Postdoctoral researcher

Project
PREP0004514

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.

Interpretable DNA/RNA Ensemble Quantification

Qualifications
  • A 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.
Research Proposal

Key responsibilities will include but are not limited to:

  • 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.
NIST Sponsor
Michael Zwolak
Group
Biophysical and Biomedical Measurement Group
Salary / Hourly Rate {Min}
$72,000.00
Schedule of Appointment
Full time
Start Date
Sponsor email
michael.zwolak@nist.gov
Work Location
Onsite NIST (Gaithersburg, MD)
Salary / Hourly rate {Max}
$72,000.00
Total Hours per week
40
End Date
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