Postdoctoral Research Associate

CHARMM is a versatile program for atomic-level simulation of many-particle systems, particularly macromolecules of biological interest.

- M. Karplus

Michigan State University, East Lansing, MI

Position Summary:

The Dickson, Feig, Vermaas, Wei, Woldring laboratories together form Team Green, a collaborative research effort funded by DARPA to predict protein structural ensembles, ligand binding affinities, and protein functions through existing bioinformatics approaches and an extensive simulation campaign. To support these efforts, Team Green is looking for up to 4 qualified postdoctoral research associates to apply molecular simulation and mathematical methods to extend and develop these predictive tools into a broadly usable pipeline.

Drs. Wei and Woldring will expect candidates with research experience and record in machine learning and deep learning modeling of biomolecular systems, structural and/or sequence bioinformatics. Research backgrounds in computational biophysics or mathematical AI are welcome.

Required Degree:
Doctorate - Biophysics, Biochemistry, Physics, Computer Science, Mathematics, Chemical Engineering, or a related field

Minimum Requirements:

A publication record commensurate with career stage and field. Relevant prior research experience. This may be developing related AI/ML methods, or implementing, or running simulations at scale, depending on the group.

Desired

Qualifications:

Day to day, the expectation will depend on the research group a successful candidate is associated with. Drs. Dickson, Feig, and Vermaas will expect that the researcher has prior experience with a programming language such as python and Unix-based operating systems such as MacOS or Linux. These tools are essential to set up, carry out, and analyze molecular simulation trajectories, and to interact with high performance computing environments needed to run those trajectories.

Thus, previous experience with these tools is beneficial but not essential:

• Python libraries like Numpy, Scipy, Pandas, Pytorch, or Matplotlib
• A programmable molecular viewer such as VMD
• Simulation engines such as NAMD, CHARMM, OpenMM, AMBER, or GROMACS
• Basic familiarity with the linux terminal

Required Application Materials:
To best evaluate candidates, please provide a list of three recommenders so that the team can reach out when you advance to that stage in addition to your CV and cover letter.

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