Scientist II/Senior Scientist, Computational Biophysics
Hybrid (Cambridge, MA; London, UK; San Francisco, CA)$140.8k - $217.8kfull-timePosted 2mo ago
About the role
Computational Biophysics Scientist to define and validate agent-usable biophysics tools, design scalable molecular simulation workflows for drug discovery, and enable automated, trustworthy workflows across GPUs.
Responsibilities
- Define the scientific requirements for agent-usable computational biophysics tools, including inputs, assumptions, and outputs.
- Design and validate molecular simulation workflows for drug discovery, including MM/GBSA and RBFE/ABFE.
- Establish standards for system setup, force field selection, parameterization, equilibration, sampling, analysis, and quality control.
- Build robust RBFE and ABFE workflows with automated checks for chemical-series compatibility and ligand-pose consistency.
- Turn biophysics protocols into reliable tools, APIs, and guardrails for LLM agents.
- Build validation benchmarks and acceptance criteria for molecular dynamics and related workflows.
- Evaluate and integrate open-source molecular simulation and free-energy tools (OpenMM, OpenFE, etc.).
- Identify and mitigate failure modes in simulation setup, parameterization, sampling, analysis, and interpretation.
- Advise teams on when biophysics workflows are appropriate and their limitations.
- Partner with ML teams to refine methods as new experimental data becomes available.
- Partner with research engineering and infrastructure teams to scale workflows across large GPU fleets with reproducibility and traceability.
Qualifications
- PhD or equivalent experience in computational biophysics/chemistry/biophysics/physics or related field.
- Hands-on experience with molecular dynamics, MM/GBSA, and free-energy perturbation methods for RBFE/ABFE.
- Practical experience with open-source molecular simulation/free-energy packages, with preference for OpenMM and OpenFE.
- Strong understanding of parameterization and validation of simulation setups.
- Demonstrated history of modeling protein-ligand binding and interpreting results for decision-making.
- Ability to reason from biophysical first principles while building practical workflows.
- Experience translating complex scientific methods into tooling requirements, review standards, and operational workflows.
- Strong cross-functional communication skills.
Skills
Required:Molecular dynamics simulationMM/GBSA and free-energy perturbation methodsBiophysics workflow designCross-functional collaboration
Nice to have:OpenMM/OpenFE
Benefits
- Full U.S. benefits: medical, dental, vision; life and disability insurance; generous PTO and holidays; parental leave; educational assistance; commuter benefits; subsidized lunch.
- International benefits tailored to region; salary ranges apply to U.S. positions.
Last updated Aug 5, 2026. Interested? Apply on the company site.
About Lila Sciences
Pioneering Scientific Superintelligence
Pioneering Scientific Superintelligence to solve humankind’s greatest challenges.
Scientific SuperintelligenceAIAutonomous LabsLife SciencesChemical SciencesMaterials Sciences
More open roles at Lila Sciences
- Staff IT Systems Engineer, Endpoints4d agoCambridge, MA · Business Operations
- Principal Network Engineer4d agoCambridge, MA · Business Operations
- Contractor, P2P Specialist4d agoCambridge, MA · Corporate Development
- Staff / Principal Research Engineer, AI Safety Mitigations4d agoHybrid (Cambridge, MA; London, UK; San Francisco, CA) · AI
- Specialist / Senior Procurement Specialist4d agoCambridge, MA · Corporate Development