Computational Scientist – Microbial Metabolic Modeling and Simulation

AV; Dayton (OH); On-site; USD 88,500 - 135,000; Full time

Benefits offered by this job

Medical, dental, vision insurance

401K with company matching

9/80 work schedule

Paid holiday shutdown

Job summary

AV is seeking a Computational Scientist in Dayton, Ohio, specializing in Microbial Metabolic Modeling and Simulation. This role involves developing genome-scale models, collaborating with lab scientists, and optimizing microbial processes for bioproduction. The ideal candidate should have a Ph.D. in a relevant field or an M.S. with experience, and U.S. Citizenship is required.

The salary range for this position is $88,500 - $135,000, along with excellent benefits including medical, dental, vision, and a 401K plan with company matching.

Qualifications

• A strong foundation in computational modeling and microbial metabolic engineering.
• Ability to translate in silico designs to practical lab applications.
• Experience in collaborating with experimental scientists.

Responsibilities

• Serve as the primary bridge between dry-lab and wet-lab operations.
• Generate, curate, and refine genome-scale metabolic models.
• Develop high-throughput computational workflows for genetic screenings.
• Analyze multi-omics and fermentation data to validate models.
• Refine modeling constraints to simulate industrial bioprocess conditions.

Skills

Microbial metabolic modeling

Simulation of metabolic fluxes

Constraint-based modeling

Collaboration with lab scientists

Peer-reviewed publications

Education

Ph.D. in Bioengineering or related field

M.S. with 2+ years of experience

Tools

COBRA toolbox

Python

MATLAB

Job description

Overview

AV is seeking a Computational Scientist specializing in Microbial Metabolic Modeling and Simulation to work with the AFRL Biological Materials and Processing Research Team to spearhead the in silico design, evaluation, and optimization of microbial hosts for advanced bioproduction and material synthesis. You will develop predictive genome-scale metabolic models (GEMs), simulate metabolic fluxes, and identify genetic intervention strategies to maximize yield, titer, and productivity of target molecules. Develop computational models of microbial systems and write code to analyze and predict microbial behavior. Collaborate closely with laboratory scientists to design experiments, interpret results, and refine models based on experimental data. Prior wet-lab experience is highly desirable, as this role requires serving as an active research partner rather than solely a computational contributor. Maintain a strong feedback loop between laboratory scientists and the modeling team, using experimental results to iteratively refine computational models and guide subsequent rounds of laboratory research, improving accuracy and accelerating discovery.

Key Responsibilities

• Translate In Silico Designs to the Bench: Serve as the primary bridge between dry-lab and wet-lab operations; take candidate metabolic pathways, knock-out strategies, and over-expression targets generated via computational modeling and translate them into actionable engineering strategies for the wet-lab team.
• Metabolic Network Reconstruction & Simulation: Generate, curate, and refine genome-scale metabolic models (GEMs) using advanced systems biology and constraint-based modeling techniques.
• High-Throughput Simulation & Selection: Develop and execute robust, automated high-throughput computational workflows (such as Flux Balance Analysis [FBA], MOMA, or regulatory flux modeling) to screen thousands of genetic perturbation strategies, isolating rare "hit" strain designs from background metabolic noise.
• Data Integration & Loop Closure: Analyze multi-omics and fermentation data (transcriptomics, metabolomics, fluxomics) to identify sequence-activity and flux-yield relationships. Feed this experimental data back into the computational models to validate predictive capabilities, troubleshoot failures, and guide the design of the next round of strain optimization.
• Model & Process Optimization: Refine modeling constraints (pH, maintenance energy, substrate uptake rates, toxicity parameters) to ensure the simulation environment reflects industrial bioprocess and fermentation conditions. Test predictive metabolic models against candidate strain performance at pilot-scale levels.

Required Qualifications

• Education: Ph.D. in Bioengineering, Chemical Engineering, Computational Biology, Bioinformatics, Biochemistry, Systems Biology, or a related field. Candidates with an M.S. and 2+ years of experience will be considered.
• Citizenship: U.S. Citizenship is required due to government facility access requirements.

Research & Technical Expertise

• Designed, optimized, and characterized microbial metabolic networks using state-of-the-art computational biology, constraint-based modeling, and systems-level approaches to predict and improve metabolic flux.
• Collaborated closely with experimental scientists to translate computational models into engineered strains and scalable biological solutions for industrial and real-world applications, maintaining a strong feedback loop between in silico predictions and laboratory validation.
• Applied metabolic engineering principles to microbial hosts including Corynebacterium, Escherichia coli, and/or Saccharomyces cerevisiae to guide strain design and pathway optimization.
• Contributed to peer-reviewed publications and incorporated this research as a significant component of a Ph.D. dissertation, demonstrating expertise in integrating computational modeling with experimental metabolic engineering.

Technical Expertise

• Proficiency in constraint-based metabolic modeling (e.g., COBRA toolbox in Python/MATLAB) and experience modeling standard industrial hosts (E. coli, yeast) and/or non-conventional microbial platforms.

Preferred Skills

• Kinetic & Dynamic Modeling: Knowledge of dynamic flux balance analysis (dFBA) or kinetic modeling of metabolic pathways.
• Familiarity with wet-lab strain construction: Understanding of advanced molecular biology techniques for strain engineering (e.g., CRISPR/Cas9, multiplex automated genome engineering, Gibson Assembly) to optimize collaboration with wet-lab peers.
• Automation & Scripting: Experience with high-throughput scripting, cloud computing, or automated pipeline workflows (Python, R, MATLAB) for scale-level simulation and data analysis.
• Fermentation Knowledge: Familiarity with bioreactor operation modes (batch, fed-batch, continuous) and the biophysical parameters governing cell growth and product synthesis.
• Multi-Omics Integration: Experience with (or willingness to learn) integration datasets (transcriptomics, proteomics, metabolomics) into metabolic flux models to help interpret experimental data and refine constraints.
• Process Scale-Up Support: Familiarity with commercial/industrial bioprocess applications and predicting metabolic shifts during scale up from laboratory- to pilot-scale bioreactors.

Clearance & ITAR

Clearance: No Clearance. ITAR Requirement: This position requires access to information subject to ITAR/EAR compliance. U.S. Citizenship is required or must qualify for export license approval. See 22 CFR 120.15. Some positions will require current U.S. Citizenship due to contract requirements.

Salary & Benefits

The Salary Range For This Role Is: $88,500 - $135,000. AeroVironment offers an excellent benefits package including medical, dental, vision, 401K with company matching, a 9/80 work schedule and a paid holiday shutdown.

About AV

AV isn’t for everyone. We hire the curious, the relentless, the mission-obsessed. The best of the best. We don’t just build defense technology—we redefine what’s possible. As the premier autonomous systems company in the U.S., AV delivers breakthrough capabilities across air, land, sea, space, and cyber. We’re an Equal Opportunity Employer and welcome all qualified applicants.