Overview
At PNNL, our core capabilities are divided among major departments that we refer to as Directorates within the Lab, focused on a specific area of scientific research or other function, with its own leadership team and dedicated budget.
Our Science & Technology directorates include National Security, Earth and Biological Sciences, Physical and Computational Sciences, and Energy and Environment. In addition, we have an Environmental Molecular Sciences Laboratory, a Department of Energy, Office of Science user facility housed on the PNNL campus.
The Earth and Biological Sciences Directorate (EBSD) leads critical research in four areas: Atmospheric, Climate & Earth Sciences, Biological Sciences, Environmental Molecular Sciences, and Global Change. Our vision is to develop a predictive understanding of biological and Earth systems in transition. We aim to understand energy and material flows within the integrated Earth system; to understand, predict, and control the response of biosystems to environmental and/or genomic changes; and to?? Model the Earth system from the subsurface to the atmosphere.?
The Environmental Molecular Sciences Division is comprised of 18 interdisciplinary research teams focused on deciphering molecular-level interactions driving biological and environmental processes across temporal and spatial scales. Through computational analysis and modeling, these findings contribute to predictive understanding of how systems respond to environmental perturbations thus enabling solutions to the nation's energy, environmental, and human health challenges. The division also manages the Environmental Molecular Sciences Laboratory, a Department of Energy, Office of Science user facility housed on the PNNL campus that accelerates the research of scientists around the world by providing access to world-class expertise, instrumentation, and computational resources.
Responsibilities
The Environmental Molecular Sciences Division's (EMSD's) Computing, Analytics, and Modeling (CAM) group focuses on advancing the science of the Environmental Molecular Sciences Laboratory (EMSL) user facility and the mission science of its sponsor, the DOE Office of Science's Office of Biological and Environmental Research (BER) mission, by delivering world-class capabilities and developments in computational science, data analytics and transformations, and modeling sciences. The group, which reports to the CAM Group Leader, works with researchers and staff in EMSL's other two science areas (Environmental Transformations and Interactions, or ETI, and Functional and Systems Biology, FSB) to deliver on EMSL's three strategic science objectives: DigiPhen (Digital Phenome), MONet (Molecular Observation Network), and MIDAS (Modeling, Integration, and Data Agents for Science). Because data and computing infrastructure systems are critical to the group's work, CAM also works closely with the group led by EMSL's Chief Data Officer.
The Computing, Analytics, and Modeling (CAM) Group within the Environmental Molecular Sciences Division at PNNL is seeking a motivated Data Scientist 2 to contribute to cutting edge AI solution for computational and modeling research across the BER mission space. The role requires experience in designing and implementing AI-based agents and agentic workflows, along with a solid understanding of key tools such as LangChain, LangGraph, and Model Context Protocol (MCP). Candidates should have a proven ability to leverage AI to accelerate the software lifecycle and improve data exploration and retrieval, as well as experience supporting various stages of the data lifecycle, including data modeling, harmonizing data models, managing distributed or federated data, and organizational data governance. Additional expertise in metabolic modeling techniques such as flux balance analysis and metabolic control analysis, and familiarity with structural biology data, particularly cryo-electron tomography, is highly desirable. Knowledge of causal inference methods and their application to complex biological systems will further strengthen the candidate's profile.
Designs, develops, documents, tests, and debugs new and existing software systems, hardware/software interfaces, and/or applications according to industry established software engineering principals and best practices. Works collaboratively within a team to execute on the full system development lifecycle including analyzing user needs to determine technical requirements; developing technical specifications based on conceptual design and requirements; developing well-crafted and documented source code; integrating hardware using software; automating manual tasks; and consulting with the end user to proto@type, configure, refine, test, and debug programs or systems to meet needs. Identifies and evaluates new technologies or methods for implementation and continuous improvement.
Drive the design and implementation of agentic workflows for scientific automation, leveraging frameworks such as LangChain, LangGraph, and the Model Context Protocol (MCP).
Develop, maintain, and support open-source scientific software, using CI/CD practices and containerized, reproducible workflows on HPC systems.
Advance CryoET data analysis capabilities through the integration of AI methods, physics-based simulations, and structural biology toolkits.
Expand systems biology modeling capabilities, including metabolic modeling, whole-cell modeling, and causal-reasoning approaches.
Communicate technical findings, including contributing to and leading the preparation of scientific output including reports, manuscripts, visualizations, stakeholder presentations, and software.
Qualifications
Minimum Qualifications:
BS/BA and 2 years of relevant experience -OR-
MS/MA -OR-
PhD
Preferred Qualifications:
Degree in Computer Science, Electrical and Computer Engineering, Bioinformatics, Statistics, Physics, Mathematics or a related field.
Agentic AI & Tools: Design and implementation of single and multi agent AI workflows for scientific automation; proficiency with LangChain, LangGraph, and Model Context Protocol (MCP); experience with LLM reasoning frameworks (e.g., ReAct) and orchestration for data analysis and metabolic engineering.
Cryo ET 3D Vision & Intelligent Retrieval: Expertise in 3D computer vision for cryo electron tomography, topologically aware protein classification, sim to real transfer, and reconstruction level signal characterization, paired with development of advanced search and retrieval systems for complex biological datasets and specialized workflows (e.g., post translational modification discovery).
AI & Autonomous Science: Interest in foundation models, multi-agent systems, and autonomous science frameworks; experience applying computational and modeling approaches across the BER mission space.
Structural & Multiomic Data: Skilled in structural biology data analysis (especially cryo-electron tomography and protein classification workflows) and multiomic approaches for metabolic and circadian regulation.
Programming & Frameworks: Proficiency in Python, PyTorch, TensorFlow, and OpenCV; experience with version control (e.g., Git) and collaborative development practices.
Data & Model Development: Skilled in preparing data for machine learning, including signal processing and feature extraction for high-dimensional datasets; familiarity with HPC environments and distributed ML training.
Data Lifecycle Management & Engineering: Experience developing and maintaining open source scientific software with CI/CD and containerized, reproducible HPC workflows; expertise in data modeling, harmonization, and management of distributed and federated data systems.
Domain-Specific AI Applications: Experience creating agentic workflows for scientific discovery and integrating AI into biological data analysis pipelines.
Biological Modeling & Analysis: Expertise in metabolic modeling (flux balance analysis, metabolic control analysis) and whole-cell modeling for spatio-temporal energy metabolism in microbial systems.
Advanced Causal Methods: Experience with causal inference and advanced causal analysis techniques for biosystems design (e.g., Causal Component Analysis, Y0-based identification).
Problem-Solving & Adaptability: Strong ability to tackle complex scientific and data challenges with attention to detail; adaptable to emerging technologies and innovative AI-driven approaches.
Collaboration & Communication: Effective in interdisciplinary environments, with proven skills in written and verbal communication across computational, biological, and data science domains.
Leadership & Initiative: Demonstrated ability to identify opportunities, advocate for them, and integrate agentic AI with deterministic workflows (e.g., ADEPT-Bio framework).
Remote & Distributed Work: Proven success working in highly distributed teams and fostering collaboration in virtual settings. Intellectual Curiosity: Enthusiasm for interdisciplinary research and continuous learning in advanced computational and biological sciences.
Hazardous Working Conditions/Environment
Not applicable
Testing Designated Position
This is not a Testing Designated Position (TDP).
About PNNL
Pacific Northwest National Laboratory (PNNL) is a world-class research institution powered by a highly educated, diverse workforce committed to the values of Integrity, Creativity, Collaboration, Impact, and Courage. Every year, scores of dynamic, driven people come to PNNL to work with renowned researchers on meaningful science, innovations and outcomes for the U.S. Department of Energy and other sponsors; here is your chance to be one of them!
At PNNL, you will find an exciting research environment and excellent benefits including health insurance, and flexible work schedules. PNNL is located in eastern Washington State-the dry side of Washington known for its stellar outdoor recreation and affordable cost of living. The Lab's campus is only a 45-minute flight (or ~3 hour drive) from Seattle or Portland, and is serviced by the convenient PSC airport, connected to 8 major hubs.
Commitment to Excellence and Equal Employment Opportunity
Our laboratory is committed to fostering a work environment where all individuals are treated with fairness and respect while solving critical challenges in fundamental sciences, national security, and energy resiliency. We are an Equal Employment Opportunity employer.
Pacific Northwest National Laboratory (PNNL) is an Equal Opportunity Employer. PNNL considers all applicants for employment without regard to race, religion, color, sex, national origin, age, disability, genetic information (including family medical history), protected veteran status, and any other status or characteristic protected by federal, state, and/or local laws.
We are committed to providing reasonable accommodations for individuals with disabilities and disabled veterans in our job application procedures and in employment. If you need assistance or an accommodation due to a disability, contact us at careers@pnnl.gov .
Drug Free Workplace
PNNL is committed to a drug-free workplace supported by Workplace Substance Abuse Program (WSAP) and complies with federal laws prohibiting the possession and use of illegal drugs.
If you are offered employment at PNNL, you must pass a drug test prior to commencing employment. PNNL complies with federal law regarding illegal drug use. Under federal law, marijuana remains an illegal drug. If you test positive for any illegal controlled substance, including marijuana, your offer of employment will be withdrawn.
Security, Credentialing, and Eligibility Requirements
As a national laboratory, PNNL is responsible for adhering to the Homeland Security Presidential Directive 12 (HSPD-12) and Department of Energy (DOE) Order 473.1A, which require new employees to obtain and maintain a HSPD-12 Personal Identify Verification (PIV) Credential. To obtain this credential, new employees must successfully complete the applicable tier of federal background investigation post hire and receive a favorable federal adjudication. The tier of federal background investigation will be determined by job duties and national security or public trust responsibilities associated with the job. All tiers of investigation include a declaration of illegal drug activities, including use, supply, possession, or manufacture within the last 1 to 7 years (depending on the applicable tier of investigation). Illegal drug activities include marijuana and cannabis derivatives, which are still considered illegal under federal law, regardless of state laws.
For foreign national candidates:
If you have not resided in the U.S. for three consecutive years, you are not eligible for the PIV credential and instead will need to obtain a favorable Local Site Specific Only (LSSO) Federal risk determination to maintain employment. Once you meet the three-year residency requirement thereafter, you will be required to obtain a PIV credential to maintain employment. The tier of federal background investigation required to obtain the PIV credential will be determined by job duties at the time you become eligible for the PIV credential.
Mandatory Requirements
Please be aware that the Department of Energy (DOE) prohibits DOE employees and contractors from having any affiliation with the foreign government of a country DOE has identified as a "country of risk" without explicit approval by DOE and Battelle. If you are offered a position at PNNL and currently have any affiliation with the government of one of these countries, you will be required to disclose this information and recuse yourself of that affiliation or receive approval from DOE and Battelle prior to your first day of employment.
Rockstar Rewards
Employees and their families are offered medical insurance, dental insurance, vision insurance, robust telehealth care options, several mental health benefits, free wellness coaching, health savings account, flexible spending accounts, basic life insurance, disability insurance, employee assistance program, business travel insurance, tuition assistance, relocation, backup childcare, legal benefits, supplemental parental bonding leave, surrogacy and adoption assistance, and fertility support. Employees are automatically enrolled in our company-funded pension plan and may enroll in our 401 (k) savings plan with company match*. Employees may accrue up to 120 vacation hours per year and may receive ten paid holidays per year.
Research Associates excluded.
**All benefits are dependent upon eligibility.
Click Here For Rockstar Rewards (https://careers.pnnl.gov/rockstar-rewards)
Notice to Applicants
PNNL lists the full pay range for the position in the job posting. Starting pay is calculated from the minimum of the pay range and actual placement in the range is determined based on an individual's relevant job-related skills, qualifications, and experience. This approach is applicable to all positions, with the exception of positions governed by collective bargaining agreements and certain limited-term positions which have specific pay rules.
As part of our commitment to fair compensation practices, we do not ask for or consider current or past salaries in making compensation offers at hire. Instead, our compensation offers are determined by the specific requirements of the position, prevailing market trends, applicable collective bargaining agreements, pay equity for the position @type, and individual qualifications and skills relevant to the performance of the position.
Minimum Salary
USD $114,000.00/Yr.
Maximum Salary
USD $182,100.00/Yr.
