PREP0004514 DNA RNA Ensemble Modeling Researcher

DNA/RNA Ensemble Modeling Researcher

Project Description:

This position will focus on theory and computation to classify DNA and RNA conformational ensembles using secondary-structure-based distance metrics and clustering. A central goal is to build hierarchical, interpretable ensemble representations that connect simulation-derived clusters to experimental measurements/observables and statistical-physics interpretation (e.g., energetic barriers and kinetic pathways). Work includes developing and validating analysis algorithms, implementing reproducible research software, and collaborating with experimental and device-focused teams to connect theory outputs to measurement needs.

Key Responsibilities: 

• Develop, test, and extend ensemble representations for DNA/RNA and relate these to experimental observables
• Implement and optimize secondary-structure distance metrics based on base-pair reorganization
• Build scalable clustering and model selection for large molecular dynamics datasets
• Presenting results at internal and external meetings and conferences
• Develop well-documented, reproducible research software and publish results

Desired Qualifications: 

• U.S. Citizen Preferred
• Ph.D. in physics, chemistry, biophysics, computational biology, applied mathematics, computer science, or a closely related field
• Demonstrated experience with biomolecular simulation and/or trajectory analysis (strong preference for nucleic acids: DNA/RNA)
• Experience with coarse-grained nucleic-acid models, e.g., oxDNA/oxRNA or closely related coarse-grained frameworks
• Practical understanding of clustering/unsupervised learning and distance-metric design
• Strong scientific programming (Python preferred; Julia a plus) and ability to write maintainable, version-controlled code
• Background in statistics/statistical physics; ability to interpret ensembles in terms of kinetics and free-energy landscapes
• Strong written and oral communication skills and ability to collaborate in a multidisciplinary team; experience analyzing experimental data from single-molecule and ensemble techniques is a plus

Other Details:

• Full-time: the participant is expected to work 40 hours a week
• Location: the participant will work at the NIST Gaithersburg Campus.
• Duration: this is expected to be a one-year position. Extensions are sometimes granted depending on the availability of funds.