Computational Protein Engineer

U.S. Citizenship is required due to government facility access and ITAR compliance.

About the role

The Biological Materials and Processing Research Team is seeking a Computational Protein Engineer to lead the de novo design and structural optimization of proteins for high-affinity ion coordination. This role focuses on computational modeling and simulation, using state-of-the-art AI and physics-based tools to engineer biological interfaces for critical material recovery. While collaboration with experimentalists is expected, the core mission is developing theoretical frameworks and computational pipelines—including bespoke forcefield generation—to model complex metal-protein interactions.

Responsibilities

• Deploy and refine advanced design suites (e.g., RFDiffusion 2/3, Rosetta, LigandMPNN) to architect novel binding pockets for polyvalent metal cations.
• Lead the development and validation of custom metal-ion forcefields for molecular dynamics (MD) simulations, ensuring accurate representation of coordination geometries.
• Utilize Density Functional Theory (DFT) and other quantum mechanics methods to calculate electronic structures and refine transition-state models for bioinorganic complexes.
• Characterize the thermodynamic landscape and conformational stability of engineered scaffolds using high-throughput structural analysis.
• Translate computational predictions into actionable design parameters for the "wet lab" team and collaborate on integrating proteins into functional materials (hydrogels/membranes).

Requirements

• Ph.D. in Computational Chemistry, Biophysics, Protein Engineering, or a related field. (Candidates with an M.S. and 5+ years of specialized experience in computational design/forcefield development will be considered).
• Deep proficiency in Molecular Dynamics (MD) simulations (GROMACS, AMBER, or NAMD) and the physics of metal-ligand coordination.
• Fluency in Python and/or C++/Rust for pipeline development and custom script generation.

Preferred Skills

• Experience with (or willingness to learn) biophysical characterization techniques (ITC, SPR, Fluorescence) to interpret experimental data.
• Experience with high-throughput liquid handling robots or automated screening workflows.
• Knowledge of protein behavior when tethered to solid surfaces (e.g., resin or silica).

Benefits

• Medical, dental, and vision coverage.
• 401K with company matching.
• 9/80 work schedule.
• Paid holiday shutdown.

Pay

The salary range for this role is $88,500 - $135,000. AeroVironment considers several factors when extending an offer, including location, role and responsibilities, work experience, education/training, and key skills.

About AV

AV isn’t for everyone. We hire the curious, the relentless, the mission-obsessed. As the premier autonomous systems company in the U.S., AV delivers breakthrough capabilities across air, land, sea, space, and cyber. From AI-powered drones and loitering munitions to integrated autonomy and space resilience, our technologies shape the future of warfare and protect those who serve. Founded by legendary innovator Dr. Paul MacCready, AV has spent over 50 years pushing the boundaries of what unmanned systems can do. Our heritage includes seven platforms in the Smithsonian—but we’re not building history, we’re building what’s next.