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Computational Biophysicist - Postdoctoral Researcher

💼 Graduate Job


🤑 $108.8K

AI generated summary

  • You need a PhD in computational sciences with experience in molecular dynamics, free energy calculations, enhanced sampling, and machine learning. Proficiency in Python or C++, high-performance computing, and strong communication skills are a must. Plus, experience in collaborating with experimental biologists and developing machine-learning models.
  • You will conduct advanced research, develop high-performance computing tools, collaborate with external partners, analyze molecular dynamics datasets, and present results at scientific meetings.

Graduate Job

Science, Software EngineeringLivermore


  • We have an opening for a highly motivated Postdoctoral Researcher to conduct research in computational biophysics and simulation, specifically with expertise in molecular dynamics simulations, enhanced sampling of rare events, machine learning, statistical analysis of molecular dynamics simulations and software development. You will be an integral member of an interdisciplinary team working with other national laboratories and companies. 
  • You will be responsible for developing new software algorithms, writing code, understanding the requirements for each simulation campaign, and creating innovative analysis tools. You will work with a team of computational biologists, physicists, material scientists, experimental biologist and computer scientists to create a novel machine-learned capability for modeling the conformational dynamics of protein complexes involved in cellular signaling pathways. This position is in the Biochemical and Biophysical Systems group of the Biosciences and Biotechnology Division.


  • PhD in computer science, computational biology, computational physics, computational chemistry or equivalent combination of education and related experience.
  • Knowledge and experience in developing novel machine-learning based methods for enhancing the sampling of rare events, using free energy methods to model protein-protein binding affinities and developing statistical analysis of large-scale molecular dynamics datasets.
  • Experience at the postdoctoral or higher level in the fields of molecular dynamics simulations, free energy calculations, transition path theory, enhanced sampling methods, machine learning, and statistical mechanics.
  • Demonstrate advanced computer skills including programming experience with Python or C++ in a UNIX environment as well as experience using large high-performance computing clusters, including the use of job schedulers such as SLURM, PBS or Flux.
  • Ability to work independently on defined research projects, as well as a member of a large team.
  • Ability to develop independent research projects as demonstrated through publication of peer-reviewed manuscripts in the field of molecular modeling and simulations.
  • Ability to travel, as necessary, to interact with sponsors, customers and collaborators.
  • Proficient written, verbal communication and interpersonal skills necessary to deliver presentations, prepare written reports and to interact with a diverse set of scientists, engineers, and other technical and administrative staff.
  • Qualifications We Desire:
  • Experience in collaborating with experimental biologists as well as understanding and using experimental data in combination with computational research.
  • Experience in developing and training machine-learning based models in high-performance computing systems.
  • Experience computing binding affinity, stability and/or other metrics using scoring functions like Rosetta.
  • Experience with parallel programming tools used to develop high performance code on GPU’s and/or CPU’s, such as OpenMP, MPI, CUDA or OpenCL.
  • Experience using collaborative programming workflows and tools such as git, Gitlab, or subversion.

Education requirements

Currently Studying

Area of Responsibilities

Software Engineering


  • Conduct advanced independent research to create a novel high performance computing capability for predicting the binding affinities and kinetics of protein-protein interactions at the atomistic and coarse-grained levels.
  • Contribute to the software development of high-performance computing tools for robust calculations of binding free-energies and kinetics.
  • Develop novel machine-learning based path-sampling methods for estimating protein binding rates and free energies.
  • Develop new workflows to analyze and visualize results from complex and large-scale molecular dynamics datasets.
  • Develop collaborations with external partners (Universities, Industry, other National Laboratories) to advance computational biology simulation efforts.
  • Prepare complex and detailed weekly progress reports to support project needs and deadlines. Prepare complex written analyses and verbal briefings, and present research results at scientific meetings.
  • Develop new and innovative research methods relevant to the needs of Laboratory programs and/or external funding agencies and interact with senior project staff and management to influence programmatic decisions.
  • Write proposals, secure funding, and establish independent research projects.


Work type

Full time

Work mode





108840 USD


  • Included in 2024 Best Places to Work by Glassdoor!
  • Flexible Benefits Package
  • 401(k)
  • Relocation Assistance
  • Education Reimbursement Program
  • Flexible schedules (*depending on project needs)
  • Inclusion, Diversity, Equity and Accountability (IDEA)