AI Scientist- Computational Chemistry

About this role:

HHMI has made a landmark $500 million commitment to support AI-driven projects and to embed AI systems throughout every stage of the scientific process in labs across HHMI. The AI initiative will be centered at HHMI’s Janelia Research Campus. Janelia has been at the forefront of AI-driven research in biology for more than 15 years. Its forward-thinking structure, centralized funding, and collaborative culture make it ideally suited to take this bold leap forward. To learn more about the initiative, visit ai.hhmi.org.

The Artificial Intelligence (AI) Scientist is an outstanding independent scientist who develops, implements, and executes innovative AI-based research projects to make biological discoveries or to generate new research tools. AI Scientists create, lead, or participate in research projects of variable scale, ranging from individual work to HHMI-wide strategic initiatives. The AI Scientist will work closely with scientists from across the broader HHMI community. They participate in, build, or supervise highly collaborative research teams consisting of other scientists, engineers, and technicians.

What We Provide:

· A competitive compensation package with comprehensive health and welfare benefits. In addition to the base salary described below, this position may also be eligible for incentive pay.

· Generous training and travel opportunities to workshops and conferences. · Access to state-of-the-art computational infrastructure and extended capabilities provided through assistance from Janelia’s Support teams and Project teams.

· A healthy work-life balance, with on-site childcare, free gyms, on-campus housing, vibrant social and dining spaces, and shuttle-bus service to Janelia from Washington, DC metro area!

· Flexible work arrangements are available.

· Relocation assistance provided for non-local candidates who wish to transition to the Washington, DC, metro area.

What You’ll Do:

· Plan, initiate, and rigorously execute independent or collaborative AI-based research; may manage personnel and budgets towards this goal.

· Plan and perform scientific duties on new and varied problems where only general objectives are stated.

· Closely collaborate with other scientists, engineers, and technicians.

· Initiate and remain flexible to transfer between projects and groups as appropriate.

· Coordinate broad phases of projects and perform advanced development work to obtain and maintain technical leadership in the field of AI.

· May assist HHMI and Janelia leadership in planning and execution of program-wide initiatives; ensures coordination with related efforts or other projects and research areas.

· Provide mentoring and leadership to others.

· Participate in the review of other projects and scientists and provide input and guidance in a collaborative and constructive way.

· Explore and develop new methods, skills, and tools. Make research outputs available through peer-reviewed scientific publications, high-quality datasets, code, and applications. Participate in patent disclosures where appropriate.

· Apply AI and computational methods, including generative molecular design, molecular property prediction, and physics-based simulation, to the development of chemical and biochemical tools such as fluorescent probes, biosensors, and imaging agents, working in close collaboration with experimental chemists and protein engineers.

· Adhere to the highest academic, scientific, and ethical standards in all professional activities.

What You Bring

· Ph.D. in Computer Science, AI, Machine Learning, Applied Mathematics, Physics, Chemistry, Chemical Engineering, Computational Chemistry, Biochemistry, Materials Science, or a related field — or equivalent combination of education and experience.

· Demonstrated record of rigorous, innovative research evidenced by peer-reviewed publications, high-quality open-source contributions, or impactful scientific applications, typically reflecting 5 or more years of research experience.

· Deep expertise in computational chemistry, molecular photophysics, or a closely related field — including experience with excited-state property prediction, fluorescent molecule or biosensor design, photoswitches, or related functional molecular systems, and familiarity with quantum chemistry methods (DFT, TD-DFT, or correlated approaches) for predicting photophysical properties such as absorption/emission spectra, quantum yield, and photostability. Candidates with this foundation who are actively building ML capabilities are strongly encouraged to apply.

· Strong working knowledge of AI/ML methods — including deep learning, probabilistic modeling, and generative or optimization-based molecular design — with an emphasis on physics-guided or mechanism-aware approaches suited to data-limited chemical domains. Proficiency in PyTorch, JAX, or equivalent frameworks, and strong programming skills in Python, Julia, C++, or Rust; experience with HPC environments and large-scale computational workflows.

· Track record of integrating computational predictions with experimental validation through active learning, Bayesian optimization, or iterative design–make–test cycles.

· Ability to work effectively in interdisciplinary teams and communicate complex technical concepts clearly to non-specialist collaborators.

· Commitment to rigorous, ethical, and reproducible research practices. Experience with molecular dynamics, docking, or free energy methods for protein–ligand modeling is desirable. Experience in program or project management is a plus.

Physical Requirements:

Remaining in a normal seated or standing position for extended periods of time; reaching and grasping by extending hand(s) or arm(s); dexterity to manipulate objects with fingers, for example using a keyboard; communication skills using the spoken word; ability to see and hear within normal parameters; ability to move about workspace. The position requires mobility, including the ability to move materials weighing up to several pounds (such as a laptop computer or tablet).

Persons with disabilities may be able to perform the essential duties of this position with reasonable accommodation. Requests for reasonable accommodation will be evaluated on an individual basis.

Please Note:

This job description sets forth the job’s principal duties, responsibilities, and requirements; it should not be construed as an exhaustive statement, however. Unless they begin with the word “may,” the Essential Duties and Responsibilities described above are “essential functions” of the job, as defined by the Americans with Disabilities Act.

Compensation Range:

In addition to the base salary described below, this position may also be eligible for incentive pay.

AI Scientist I: 5+ years’ experience - $182,160.80 (minimum)- $227,701.00 (midpoint) - $296,011.30 (maximum)

AI Scientist II : 10+ years’ experience - $213,564.00 (minimum) - $266,955.00 (midpoint) - $347,041.40 (maximum)

AI Scientist III: 15+ years’ experience including program/project management experience - $245,145.60 (minimum) - $306,432.00 (midpoint) - $450,000.00 (maximum)

Pay Type:

Annual

HHMI’s salary structure is developed based on relevant market data. HHMI considers a candidate’s education, previous experience, knowledge, skills and abilities, as well as internal equity when making job offers. Typically, a new hire for this position in this location is compensated between the minimum and midpoint. Your recruiter can share more about the specific pay range during the recruitment process.