Computational Protein Engineer

Position Overview

The Biological Materials and Processing Research Team is seeking a Computational Protein Engineer to spearhead the de novo design and structural optimization of proteins for high-affinity ion coordination. This role is primarily focused on computational modeling and simulation, using state-of-the-art AI and physics-based tools to engineer biological interfaces for critical material recovery.

While the candidate will collaborate with experimentalists, the core mission of this role is to develop the theoretical frameworks and computational pipelines—including bespoke force field generation—necessary to model complex metal-protein interactions.

• Computational Design & Generative AI: Deploy and refine advanced design suites (e.g., RFDiffusion 2/3, Rosetta, LigandMPNN) to architect novel binding pockets for polyvalent metal cations.
• Force field Development: Lead the development and validation of custom metal-ion force fields for molecular dynamics (MD) simulations, ensuring accurate representation of coordination geometries.
• Quantum Chemistry: Utilize Density Functional Theory (DFT) and other QM methods to calculate electronic structures and refine transition-state models for bioinorganic complexes.
• Structural Bioinformatics: Characterize the thermodynamic landscape and conformational stability of engineered scaffolds using high-throughput structural analysis.
• Interdisciplinary Interface: Translate computational predictions into actionable design parameters for the "wet lab" team and collaborate on the integration of proteins into functional materials (hydrogels/membranes).

• Education: 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/force field development will be considered).
• Technical Expertise: Deep proficiency in Molecular Dynamics (MD) simulations (GROMACS, AMBER, or NAMD) and the physics of metal-ligand coordination.
• Programming:
  Fluency in Python and/or C++/Rust for pipeline development and custom script generation.
• Citizenship: U.S. Citizenship is required due to government facility access requirements; U.S. citizen or lawful permanent resident needed for ITAR/EAR compliance.

• Laboratory Familiarity: Experience with (or willingness to learn) biophysical characterization techniques (ITC, SPR, Fluorescence) to help interpret experimental data.
• Automation: Experience with high-throughput liquid handling robots or automated screening workflows.
• Bio-Interfacial Modeling: Knowledge of how proteins behave when tethered to solid surfaces (e.g., resin or silica).

The salary range for this role is: $88,500 - $125,475. AV offers an excellent benefits package including medical, dental, vision, 401(k) with company matching, a 9/80 work schedule, and a paid holiday shutdown.

No Clearance.

This position requires U.S. citizenship or lawful permanent residency to comply with ITAR and EAR regulations.

We are proud to be an EEO/AA Equal Opportunity Employer, including disability/veterans. Aero Vironment, Inc. is an Equal Employment Opportunity (EEO) employer and welcomes all qualified applicants. Qualified applicants will receive fair and impartial consideration without regard to race, sex, color, religion, national origin, age, disability, protected veteran status, genetic data, sexual orientation, gender identity or other legally protected status.