PME Student Manual

Students entering the Pritzker Molecular Engineering (PME) PhD program in 2021 or later are expected to fulfill the following course requirements. Courses used to meet program requirements must be completed with grades of B or higher.

• Three Thematic Core Courses
• Four In-Depth Courses (related to your chosen research field)
• Two Broad Elective Courses

In consultation with their Primary Academic Research Advisor(s) and Primary PhD Program Advisor (if applicable), students select core, in-depth, and elective courses from a portfolio of graduate level courses.

In order to be eligible for candidacy, students must complete all Thematic Core and In-Depth Courses by the end of Winter Quarter of the second year. Students are strongly urged to complete at least half of their course requirements in the first year.

Thematic Core Courses, designed specifically for students in each of the three PME research themes, teach fundamental principles, methodologies, and/or systems. These courses aim to provide a foundation for advanced coursework and research in the thematic areas.

*Students who have already taken an advanced quantum class can replace PHYS 34100 with either MENG 37400 Advanced Quantum Information or MENG 37200 Quantum Dissipation and Quantum Measurement.

*********************************************************

PME Interdisciplinary Core Courses*, designed specifically for PME students, teach fundamental principles, methodologies, and/or systems that serve multiple engineering fields. These courses foster interdisciplinary understanding and collaboration. 

• MENG 31100 Math Methods in Molecular Engineering
• MENG 31200 Thermodynamics and Statistical Mechanics
• MENG 31300 Transport Phenomena
• MENG 31400 Advanced Quantum Engineering
• MENG 33100 Biological Materials
• MENG 35100 Introduction to Polymer Science
• MENG 36600 Electronic and Quantum Materials for Technology

*Students who matriculated prior to Autumn 2021 are expected to complete a total of three Interdisciplinary Core courses in place of the Thematic Core course requirement. 

In-Depth Courses can include PME courses as well as courses from fellow STEM departments such as physics, chemistry, biophysics, computer science, and biological sciences. These courses give students specialized knowledge in their research field of choice. In-depth courses must be graduate-level and can be in any STEM area with the approval of the research adviser.

Broad Elective Courses serve to help students develop skills in leadership, communication, technology development, and product design. They also serve to help students acquire or renew basic understanding in STEM subject areas.  Students should also consider courses in other divisions such as public policy, business, or the humanities.

All first-year PME graduate students are required to register for and attend the PME Research Professionalization Seminar (MENG 40300). 

MENG 40300 provides an overview of the types of competencies and non-academic knowledge associated with successful research. Grades for this course are pass/fail and are based on participation and attendance. Students who miss more than two classes and/or who do not complete the Responsible Conduct of Research training receive a failing grade.

All graduate students in the PME participate in the advisor matching process during their first year. The vibrant and diverse research activities pursued by PME faculty members offer students a very broad range of research opportunities. The PME’s highly interdisciplinary environment also provides opportunities to work with multiple faculty members within the school as well as with faculty throughout the University of Chicago and Argonne National Laboratory. Advisors begin working closely with students during their first year of study with annual reviews of progress throughout their studies and research.

There are numerous ways in which students can engage prospective advisors including but not limited to during orientation week at the poster session or match talk presentations; in lab/group meetings, individual faculty meetings, or reading groups; and in their courses. These opportunities give new students an overview of the types of research being pursued at PME, encourage them to consider possibilities for their own interdisciplinary research, and provide students the opportunity to ask questions and engage with individual faculty members whose research interests them most. Students are expected to follow up individually with the advisors they are most interested in working with. They should take the time to review the research that the advisors are working on and to engage the graduate students affiliated with the advisors. Students are strongly encouraged to consider more than one advisor as they engage this process.

Students must start their PhD research projects by the beginning of the spring quarter of their first year. As such, they must match with a primary academic research advisor before the end of the winter quarter of their first year and can match with a PME faculty member, a UChicago faculty member not in the PME, or an Argonne scientist approved to supervise students through the GRC. If one of the latter two, students will also need to arrange for a PME faculty member to serve as the Primary PhD Program Advisor who will be responsible for reviewing the student’s academic progress and serving on all committees related to candidacy and thesis defense. The advisor match will be formally confirmed with the advisor's signature on the PME PhD Advisor Match Form. Once a match with an academic research advisor has been made, first-year students are expected to consult with their advisors on course selection and progress.

If a student fails to match, then the student will no longer be in good academic standing and will be placed on academic probation. The student will be supported centrally by the PME for the spring quarter to give the student additional time to match with a primary academic research advisor and may enroll in any allowable 300 units of credit during this period. If the student fails to match by the end of the spring quarter, the student will have to leave the program and will no longer be financially supported.

To make academic progress on the PhD research project, students must be continuously engaged with a primary academic research advisor. If at any time and for any reason a student is not being advised and financially supported by a primary academic research advisor, the student and a primary academic research advisor must inform the Director of Graduate Studies of appropriate PME PhD degree program immediately. From the notification date through the end of the quarter, and the following quarter, the student will be supported centrally by the PME to give the student time to match with a new primary academic research advisor and research project. If the student fails to match with a new primary academic research advisor and research project in this time frame, the student will have to leave the program and will no longer be financially supported. Note that under these circumstances, students have typically fulfilled to requirements to graduate with a terminal master’s degree.

PME graduate students pursue candidacy for the PhD in their second year. Students develop and present a research proposal describing the objectives, approaches, and expected outcomes of their PhD thesis work. To be admitted to candidacy, students must also successfully complete all core courses and all in-depth courses. Altogether, admission to candidacy depends on an evaluation of academic performance, research performance, the research proposal, and oral review.

The proposal should be prepared in the formats outlined by the National Science Foundation or the National Institutes of Health in their guides on grant proposals. It will be presented to a faculty review committee for approval. Students being reviewed shall submit their completed research proposal by the end of January in the winter quarter.

Students will have 25 minutes at the beginning of the review to present without interruptions and shall personally make arrangements for room reservations and any required projection equipment needed for their review. A full two hours will be scheduled for each review. 

The Faculty Candidacy Review Committee is composed of three to four faculty members including the student’s Primary Academic Research Advisor and Primary PhD Program Advisor, if applicable. At least two of the members must be PME faculty. The candidacy committee should be composed in consultation with and approved by the Primary Academic Research Advisor.

Admission to PhD candidacy depends only in part on the results of the proposal and oral review. Performance in research and in coursework is also considered in committee deliberations. The outcome of the candidacy review will be communicated to the student by the committee chair immediately following committee deliberations. There are three possible outcomes for the candidacy review:

• Pass
• Deficient with opportunity to retake: Students in this category have presented proposals that are promising but have failed to meet the standard of an absolute pass (e.g. missing data, missing coursework, incomplete understanding of the subject matter, etc.). They will be given the opportunity to retake the exam by the end of the Spring Quarter. If the student fails the second attempt, they will no longer be considered in good standing and must leave the graduate program. 
• Fail: Students in this category have presented proposals that are well below the standard of an absolute pass and are indicative of an inability to pursue independent research at the doctoral level. They may also be failing in coursework and/or engagement in laboratory research. Such students will not be given the opportunity to retake the exam and are no longer considered to be in good standing. The student must leave the graduate program by the end of the Spring Quarter.

Students who are not admitted to candidacy because of an unsatisfactory proposal, a poor record of research, and/or unsatisfactory coursework performance may appeal the candidacy outcome in a letter to the PME Dean and to the Vice Dean for Education and Outreach. If the student feels that there are extenuating circumstances that should be considered, those reasons should be clearly articulated in the letter of appeal.

The PME requires that all PhD students engage in meaningful teaching experiences.

Students must either complete two quarters as a Teaching Assistant for a course, or one quarter as a Teaching Assistant for a course and the equivalent of a second TAship credit in an approved alternative activity (or activities). The availability of approved alternatives is limited, and the list of approved alternatives may change. Most students fulfill this requirement with two TAships.

Teaching assignments are determined based on department need, although some consideration may be given to student preferences.

Although it is possible for students to serve as TAs in their first year, most students fulfill this requirement in the second, third, and fourth years. The TA requirement must be completed before graduation.

It is generally expected that students will meet their TA requirements by serving as a TA for PME courses, but occasionally students receive TA credit for TAing a course outside of PME. These requests are considered on a case-by-case basis, and decided primarily on the appropriateness of the course and the ability of PME to meet its own TAing needs. Not every request can be accommodated.



Students interested in TAing a course outside of PME should first discuss with their advisor, and then send their request to an Assistant Director of Academic Programs.

Doctoral dissertations are original contributions to scholarship.  Every student in the PME PhD program is required to prepare, submit and defend an original dissertation thesis project. Detailed instructions and guidelines on how to meet requirements for University of Chicago dissertations are available in the University's student manual, in the University-Wide Requirements for the PhD Dissertation, and on the Dissertation Office website. Students are urged to review these resources early in the writing process. The final copy of the dissertation must be uploaded to the Dissertation Office site by the deadline specified by the Dissertation Office each quarter.

The Dissertation Defense Committee is composed of three to four faculty members including the student’s Primary Academic Research Advisor and Primary PhD Program Advisor, if applicable. At least three faculty members from the University of Chicago and at least two faculty members from PME must be on the committee. The thesis committee should be composed in consultation with and approved by the Primary Academic Research Advisor and Primary PhD Program Advisor, if applicable. The student is responsible for organizing the logistics of the thesis defense.

Students who transfer to the University with their PI and have completed candidacy prior to transferring should provide a list of their committee members to the PME Dean of Students office by the end of their first quarter in residence.

Deadlines for a particular quarter may vary slightly. Be sure to check with the PME Dean of Students Office for the quarter in which you plan to graduate. Helpful information can be found at the links below.

• PME Defense and Graduation Information Sheet
• Dissertation Checklist
• Dissertation Deadlines
• Degree Conferral & Convocation Dates

A fee of $65 will be charged for each degree application that is canceled after the end of the fifth week of the quarter in which it is filed. Note: A degree application is valid only for the quarter in which it is made.

The University of Chicago is a community of scholars dedicated to research, academic excellence, and the pursuit and cultivation of learning. Every member of the University—student, faculty, and staff—makes a commitment to strive for personal and academic integrity; to treat others with dignity and respect; to honor the rights and property of others; to take responsibility for individual and group behavior; and to act as a responsible citizen in a free academic community and in the larger society. In this context, complaints, concerns, and allegations of abuse of authority are taken seriously. Confidentially will be preserved when appropriate.

• View all grievance policy procedures for the Pritzker School of Molecular Engineering here (PDF)