preferred qualifications

• Familiarity with AI/ML frameworks such as PyTorch, TensorFlow, or JAX.

• Demonstrated experience/interest with GPU programming (e.g., CUDA, OpenCL).

• Prior experience with diffraction data analysis software (e.g., DIALS, XDS, Phenix).

• Knowledge of SLURM or similar for job management in a compute cluster environment.

• Experience or strong interest in beamline operations or scientific user facilities.

This is a fixed-term staff position, expected to be a 2-year appointment with the possibility of

extension up to a full 32 months, contingent upon project needs and funding.

Application materials should include a cover letter, a statement of research area including a

summary of accomplishments, a curriculum vitae (CV), a list of publications, and names of

three references for future letters of recommendation.

Please email all application materials to Dr. Derek Mendez; [email protected]

SLAC is a U.S. Department of Energy (DOE) laboratory operated by Stanford University

and based in Menlo Park, CA. The Macromolecular Crystallography Group is part of the

Structural and Molecular Biology division of the SSRL directorate.