Process Systems Engineer

  • Lilly
  • Indianapolis, Indiana
  • Full Time

At Lilly, we unite caring with discovery to make life better for people around the world. We are a global healthcare leader headquartered in Indianapolis, Indiana. Our employees around the world work to discover and bring life-changing medicines to those who need them, improve the understanding and management of disease, and give back to our communities through philanthropy and volunteerism. We give our best effort to our work, and we put people first. Were looking for people who are determined to make life better for people around the world.

Lillys Product Research and Development (PRD) is involved in key activities for the development of active pharmaceutical ingredients from pre-clinical phases through commercialization of drug substances and drug products for biologics, small molecules, synthetic oligonucleotides, peptides, conjugates and other modalities. Our scientists develop key technical and business solutions across the portfolio using their deep technical expertise to speed up testing of the clinical hypothesis and overall drug development. PRD tackles this diversity of responsibilities by recognizing that an even greater diversity of talents and cultures is necessary to deliver the next generation of life changing medicines to patients.

PRD is seeking outstanding process system engineering candidates to work within the Process Systems Engineering team. The position presents an opportunity to develop and apply computerized model-based solutions to accelerate the development of new medicines. It also presents the chance to work side by side with chemists, analytical chemists, formulation scientists, engineers and biologists to develop new technical solutions to accelerate our portfolio. This position will be based in Indianapolis where research is conducted in a new, state of the art development facility. The ideal candidate must demonstrate a history of strong technical depth, scientific leadership, and a willingness to promote a collaborative, team-based approach to problem solving.

The responsibilities and opportunities for this role include:

  • Apply process systems engineering fundamentals towards designing and optimizing pharmaceutical manufacturing processes including but not limited to solids operations, chemical reactions, separation processes, bioprocessing (upstream/downstream) using modeling, simulation and optimization tools in conjunction with data analysis.
  • Design appropriate strategies to apply a variety of computational tools to support the development and scale-up of pharmaceutical manufacturing processes.
  • Implement and execute the necessary data analysis, models and/or simulations to support to the design or scale-up of pharmaceutical manufacturing processes.
  • Analyze and interpret data collected from laboratory experiments and/or from manufacturing (including parameter estimation).
  • Actively participate in the design of process conditions for process understanding (experiments) or for material production in manufacturing (nominal conditions).
  • Understand and utilize thermodynamics and material characterization techniques as an informing factor to model-based solutions.
  • Develop user-friendly computational tools to be deployed across PRD to support the development of specific manufacturing platforms.
  • Train the PRD general community in the use of platform computational tools.
  • Serve as a member of integrated commercial teams responsible for the development and demonstration of new processes.
  • Take leadership in the supervision of the compliance with regulations, guidelines, procedures, and practice governing drug research and development, including the departmental and corporate standard operating, good manufacturing practices, and safety procedures.
  • Collaborate closely with multifunctional organizations such as Product Delivery, Project Management, Quality, Manufacturing, and Regulatory to execute and deliver material and information for clinical trials and regulatory submissions.
  • Develop the external manufacturing network, oversee activities and install key capabilities within contract manufacturing organizations (CMOs).
  • Engage in a highly collaborative work environment across and beyond PRD and Lilly, including external academic researchers and pre-competitive collaborations.
  • Direct and mentor less experienced scientists and engineers to deliver the portfolio and innovation projects.
  • Promote diverse thought and experience to deliver innovative solutions that address unmet technical needs.
  • Publish and present original research externally, author internal technical documents and develop and document control strategies for new product registration applications (manufacturing process and development history portions).

Additional Skills and Preferences:

  • Experience across multiple disciplines of process systems engineering (modeling, optimization, control, statistics, numerical methods, programming).
  • Knowledge and experience building fundamental, empirical or hybrid models as appropriate.
  • Awareness of simulation tools across scales (DEM,CFD, FEM, PBM etc)
  • Experience in parameter estimation and handling of data uncertainty.
  • Familiarity with techno economic evaluations, supply chain, production planning and operations research related modeling and optimization.
  • Experience with modeling and simulation and data analytics software packages (e.g Python, MATLAB, gPROMS, Aspen +, GAMS, Pyomo, R).
  • Knowledge and familiarity with data generating sources and automation architectures.
  • Good foundations in numerical methods, optimization, thermodynamics, and transport phenomena.
  • Excellent oral communication and documentation skills.
  • Demonstrate ability to effectively collaborate with multidisciplinary teams.
  • Demonstrate leadership behaviors with ability to accept challenges, seek opportunities to remove barriers, influence without authority, and lead in areas of uncertainty
  • Demonstrate exemplary teamwork/interpersonal skills
  • Demonstrate problem solving, attention to detail and result oriented behaviors in a fast-paced environment.

Basic Requirements:

  • PhD in Chemical Engineering or related discipline.

Additional Information:

  • Travel: 0 to 10%
  • Position Location: Indianapolis, IN.

Lilly is dedicated to helping individuals with disabilities to actively engage in the workforce, ensuring equal opportunities when vying for positions. If you require accommodation to submit a resume for a position at Lilly, please complete the accommodation request form ( ) for further assistance. Please note this is for individuals to request an accommodation as part of the application process and any other correspondence will not receive a response.

Lilly is proud to be an EEO Employer and does not discriminate on the basis of age, race, color, religion, gender identity, sex, gender expression, sexual orientation, genetic information, ancestry, national origin, protected veteran status, disability, or any other legally protected status.

Our employee resource groups (ERGs) offer strong support networks for their members and are open to all employees. Our current groups include: Africa, Middle East, Central Asia Network, Black Employees at Lilly, Chinese Culture Network, Japanese International Leadership Network (JILN), Lilly India Network, Organization of Latinx at Lilly (OLA), PRIDE (LGBTQ+ Allies), Veterans Leadership Network (VLN), Womens Initiative for Leading at Lilly (WILL), enAble (for people with disabilities). Learn more about all of our groups.

Actual compensation will depend on a candidates education, experience, skills, and geographic location. The anticipated wage for this position is

$129,000 - $209,000

Full-time equivalent employees also will be eligible for a company bonus (depending, in part, on company and individual performance). In addition, Lilly offers a comprehensive benefit program to eligible employees, including eligibility to participate in a company-sponsored 401(k); pension; vacation benefits; eligibility for medical, dental, vision and prescription drug benefits; flexible benefits (e.g., healthcare and/or dependent day care flexible spending accounts); life insurance and death benefits; certain time off and leave of absence benefits; and well-being benefits (e.g., employee assistance program, fitness benefits, and employee clubs and activities).Lilly reserves the right to amend, modify, or terminate its compensation and benefit programs in its sole discretion and Lillys compensation practices and guidelines will apply regarding the details of any promotion or transfer of Lilly employees.

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Job ID: 523363931
Originally Posted on: 6/2/2026

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