Computational Protein Engineer

AeroVironment•Bath Township, OH

5d•$88,500 - $125,475•Onsite

About The Position

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 forcefield generation—necessary to model complex metal-protein interactions.

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.
U.S. Citizenship is required due to government facility access requirements.

Nice To Haves

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

Responsibilities

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.
Forcefield Development: Lead the development and validation of custom metal-ion forcefields 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).