Current PhD Students

PME Student Manual

The Pritzker School of Molecular Engineering (PME) Divisional Student Manual is a set of academic policies and requirements that apply to all students in the molecular engineering doctoral program.

In addition to this manual, please review the following web pages for specific aspects of our program:

If you are looking for... Visit
An overview of our courses and the core competencies they build Courses and Core Competencies
Detailed course descriptions and instructor and prerequisite information Course Catalog
University policies and regulations University Student Manual

A new set of PME PhD program course requirements will be implemented beginning Autumn 2021. All PME PhD students entering in Autumn 2020 are encouraged to follow the new set of course requirements in its entirety. Rising second-year students who elect to follow the new requirements will not be required to take the winter-spring PME Core sequence.

In the Pritzker Molecular Engineering (PME) PhD program, students are expected to fulfill the following course requirements*:

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

New course requirements* (beginning Autumn 2021):

  • Five PME Core Courses
    • Thematic Core Courses (3)
    • PME Core Sequence Courses (2, offered in Winter and Spring 2021)
  • Four In-Depth Courses (related to your chosen research field)
  • Two Broad Elective Courses

Incoming students who elect to follow the new set of course requirements will complete three thematic core courses, four in-depth courses, two broad elective courses, and the PME core sequence for a total of eleven courses.

*In order to be eligible for candidacy, students must complete all 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.

Courses used to meet program requirements must be completed with grades of B or higher.

In consultation with the faculty advisor, students will select core and in-depth courses from a portfolio of graduate level courses. Though we only require nine courses under the old requirements, and eleven courses under the new requirements for the PhD program, we encourage you to take additional relevant courses in areas across the University.

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. Current PME Core Courses are listed below:

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

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.

(Note: The PME-only section of ENGL 30000 Academic and Professional Writing (Little Red Schoolhouse) offered in Autumn may not be counted toward PME graduation requirements because it is not a full, quarter-long course. Interested students are still encouraged to register.)

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.

Immuno-Engineering (3) MENG 33100 Biological Materials
  MENG 33200 Principles of Immunology
  Choose one of the following:  
  1. MENG 33110 Stem Cell Biology, Regeneration, and Disease Modeling
  2. MENG 33130 Proteomics and Genomics in Biomolecular Engineering
     
Materials Systems for Sustainability and Health (3) MENG 31100 Math Methods in Molecular Engineering
  Choose two of the following:  
  1.MENG 31200 Thermodynamics and Statistical Mechanics
  2.MENG 31300 Transport Phenomena
  3.MENG 35100 Introduction to Polymer Science
  -OR-
  CHEM 39000 Solids, Materials, Surfaces
     
Quantum Engineering (3) MENG 31400 Advanced Quantum Engineering
  PHYS 34100 Graduate Quantum Mechanics-1*
  PHYS 34200 Graduate Quantum Mechanics-2

*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 Core Sequence, this sequence covers grand challenges and fundamental science and engineering concepts in the three PME themes, Immuno-Engineering, Materials Systems for Sustainability and Health, and Quantum Engineering, from a general interest perspective.   

 

The vibrant and diverse research activities pursued by Pritzker School of Molecular Engineering (PME) faculty members provide students with a broad range of research opportunities. Our interdisciplinary environment offers many opportunities for students to work with multiple faculty members within PME and/or with faculty in other partner institutes at the University of Chicago and Argonne National Laboratory.

Advisers begin working closely with students during their first year of study, with annual reviews of progress throughout their studies and research.

First-year students are required to attend the first-year Adviser Match Talks, which consist of a series of research presentations given by PME faculty and research advisers from partner institutions/divisions. These presentations 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 advisers they are most interested in working with. They should take the time to review the research that the advisers are working on and to engage the graduate students affiliated with the advisers. Students are recommended to consider more than one adviser as they engage this process.

Near the end of their first term of study, all doctoral students will be expected to secure a primary academic adviser who will guide them through the course of their doctoral research. The adviser match will be formally confirmed with the adviser's signature on the PME Adviser Match Form. Once a match with a research adviser has been made, first-year students are expected to consult with their advisers on Winter Quarter course selection.

Students planning to work with faculty outside of the school should consult with the deputy dean of education and outreach early in their deliberative process. To work with a primary research adviser outside of PME, students must secure: 1) formal commitment from the non-PME faculty member both describing the research to be performed and agreeing to provide financial support; 2) the agreement of an PME faculty member to serve as primary academic adviser, responsible for reviewing the student’s academic progress and serving on all committees related to candidacy and thesis defense, and; 3) formal approval from the deputy dean of education and outreach.

In addition, students must submit a brief research proposal and explain why they wish to work under the supervision of an adviser outside of PME. All decisions to approve non-PME faculty as primary advisers will be made in consultation with the PME faculty body.

During their second year of study, students pursue candidacy for the PhD. To be admitted to candidacy, students must successfully complete all core courses and all in-depth courses. In addition, they must develop a research proposal describing the objectives, approaches, and expected outcomes of their PhD thesis work. Altogether, admission to candidacy will depend on an evaluation of academic performance, research performance, and the research proposal. This process should be completed no later than March 12.

December 1, 2020

Deadline for students to submit to lisaa@uchicago.edu:

  1. a title,
  2. a short abstract of proposed research,
  3. a list of the candidacy review committee members,
  4. and a confirmed date, time, and place for the review.

January 31, 2021

Deadline for students to submit the full research proposal to lisaa@uchicago.edu and to the members of the candidacy committee.

March 12, 2021

Deadline for completion of candidacy review.

  • The outcome of the candidacy review will be communicated to the student by the chair of the committee immediately following committee deliberations. Candidacy outcomes will then be confirmed via official letter within two business days of the review. 
  • Any questions regarding the research proposal for candidacy should be addressed to the student's research adviser. If any issues or difficulties arise, students are encouraged to speak to the deputy dean of education and outreach or to the dean of students.

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 January 29.

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 shall be composed of three to four members and should include the student’s primary research adviser (and primary academic adviser, if applicable). At least two of the members must be PME faculty. The Faculty Candidacy Review Committee should be composed in consultation with and approved by the primary research adviser.

It is the responsibility of the student to submit a project title, a short abstract, and a confirmed schedule for the review by December 1. All candidacy reviews for second-year students will take place between early February and early March. Any and all changes pertaining to committee composition and candidacy review dates will need approval from the deputy dean of education and outreach.

The outcome of the candidacy review will be communicated to the student by the chair of the committee immediately following committee deliberations. A letter confirming the outcome will be sent to the student within two business days of the review. 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. The student will receive support for one additional quarter with an opportunity for a terminal MS degree.
  • 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. Such students 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 will receive support for one additional quarter with an opportunity for a terminal MS degree. The student must leave the graduate program by the end of the Spring Quarter.

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.

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 deputy dean of 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.

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.

Each PhD Thesis Committee is composed of three to four members. The committee should include the student’s primary research adviser (and primary academic adviser if applicable), at least three faculty members from the University of Chicago, and at least two faculty members from PME. The thesis committee should be composed in consultation with and approved by the primary research adviser (and primary adviser if applicable). 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 dean of students by the end of their first quarter in residence. The student is responsible for organizing the logistics of the thesis defense.

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 (typically by week seven).

Before the dissertation is officially uploaded to the Dissertation Office, students must submit the Departmental Approval Form to the PME Dean of Students with approval signature(s) from the dissertation committee chairperson(s) and committee members. (The form will be sent to students from the Dean of Students Office a week before the dissertation defense date.)

At least 15 days in advance of the scheduled dissertation defense, PME PhD candidates must submit copies of the final thesis along with defense scheduling details to Lisa Abston lissa@uchicago.edu in the PME Dean of Students Office. The thesis and schedule will be then be shared with members of the dissertation committee. 

Week 10 of quarter prior to anticipated graduation quarter

Deadline to submit Intent to Distribute and Defend Form to rpopoff@uchicago.edu.

Review Dissertation Office webpage.

Friday of week 1

Deadline to submit the application to graduate via my.uchicago.edu portal. Note: It is recommended that students defend their dissertation and complete all required revisions before applying to graduate.

Wednesday of week 4

Deadline for optional dissertation draft review through UChicago Dissertation Office.

Friday of week 4

Last feasible date to defend thesis

Friday of week 5

Last day to withdraw degree application**

Week 5 - Week 6

Format dissertation for publication. All dissertations must follow the formatting and submission requirements stated in the University-Wide Requirements for the PhD Dissertation, available from the Dissertation Office on the first floor of the Regenstein Library.

Friday of week 7

Final submission of dissertation due to dissertation office by 4:30pm. PhD candidates who miss this deadline will not be eligible to graduate until the following quarter.

Friday of week 10 (summer, autumn, winter) or Saturday of week 11 (spring only)

Graduation (Convocation Ceremony only in June)

* This timeline serves as a general summary. Deadlines for a particular quarter may vary slightly. Be sure to check the dissertation office deadlines for the quarter in which you plan to graduate.

** A fee of $65 will be charged for each degree application that is cancelled 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.

Pedagogical training is a component of our doctoral education. PME requires that all graduate students engage in meaningful teaching experiences. Most students will satisfy this requirement by serving as a teaching assistant (TA).

Students can also propose a meaningful teaching equivalent to be approved by the deputy director for education and outreach and the dean of students. Proposed equivalents must have clearly articulated pedagogical learning goals and objectives.

Students are not expected to complete their teaching requirement in their first year, but may be asked to be a TA as needed in any year thereafter. While there is some consideration of student preferences in teaching assignments, assignments overall are determined by departmental need.

  • Students who entered the doctoral program in 2017, 2016, 2015, and 2014 must either complete two quarters as a TA or one quarter as a TA and one approved equivalent.
  • Students entering the doctoral program after 2017 must either complete two quarters as a TA or one quarter as a TA and two approved equivalents.

Approved teaching equivalents are educational and training programs that support graduate students’ development of pedagogical, mentoring, and teaching competencies. Each of these programs is designed with student-centered learning goals and outcomes, and is supported by research-based curricular materials. Current approved half-credit equivalents include:

If you are interested in proposing a teaching equivalent program, please make an appointment with the Dean of Students and the Educational Training and Outreach Coordinator to discuss how to clearly articulate pedagogical learning goals, and describe the professional skills and competencies you will develop as a graduate student through participation in the proposed program.

The academic record of all first-year Pritzker Molecular Engineering graduate students will be reviewed at the end of every quarter. Students should aim to complete at least half of their course requirements by the end of their first year of study. In addition to coursework requirements, students are expected to demonstrate consistent engagement and reasonable progress in their laboratory research.

First-year students are encouraged to meet with their adviser and/or the dean of students at least once each term to ensure that they understand the requirements of the doctoral program, that they are managing the balance of coursework and research appropriately, and that they are aware of sources of support both within PME and within the broader university.

The academic progress of all PME students will be evaluated annually during the summer term. Students in all years will be asked to describe what they have accomplished toward the degree during the past academic year (both coursework and research). Advisers will be asked to review the accomplishments with their students. The report of academic progress, signed by both the student and the adviser (including the primary academic adviser if applicable), will be reviewed by the deputy dean of education and outreach. Once the student has been advanced to candidacy, academic progress may also be reviewed by the members of the thesis committee in conjunction with the deputy dean of education and outreach.

All PME students are expected to complete the doctoral program within a period of five years in order to remain in good standing. To support this expectation and facilitate progress in their research, students are strongly recommended to complete all  required coursework by the end of their second year. Cases of students who are not progressing satisfactorily will be raised for discussion with the PME faculty body.

The PME is invested in the overall success and well-being of our students.  Any student who is experiencing difficulties that might hinder their performance in the classroom or in the laboratory, or that might otherwise negatively affect their annual review should reach out to the dean of students or to the deputy dean of education and outreach. Early attention to such difficulties will facilitate appropriate support and access to resources.

In order to remain in good standing, students that have not advanced to candidacy must earn a quality grade of "B" or better in each of their non-research based courses. Students failing to meet this requirement will be placed on academic probation and be expected to earn quality grades of "B" or better in each of their non-research based courses in the following quarter; after which they will be automatically returned to good standing. Students who remain on academic probation for more than two quarters may be asked to leave the doctoral program. If a student anticipates that they might earn a grade below a "B", they should speak with the Dean of Students as soon as possible to discuss their options. If a student that has passed candidacy receives a course grade below a “B” in a non-research based course, they will not be placed on academic probation. However, such courses cannot be used toward the nine courses required for graduation.

Proper acknowledgment of another's ideas, whether by direct quotation or paraphrase, is expected. If any written or electronic source is consulted and material is used from that source, directly or indirectly, the source should be identified by author, title, and page number, or by website and date accessed. Any doubts about what constitutes "use" should be addressed to the instructor.

Review the Academic Policies section of the University Student Manual for more information.

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, grievances and unfair treatment are taken seriously.

Students with a question about a grade received in a course should consult with the instructor first. Students should note that faculty members have the authority to assess the academic performance of their students. Under normal circumstances, only the instructor who gave the course, examination, or evaluation has the authority to change the assessment of the students' performance. Similarly, the evaluation of students' academic progress and standing in the program is the prerogative of the departmental faculty. 

Students who are concerned with the assessment of their research progress and accomplishment of academic milestones should consult first with their research adviser to better understand expectations and the structure of assessment. Again, students should note that faculty members have the authority to assess the academic performance of their students and the evaluation of students' academic progress and standing in the program is the prerogative of the departmental faculty. 

Students who are concerned with academic issues not related to grades, research, or academic progress, can consult with their research/academic adviser, the deputy dean of education and outreach, or the dean of students. If a student is not certain whom to approach, consultation with one of these individuals may help in determining who would be the most appropriate person to answer their question. Whoever ultimately responds to the student's concern will base their response on either metrics laid out in the syllabus or policies and practices established by the division, university, or government.

Students with a grievance may bring it to the attention of their research/academic adviser, the deputy dean of education and outreach, or the dean of students. In case of a grievance related to academic assessment brought by a student about an instructor for a course grade or the departmental faculty for academic progress, the resolution process addresses whether the assessment was made impartially, solely based on academic performance, and conducted using standard procedures. For grievances related to other academic matters, the resolution process addresses whether the established policies and practices were appropriately applied.

The academic official to whom the student brought the grievance will meet with the student to discuss and resolve the grievance. This official may consult as appropriate with other faculty and/or the dean of students (or designee) to resolve the matter. The official will discuss the outcome of the review in a meeting with the student and follow up in writing. Should the matter remain unresolved, the student may bring the grievance to the attention of the dean of students (or designee). The student should submit the grievance, the written response to the grievance, and an articulation of why the matter is still unresolved in writing to the dean of students. The dean of students will review the written materials, may ask the student for clarification, may consult with the official who initially responded to the grievance and/or the chair or program director and the academic dean, and will make a final determination. The dean of students will discuss the outcome of the review in person with the student and follow up in writing.

Students with questions about the procedures may contact the dean of students.

Students may also avail themselves of the Office of the Student Ombudsperson to resolve a concern.

Complaints about sexual harassment or discrimination and harassment on the basis of race, color, religion, sex, sexual orientation, gender identity, national or ethnic origin, age, disability, veteran status, genetic information, or other protected classes under the law are addressed under the University's policy on harassment, discrimination, and sexual misconduct

Complaints about student conduct involving possible violation of University policies and regulations and other breaches of standards of behavior expected of University students should be brought promptly to the attention of the dean of students of the academic area of the accused student. It is important that these complaints be explored and judged in accordance with University policies and procedures. Please see University Disciplinary Systems for more information.