The PhD Degree

• Overview
• Steps to the PhD
• Course Requirements
  • Core Courses
  • Lab Requirement
  • Core Course and Lab Waivers
  • Breadth Requirement
  • Sample Schedules
• Teaching and Graduate Seminars
• The Comprehensive Exam
• The Oral Exam
• The Doctoral Defense
• General Policies
  • Professional Conduct
  • Good Standing
  • Tuition Waivers
  • Graduate Funding
  • Leave of Absence
• Concentrations
  • Astronomy Concentration
  • Physical Biology Concentration

Overview

Students in the Ph.D. program gain a solid background in the breadth of physics and astronomy, and demonstrate their ability to carry out research and overcome new challenges in a specific area of interest. These students often go on to traditional research positions at universities and national labs as well as to industrial labs. Other careers pursued by PhD graduates might include medical physics, analysis in technological and financial settings, and data science.

The learning goals for the PhD degree are as follows:

• Should have mastered core physics and should be familiar with areas of physics outside their research specialty.
• Should be able to think independently and have acquired critical reasoning skills.
• Should be an expert in their research specialty and have demonstrated the ability to conduct original research.
• Should be able to communicate research results to an audience of physicists.

Beyond the standard Ph.D. in Physics, our program offers two concentrations for students with more specific interests: a Ph.D. Degree in Physics with Concentration in Astronomy and a Ph.D. Degree in Physics with Concentration in Physical Biology. Full requirements for the standard program and concentrations, along with the funding package and tuition waiver typical of a PhD, are given in the sections below.

Steps to the PhD

Becoming a Ph.D. in Physics happens in two phases: first advancing to candidacy by completing coursework and passing your exams, then conducting original doctoral research and defending it. The tables below lay out both phases in order; every milestone in them is covered in full detail in its own section further down this page.

Phase I: Advancing to Candidacy

Advancing to candidacy means finding an advisor, completing the core and required coursework, and passing both the Comprehensive Exam and the Oral Exam – these don’t have to happen in a fixed order, and the Oral Exam is often completed while coursework or the Comprehensive Exam are still in progress. Each is covered in its own section below.

You must advance to candidacy at least one year before you defend your doctoral thesis.

Phase II: Doctoral Research

Once you’ve advanced to candidacy, the focus shifts to research: working with your advisor, checking in periodically with your thesis committee, and ultimately writing and defending your dissertation.

Most students follow this path exactly as described above. Two concentrations – an Astronomy Concentration and a Physical Biology Concentration – modify some of these requirements for students with more specific interests; see the bottom of this page for details.

Course Requirements

Only courses with a grade B or better are counted towards the Ph.D. degree.

Core Courses

One of the requirements for advancement to candidacy is demonstration of command of four core areas of physics: Classical Mechanics (PHY 501), Electricity and Magnetism (PHY 505), Quantum Mechanics (PHY 511/512) and Statistical Mechanics and Thermodynamics (PHY 540). Most students should take the core courses during their first year.

Lab Requirement

PHY 515 or PHY 517 – both laboratory courses provide an introduction to the special problems of experimental physics and astronomy. Students perform a number of classical and instructive experiments to learn why and how we acquire the knowledge upon which physics is based.

Core Course and Lab Waivers

Waivers may be granted for required courses – core courses, breadth requirements, teaching experience, PHY 515, etc. – on the basis of work done at other universities. Requests must be made during the first semester of study at Stony Brook, directed to the Graduate Program Director; a transcript alone is not sufficient, so the student should also bring supporting documentation such as a detailed course syllabus, course WEB pages, and homework assignments.

For a core course specifically, a waiver can be granted two ways: by taking advanced graduate courses covering equivalent material elsewhere, subject to approval by an Advising Committee appointed by the Graduate Program Director; or by a sufficiently good performance on the corresponding subject of the placement examination, given at the Placement level at the beginning of the Fall semester (2nd-year students and beyond need permission from the Graduate Program Director to take the placement exam).

In the case of the Graduate Laboratory course (PHY 515 or PHY 517) all materials associated with the course taken elsewhere should be presented: syllabus, the faculty supplied instructions or “write-ups” of the experiments done by the student, the laboratory logbook in which the student recorded the day-to-day results of each experiment, and the final written report for each experiment, together with the grades for each of those. Students seeking a waiver in PHY 515 or PHY 517 should submit all materials to faculty teaching the course soon after arrival to Stony Brook. Instead of fully waiving the course requirement, waivers are sometimes granted for individual experiments.

Breadth Requirement

All Ph.D. students must take at least three advanced courses in three different areas of physics and astronomy or a related area chosen from a list of courses and areas approved for this purpose (see table below) or courses approved by the graduate program director. No more than one course from the PHY 680 or PHY 690 series or outside the Department of Physics and Astronomy can be used to fulfill this requirement.

Areas and Courses eligible for the Breadth requirement

Students in the Astronomy track have the option to take three of the astronomy courses (PHY 521-524, 620) rather than the above.

Students completing the Astronomy Concentration or the Physical Biology Concentration satisfy this requirement differently – see those sections at the bottom of this page.

Sample Schedules

How quickly you approach the core courses should depend on your level of preparation. Please do not underestimate these courses and overestimate your own preparation! Remember that you also need to do breadth, grad lab, grad seminars. Here are some example plans you could follow, slowest at the top, fastest at the bottom.

Teaching and Graduate Seminars

Teaching

PHY 600 Teaching (two semesters) – because teaching and research are inextricably intertwined in a scientist’s career, all Ph.D. students are required to teach (be a TA) for two semesters. Many do this for a second year. The first introduction to teaching begins during the orientation week: entering students participate in a TA training, required for all new TA’s. Usually graduate students will conduct laboratory sections associated with undergraduate courses. Senior faculty members closely supervise this effort. Students normally do their teaching concurrently with their own first year courses, and earn 0-3 academic credits per semester in PHY 600.

Graduate Seminars

Two out of three of PHY 598, PHY 599, and PHY 664 are required of all Ph.D., M.S.I., and M.A. students. Almost everybody should take them during their first two semesters at Stony Brook, as they provide a good way to get acquainted with the department. The courses cover different areas of physics and can be taken in any order.

In these seminars, students gain experience presenting research topics to an audience of their peers. This requires different skills than the core courses: the level of knowledge between speaker and listeners is nearly on a par, and the motivation for the activity is different too. This prepares graduate students for presenting research at seminars and scientific meetings, as well as for their own thesis defense.

PHY 664 Astro Journal Club was added as an alternative to one of 598 and 599 in Fall 2025. PHY 664 is expected to satisfy the degree requirement for two semesters of a seminar course. Although formally this is still pending approval from the Graduate School, we recommend that students interested in Astronomy take PHY 664 in lieu of one of 598 and 599, starting in the Fall 2025 semester.

The Comprehensive Exam

The comprehensive exam, which also plays the role of a Placement Exam, is offered over four days, and covers classical mechanics (CM), relativity, electricity, magnetism and optics (EM), quantum mechanics (QM) and statistical mechanics and thermodynamics (SM). The exam takes place in August and in January during the week before the start of classes.

All PhD students are required to pass the Comprehensive exam before the start of their third year as a PhD student. The minimum requirement for passing this exam is passing three subjects at the PhD level and one subject at the Master level. Admission to the fifth semester of graduate study is contingent upon passing the comprehensive exam or by explicit approval of the Graduate Program Director. We encourage all first-year students to take the Comprehensive exam for practice. There is no expectation by the Department that such students will pass, although some do. There is absolutely no disgrace in an unsuccessful attempt.

Most students with an American bachelor’s degree and no additional advanced studies have passed the Comprehensive by the beginning of the fourth semester; many pass earlier. Students with more advanced background often pass in the first year. In some cases, students pass the comprehensive exam at the beginning of the fifth semester, but this is not encouraged. In such cases, the Oral exam should be completed beforehand so that a student’s status in the department is clear immediately after the written exam results are available.

The comprehensive exam can be passed at three different levels. The highest level is at the placement level, then all three problems in a given subject area have to be passed at a high level set by the faculty. Students passing at this level are exempt from the corresponding core course requirement. The second pass level is the PhD level – at this level students have to pass only two of the three problems at a lower level than the placement level. The lowest pass level, also for two out of the three problems for each subject, is as the Master level. The passing level is set by the faculty and is lower than the PhD level. The comprehensive exam is passed in each subject separately. The level is roughly that of the midterm and final examinations in the core courses. With regard to academic integrity, religious observances, disabilities, etc., this exam follows the university wide guidelines for courses and exams. One hand written page of notes (both sides) is allowed for each subject.

The Comprehensive Exam is prepared by the Graduate Examinations Committee. The Department’s faculty meets to discuss the results of the Comprehensive exam about one week after each exam. After that meeting, the answer books are available in the Department office for inspection by the students for grading errors, or for removal by the appropriate student. No grade changes are allowed to an exam book after it has left the office. It is a student’s responsibility to ask a professor to regrade a particular question, and this must be done in the office. A large number of small grade changes is not an acceptable way to make a significant change in a total score. Unclaimed books may be discarded after four weeks.

Waivers: A transfer student who has been admitted into the Ph.D. program in Physics at Stony Brook and who has passed a written comprehensive examination as a matriculated student in the doctoral program of the physics or astronomy department at another university may request a waiver of the written comprehensive examination. To request such a waiver a student should:

• First, discuss the situation with the Graduate Program Director.
• Submit to the Graduate Examination Committee a copy (in English or in the original language with an English translation) of the examination which the student passed.
• Supply a signed statement by the Chair or Graduate Program Director of the student’s previous university certifying the maximum possible grade on the examination, the minimum grade for a pass at the Ph.D. level, and the grade obtained by the student.

The Graduate Examinations Committee will consider both the level of the test and the quality of the student’s performance in deciding whether to recommend to the faculty that the student be exempted from taking the written comprehensive exam at Stony Brook.

The Oral Exam

The oral exam consists of a presentation of an approved research topic in physics or astronomy to a committee of at least three faculty members, prepared under the guidance of one of them. The committee members must be approved in advance by the Graduate Program Director. The committee should contain at least one experimentalist and one theorist, and at least one member whose research specialty is different from the student’s field of research. At least half of the committee, and the chair, must be full-time faculty, and the chair cannot be the student’s future advisor.

The faculty advisor for the oral exam will generally become the student’s thesis advisor. This exam is a demonstration that the student is capable of beginning Ph.D.-level research; it is not necessary to show a completed research project. In addition, upon passing the exam, an advisor is asked to commit to supporting the student academically going forward, and, where possible, with funding.

Students are encouraged to complete the Oral Exam by the start of their sixth semester at Stony Brook. The formal deadline is before the start of the seventh semester (the start of their fourth year). Students may take the Oral Exam while still completing their coursework and the Comprehensive Exam – there’s no requirement to finish those first.

In some cases a student may pass the Oral Exam on time but not have a thesis advisor committed to continuing – either because one hasn’t been identified yet, or because the oral-exam advisor decides at this point not to continue. In this case, the student must find a new advisor to remain in Good Standing.

For how to assemble your committee, choose a topic, and submit the required forms, see The Oral Exam in Resources.

The Doctoral Defense

This is the last exam taken by a Ph.D. student at Stony Brook: an oral defense of the thesis before the Thesis Defense Committee. All defense committees are subject to approval by the Graduate Program Director; usually, the student’s Oral Exam committee serves as its core.

The committee has at least four members: at least three from the Department (full-time or adjunct), typically the three members of the student’s Oral Exam Committee, plus one external member from outside the Department – a scientist from another department at Stony Brook or another institution, who is not a collaborator or co-author, and who can give an independent evaluation of the thesis work. At least half of the committee, including the chair, must be full-time faculty, and the chair cannot be the student’s advisor. The committee should include at least one experimentalist, one theorist, and one member from a research field other than the thesis topic; the external member may also fill the experimentalist or theorist role.

The advisor, chair, and student must be physically present for the defense. Other members are preferred to attend in person but may participate virtually.

For the full step-by-step checklist – filing for graduation, forming and getting your committee approved, writing the thesis, submitting the defense announcement, and collecting signatures and submitting to ProQuest – see the steps to The Doctoral Defense in Resources.

General Policies

The sections below cover departmental and University policy on conduct, academic standing, tuition, and funding – as distinct from the academic requirements and milestones described above.

Professional Conduct

Graduate students are expected to conduct themselves professionally – both in everyday interactions with colleagues and in their research – and to meet the same ethical standards as any other member of the University and physics communities. The Department is committed to the ethical standards of our professional society, the American Physical Society, and expects every member of our community to uphold them. Rather than restate that expectation here, this section points to where it’s actually defined.

Day-to-day conduct toward colleagues, students, and staff is governed by the University’s Code of Student Responsibility, published by Community Standards, whose “Respect for Persons” provisions prohibit harassment and discrimination; sexual misconduct is covered separately under Section VII. Concerns can be raised with the Office of Equity and Access or Title IX. Because graduate students also teach, university policy additionally bars personal or business relationships with students you supervise or grade.

Research conduct falls under the University’s Responsible Conduct of Research and Scholarship policy; students on grant-funded research may be required to complete related training as a condition of that funding. Fabrication, falsification, and plagiarism in research are handled by the University’s Research Integrity Officer – see the Office of Research Compliance’s Research Misconduct page for how to report a concern; the same behavior in coursework – including the Comprehensive Exam – instead falls under the Academic Integrity Policy.

For physicists specifically, the APS Ethics Standards are worth reading in full: they cover both halves of this at once – treating colleagues and students fairly and respectfully, and conducting research honestly, including proper authorship and prompt correction of honest error.

Violations of these standards, in fact or in spirit, are handled by the appropriate University office: Community Standards for conduct, the Academic Judiciary for coursework integrity, the Office of Equity and Access for harassment and discrimination, Title IX for sexual misconduct, and the Office of Research Compliance’s Research Misconduct process for research. Decisions to dismiss or place a student on probation for conduct are made by the Graduate School and these offices, not the Department. The Department’s own Good Standing review below is reserved for academic progress, though professional conduct is also a factor in ongoing TA support – see Graduate Funding below.

Good Standing

Good standing means a student is meeting the requirements of the degree program and making satisfactory progress toward the degree. A student can also lose good standing through inappropriate conduct, as discussed in Professional Conduct above.

Responsibility for the Degree Requirements. A student is responsible for keeping their own degree steps on track, and neglecting this responsibility can also affect good standing, just like coursework, conduct, or progress toward the degree. If a student ever does fall out of good standing, for any reason, it’s on them to reach out and work promptly with the Graduate Program Director on a plan to get back on track. Better still, a student who sees trouble coming is encouraged to reach out early, before it becomes a good-standing issue.

Advisor and Oral Exam. Students are expected to find an advisor and complete the Oral Exam by the formal deadline – the end of their third year – since an advisor is required both for the Oral Exam and for advancing to candidacy. The Oral Exam can be repeated as long as the student is within this deadline. A student who reaches the deadline without an advisor committed to continuing is no longer in good standing.

Teaching. TA performance is evaluated each semester by the supervising faculty member. Sustained unsatisfactory performance can put a student’s good standing at risk, and can result in the loss of TA funding (see Teaching and Graduate Funding above).

Core courses. Students are required to take the core courses, except if they passed the relevant Comprehensive Exam at the placement level or received a course waiver. If a student has not passed out of the course and does not pass the course with a grade B or better, they can either take the course again or pass the Comprehensive Exam at the doctoral level. A student with unusual mitigating factors (such as medical leave), can petition the Graduate Program Director for a “make-up” oral exam. The “make-up” oral exam may be set up to test the student’s knowledge in the particular area. For example, if a student got a B- in PHY 505 then the exam will cover “Electricity and Magnetism”. The time of the exam, and the three-member exam committee, will be chosen by the Graduate Program Director and will typically involve the core course instructor.

Comprehensive exam. If a PhD student has not passed the comprehensive exam at the beginning of their fifth semester, an ad hoc committee shall be set up. This committee will be chaired by the graduate program director and include the chair of the exam committee and any advisor if the student has started working with a professor. Additional members as considered appropriate may be added at the discretion of the graduate program director. This committee will decide whether the student shall be given an Oral Exam in the relevant subject(s), whether there are additional comprehensive exam attempts to be given, or whether they will have to leave the program. The criteria on which the decision will be made include past performance on the comprehensive exam, the standing of the student with regard to required courses, and their demonstrated potential to proceed to full-time Ph.D. research. It is the department’s general policy that if progress on these three criteria is satisfactory a student will be granted an opportunity to either take the written exam again or have an Oral Exam. A student who is denied this opportunity and asked to leave the program may appeal through the Graduate School’s own Probation, Conduct and Grievances process.

Time limit to degree. Like all Stony Brook doctoral students, students must complete the Ph.D. within seven years of reaching 24 graduate-level credits (G4 status, usually the end of the first year) – the Graduate School’s University-wide time limit. See Time Limit Extension in Resources for how to request more time if you need it – the request is reviewed by the Graduate Program Director together with your advisor.

Letter of Concern. Before a situation rises to the level of formal probation, the Graduate Program Director may send a student an informal Letter of Concern – flagging a specific problem (a missed milestone, slow research progress, TA performance, etc.) and what’s expected going forward. This is not a formal action and does not appear on a student’s record; it’s meant to give a student the chance to correct course early.

Probation. The Graduate School applies its own academic standards to all doctoral programs: a cumulative graduate GPA below 3.0 in courses numbered 500 or above triggers academic probation, for a maximum of two semesters. A student must return their GPA to 3.0 by the end of the second probation semester or will not normally be permitted to continue – see the Graduate Catalog’s Probation, Conduct and Grievances policy for the full requirements, including the required notification letter and the process for appealing a decision.

Departmental Probation. In addition, the Department may place a student on probation for insufficient progress on the degree requirements – for example, not finding an advisor or not passing the Comprehensive Exam on time. In this case, a probation committee shall be set up: no fewer than three faculty, chaired by the graduate program director and including the student’s advisor, if one has been identified. Additional members as considered appropriate may be added at the discretion of the graduate program director. This committee will evaluate the student’s overall progress in the degree program and set a realistic timeframe – usually one semester – to address the identified issues. A student who remains on probation past this timeframe, without resolving or progressing on the underlying issues, may be dismissed from the program, at the discretion of the probation committee.

Appeal. A student who believes they have been unfairly dismissed may appeal. The primary avenue is the Program Grievance and Appeals Committee (GPGAC), described in the Graduate School’s Probation, Conduct and Grievances policy – an ad hoc committee, with no fewer than four members split evenly between faculty and graduate students, that the student must request be convened. The GPGAC’s review is limited to whether proper procedure was followed and policy was fairly applied – it does not re-evaluate the underlying academic judgment, such as whether the student had in fact met the degree requirements. If the matter isn’t resolved at this level, it can be escalated to the Dean of the Graduate School and, from there, the Graduate Council Appeals Committee (GCAC), whose decision is advisory to the Dean; the decision of the Vice Provost for Graduate Education is final.

Tuition Waivers

If properly handled, Ph.D. students do not pay tuition, which is covered by a tuition scholarship. However, serious problems can arise for those who fail to follow instructions, respond to notices, or submit forms on time – sometimes resulting in large, irretrievable financial losses. Two things put this coverage at risk if you don’t follow through on them:

• New York State residency. Establish residency as soon as you’re eligible – see New York State Residency in Resources for the requirements, documentation, and deadlines.
• Your credit load. Register for the number of credits your tuition waiver requires each semester – see Registering for Classes and Credits in Resources for the current requirements and what happens if you go over.

Graduate Funding

Doctoral students are typically supported as a Teaching Assistant (TA) during their first two years, as outlined in their offer letter. After that, students are expected to find an advisor and move to research-grant support as a Research Assistant (RA). Some students have different arrangements, for example through graduate fellowships.

Doctoral students can also be supported as a TA during the summer. The TA Allocation Committee, described below, makes these decisions. First-year students requesting summer support receive strong preference. In Fall 2026, for example, every first-year student who requested summer support received eight weeks of it.

Students sometimes need additional funding. This can happen if a student has not yet found an advisor able to provide funding, or if an advisor’s funding is unexpectedly interrupted. In these cases, the Department may be able to provide extra TA support.

The TA Allocation Committee decides whether extra TA support is warranted. Its members are the Graduate Program Director (Derek Teaney), the Graduate Coordinator (Donald Sheehan), the Undergraduate Program Director (Dominik Schneble), and the Undergraduate Astronomy Director (Michael Zingale). The committee weighs:

1. Availability of TA lines.
2. How many semesters of extra TA support the student has already received.
3. Whether the student is in good academic standing and making research progress.
4. The student’s past performance as a TA and their professional conduct.
5. Any mitigating factors.

A third-year student in good standing who needs more time to find an advisor or settle into a research group will almost always receive additional funding. To date, the only students denied this funding have had serious, ongoing problems with professional conduct or with academic and research progress.

Leave of Absence

Parental Leave. Eligible students can take up to 12 weeks of leave for a birth, or 6 weeks for an adoption or foster placement. You’ll keep your full-time registered status, benefits, and funding, plus get an automatic one-semester extension on program deadlines. See the Graduate School’s Parental Leave Policy for eligibility, and submit the Parental Leave Application with supporting documentation, ideally 30 days ahead. International students should also check with Visa and Immigration Services.

Other Leave (e.g., Medical Leave). If you need to take leave for another reason, such as a medical issue, we want to make this as manageable as possible. Submit a Request for Leave of Absence form to the Graduate School. The Graduate Catalog covers the full policy and is worth reading. A leave is typically granted for up to a year, and can be extended for an additional year on review.

If possible, work out a re-entry plan with the Graduate Program Director and your advisor. You can use the Re-Entry Plan Template on the Graduate School’s Student Resources page as a starting point. The plan should cover funding, and whether your research will remain timely when you return. In the current funding environment, we can’t promise your grant funding will still be available upon your return, but if it isn’t, the TA Allocation Committee described above can consider funding you as a TA.

Concentrations

Beyond the standard PhD, we offer two concentrations for students with more specific interests. Each has slightly different requirements from the default track, particularly around the breadth and laboratory courses.

Astronomy Concentration

Students may elect to earn a Ph.D. in Physics with a concentration in Astronomy. (Note: you can work with an advisor in Astronomy without earning this concentration.) To complete the Ph.D. with this concentration, students need to take three courses chosen from PHY 521, 522, 523, 524 (the core astronomy sequence) and PHY 620 (Modern General Relativity) – that is, any three out of the five. The four core astronomy courses rotate on a four-semester cycle, one course per semester, while PHY 620 is offered every year. Students completing the astronomy concentration satisfy the standard breadth requirement in this manner. A possible astronomy sequence looks like this:

The particular order of the astronomy courses is determined by the actual course offering in those semesters. The order PHY540/PHY505 and PHY511/PHY512 can be switched according to the preference of the student. PHY 515 or PHY 517 (discussed above) can be taken in any semester during the first two years.

Physical Biology Concentration

This is an interdisciplinary concentration in connection with the Laufer Center for quantitative biology. Students usually declare their interest in this concentration not later than the end of the first semester. Postponing this decision will result in a loss of time. The main difference with the default physics concentration is a reduction of core courses by one course while several physical biology courses are required. Instead of the graduate lab students do rotations with faculty associated with the Laufer center. Also the Graduate Seminar is substituted by the Laufer Center Journal Club. The requirements for a Ph.D. Degree in Physics with Concentration in Physical Biology are as follows:

• Four Physics core courses: Electrodynamics (PHY 505), Quantum Mechanics I (PHY 511), Statistical Mechanics (PHY 540) and either Classical Mechanics (PHY 501) or Quantum Mechanics II (PHY 512).
• Two Core Courses in Physical Biology: Physical Biology (PHY 558) and Biological Dynamics and Networks (PHY 559)
• Biology For Physical Scientists (PHY 561)
• Two semesters of Teaching (PHY 600)
• Two semesters of Lab Rotations (PHY 584 / AMS 531)
• Two semesters of the Laufer Center Journal Club (PHY 665 / AMS 532)
• Two Life Science courses from an approved list. Currently, the following courses have been approved: Biomolecular Structure and Analysis (CHE 541), Molecular Genetics (MCB 503), Structural Biology and Spectroscopy (MCB 512), Graduate Biochemistry I (MCB 520), Cell Biology (MCB 656), Introduction to Neuroscience I (BNB 561), and Introduction to Neuroscience II (BNB 562)
• Passing of the Comprehensive Exam.
• An oral exam on a topic in Physical Biology
• Student should find an advisor working on the topic of Physical Biology

All courses have to be passed with a grade of B or better.

A typical course sequence for students in the Physical Biology concentration looks something like:

Additional information on the Concentration in Physical Biology can be found on the webpage of the Laufer Center which also has a list of course requirements.