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.