Scientist II/Senior Scientist, Computational Biophysics

Responsibilities

We are representing a confidential AI-driven life sciences organization seeking a computational biophysics expert to ensure molecular simulation and free-energy methods are scientifically rigorous, reliable, and suitable for automated drug discovery workflows.

In this role, you will:

• Define scientific requirements and validation standards for computational biophysics tools used in automated workflows, including acceptable inputs, assumptions, and decision-grade outputs
• Design and validate molecular simulation workflows for drug discovery, including MM/GBSA and free-energy perturbation methods for relative and absolute binding free energies (RBFE/ABFE)
• Establish standards for system setup, force field selection, molecular parameterization, equilibration, sampling, analysis, and quality control
• Build robust RBFE and ABFE workflows with automated checks for chemical-series compatibility, ligand-pose consistency, and other critical validation criteria
• Collaborate with research engineers to convert biophysics protocols into reliable tools, APIs, and guardrails for AI agent invocation
• Develop validation benchmarks and acceptance criteria for molecular dynamics and binding free-energy workflows
• Evaluate and integrate open-source molecular simulation packages, particularly OpenMM, OpenFE, and related tools
• Identify and mitigate failure modes across simulation setup, parameterization, sampling, analysis, and interpretation
• Provide expert guidance on when biophysics workflows are appropriate, what evidence they can support, and where limitations matter
• Partner with ML teams to refine molecular simulation methods as new experimental data becomes available
• Work with infrastructure teams to scale validated workflows across large GPU fleets with full reproducibility and traceability

What We're Looking For

Required qualifications:

• PhD or equivalent experience in computational biophysics, computational chemistry, chemical physics, biophysics, physics, chemistry, or related field
• Deep hands-on experience with molecular dynamics simulation, MM/GBSA, and free-energy perturbation methods for RBFE and ABFE
• Practical experience with open-source molecular simulation and free-energy packages, with strong preference for OpenMM and OpenFE
• Strong understanding of molecular system parameterization and validation of scientifically sound simulation setups
• Demonstrated history of modeling protein-ligand binding and interpreting results for scientific decision-making
• Ability to apply biophysical first principles while building practical workflows for cross-functional teams
• Experience translating complex scientific methods into tooling requirements, review standards, and operational workflows
• Strong communication skills and comfort collaborating with computational scientists, ML researchers, research engineers, and drug discovery teams

Valuable additional experience:

• Industry drug discovery experience, especially in structure-based or computational discovery programs
• Familiarity with large-scale GPU simulation infrastructure or distributed scientific computing
• Experience building automated or semi-automated scientific workflows
• Knowledge of cofolding, structure prediction, or ML-assisted molecular modeling methods
• Experience defining benchmark suites, regression tests, or validation harnesses for scientific software
• Experience designing perturbation maps for robust RBFE statistics
• Experience integrating machine-learned interatomic potentials or hybrid force-field simulations
• Experience with active learning or fine-tuning of simulation parameters against experimental data
• Comfort working with LLM agents or agentic workflow systems

How We Work With You

Our talent team at Get A Job.ai partners with leading organizations to connect exceptional candidates with career-defining opportunities. When you apply through our platform, a dedicated recruiter will review your background and conduct an initial screening. If there's a strong match, we'll submit your profile to our client and guide you through their interview process. Please note that all applications must go through Get A Job.ai—direct contact with the client is not part of this process.

Pay

Compensation details will be discussed during the screening process and will reflect your background, expertise, and expected impact.

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