Doctor of Philosophy
PhDOverview
The Department of Applied Physics offers qualified students with backgrounds in physics or engineering the opportunity to do graduate coursework and research in the physics relevant to technical applications and natural phenomena. These areas include accelerator physics, biophysics, condensed matter physics, nanostructured materials, quantum electronics and photonics, quantum optics and quantum information, space science and astrophysics, synchrotron radiation, and applications.
Faculty members and various members of other departments such as Biology, Chemistry, Electrical Engineering, Materials Science and Engineering, Physics, the SLAC National Accelerator Laboratory, and faculty of the Medical School engaged in related research fields supervise student research.
Research activities are carried out in laboratories including the Geballe Laboratory for Advanced Materials (GLAM), the Edward L. Ginzton Laboratory (GINZTON), the Hansen Experimental Physics Laboratory (HEPL), the SLAC National Accelerator Laboratory, the Center for Probing the Nanoscale, and the Stanford Institute for Materials and Energy Science (SIMES).
This program is full time, doctoral students in the Applied Physics PhD program are expected to maintain a significant physical presence on campus throughout their graduate studies. This ensures that students have access to advisors and mentors, libraries, and other resources that support timely progress towards completion of degree requirements. Additionally, being on campus ensures that students are part of the academic and campus community which supports continued professional development.
Requirements
Program Requirements
Requirements Overview
The program leading to a PhD in Applied Physics consists of coursework, research, qualifying for PhD candidacy, a research progress report, a university oral examination, and a dissertation.
Courses in Physics and Mathematics to overcome deficiencies, if any, in undergraduate preparation
Basic graduate courses: These requirements may be totally or partly satisfied with equivalent courses taken elsewhere, pending the approval of the graduate study committee; Letter grades are required for all courses
Students are expected to complete the specified course requirements by the end of their third year of graduate study
Coursework
PhD candidates must complete a minimum of 135 units. These courses must be numbered 100+.
Out of the 135 units, a student must complete a minimum of 30 units of approved courses in engineering and science. Core Course requirements outlined below make up 12-15 of these 30 units and must be taken for a letter grade. 18 of these 30 units must be advanced course work numbered 200+ to fit the particular interests of the individual student and must also be taken for a letter grade.
Additional units of courses as needed to meet the minimum residency requirement of 135 units. Research units, directed study, seminars, and curricular practical training included.
Core Course Requirements
All PhD students must complete at least one approved graduate course (for a letter grade) in each of any four of the following five areas:
Quantum Mechanics
Statistical and Condensed Matter Physics
Classical Physics
Methods
Biophysics
A course that appears in multiple categories may be used to satisfy only one core requirement. The flagship course, offered every year by the Applied Physics department in each area is listed in each area. Students unfamiliar with a topic area are strongly encouraged to begin with the flagship course, or another more introductory course as needed. Discussions with the academic advisor will help students determine their appropriate curriculum. Students with prior background may choose any approved course in that category.
Total coursework: Students must complete a minimum of 18 units of courses numbered 200 or above in science or engineering, including the four core courses above.
Letter grade: All courses used to satisfy program requirements must be taken for a letter grade.
Double-counting: A course that appears in multiple categories may be used to satisfy only one core requirement.
Units to Reach PhD University Minimum: An additional 105 units are needed to meet the University minimum residency requirement of 135 units of completed course work. This requirement is typically fulfilled primarily by directed study and research units, as well as 1-unit seminar courses.
Waiver and Substitution Policy
Students with equivalent prior coursework may petition the Graduate Studies Committee for a substitution (not a waiver). Under a substitution, the student takes a different advanced course in a related area rather than skipping the requirement; the total number of required courses remains the same. Students considering a substitution should consult with their academic advisor to assess their preparation and identify an appropriate alternative course.
Petitions should include the syllabus and transcript from the prior course. The committee chair reviews for equivalency.
Outright waivers (reducing the number of courses) are granted only in rare circumstances.
Milestones
Third-Year Progress Meeting: this is to discuss the progress toward the formulation of thesis research and completion of the other degree requirements. This is not an examination and there is no recorded evaluation. It must occur by the end of spring quarter of the third year. The third-year progress committee consists of the student’s research advisor and one additional faculty member. This second member of the committee can be the academic advisor or another Applied Physics faculty member of the student’s choosing.
Fourth-Year Progress Report: this is normally completed before the end of winter quarter of the fourth year of enrollment in graduate study at Stanford. The Progress Report should not be viewed as an exam; rather, it is an informational discussion between students and the group that will be their Dissertation Reading Committee. Students share research results to date and get input on future research plans leading to degree conferral. The student arranges to give an oral research progress report presentation should not take more than 45 minutes, with an additional 15 minutes for questions.
Core Course Requirements
Complete at least 1 course in each of any 4 of the following 5 areas.
Quantum Mechanics
Flagship course: APPPHYS 203 is strongly recommended for students unfamiliar with this topic area.
APPPHYS 203
Atoms, Fields and Photons
APPPHYS 228
Quantum Hardware
APPPHYS 282
ULTRACOLD QUANTUM PHYSICS
APPPHYS 283
Ultrafast Quantum Physics
EE 224
Quantum Control and Engineering
PHYSICS 230
Graduate Quantum Mechanics I
PHYSICS 231
Graduate Quantum Mechanics II
PHYSICS 234
Advanced Topics in Quantum Mechanics
PHYSICS 330
Quantum Field Theory I
PHYSICS 331
Quantum Field Theory II
PHYSICS 332
Quantum Field Theory III
PHYSICS 430
Quantum Error Correction
Statistical and Condensed Matter Physics
Flagship course: APPPHYS 204 is strongly recommended for students unfamiliar with this topic area.
APPPHYS 204
Quantum Materials
APPPHYS 229
Statistical Mechanics of Learning and Computation
APPPHYS 230
Renormalization Group and Randomness
APPPHYS 270
Magnetism and Long Range Order in Solids
APPPHYS 272
Solid State Physics
APPPHYS 273
Solid State Physics II
APPPHYS 280
Phenomenology of Superconductors
APPPHYS 285
Physics of Disordered Systems
CHEMENG 466
Polymer Physics
PHYSICS 212
Statistical Mechanics
PHYSICS 372
Condensed Matter Theory I
PHYSICS 373
Condensed Matter Theory II
Classical Physics
Electrodynamics and Optics
Flagship course: APPPHYS 201 is strongly recommended for students unfamiliar with this topic area.
APPPHYS 201
Electrons and Photons
APPPHYS 220
Advanced Topics in Accelerator Physics
APPPHYS 325
Synchrotron Radiation and Free Electron Lasers: Principles and Applications.
EE 236A
Modern Optics
EE 236B
Guided Waves
EE 236C
Lasers
EE 242
Electromagnetic Waves
EE 292L
Computational Electromagnetics
EE 336
Nanophotonics
EE 346
Introduction to Nonlinear Optics
MATSCI 341
Quantum Theory of Electronic and Optical Excitations in Materials
PHOTON 366
Light and Plasma
PHYSICS 220
Classical Electrodynamics
Continuum Mechanics
Note: There is no flagship course for Continuum Mechanics.
Methods
Laboratory Courses
Flagship courses: APPPHYS 214 or APPPHYS 232 are strongly recommended for students unfamiliar with this topic area.
APPPHYS 214
Experimental Methods for Quantum Materials
APPPHYS 222
Principles of X-ray Scattering
APPPHYS 232
Advanced Imaging Lab in Biophysics
EE 234
Photonics Laboratory
EE 235
Molecular and Cellular Engineering Lab
EE 235A
Analytical Methods in Biotechnology I
EE 251
High-Frequency Circuit Design Laboratory
EE 312
Integrated Circuit Fabrication Laboratory
ENGR 241
Advanced Micro and Nano Fabrication Laboratory
MATSCI 171
Energy Materials Laboratory
MATSCI 172
X-Ray Diffraction Laboratory
MATSCI 173
Mechanical Behavior Laboratory
MATSCI 322
Transmission Electron Microscopy Laboratory
MATSCI 326
X-Ray Science and Techniques
MATSCI 327
Transmission Electron Microscopy Analysis and Simulation
PHYSICS 301
Graduate Observational Astrophysics
Computational Courses
Note: There is no flagship course for Computational Courses.
CME 206
Introduction to Numerical Methods for Engineering
CME 213
Introduction to parallel computing using MPI, openMP, and CUDA
CS 221
Artificial Intelligence: Principles and Techniques
CS 224N
Natural Language Processing with Deep Learning
CS 224R
Deep Reinforcement Learning
CS 228
Probabilistic Graphical Models: Principles and Techniques
CS 229
Machine Learning
CS 236
Deep Generative Models
EE 292L
Computational Electromagnetics
EE 364A
Convex Optimization I
EE 364B
Convex Optimization II
ME 469
Computational Methods in Fluid Mechanics
Mathematical Methods Courses
Note: There is no flagship course for Mathematical Methods Courses.
APPPHYS 223
Stochastic and Nonlinear Dynamics
CME 308
Stochastic Methods in Engineering
EE 276
Information Theory
EE 278
Probability and Statistical Inference
MATH 220A
Partial Differential Equations of Applied Mathematics
STATS 200
Introduction to Theoretical Statistics
Biophysics
Note: There is no flagship course for Biophysics.
APPPHYS 205
Introduction to Biophysics
APPPHYS 235
Biotransport Phenomena
APPPHYS 237
Quantitative Evolutionary Dynamics and Genomics
APPPHYS 294
Cellular Biophysics
CHEMENG 320
Chemical Kinetics and Reaction Engineering
18 Units of Additional Advanced Courses in Science and/or Engineering
At least one science/engineering-based course in each of two areas other than the student’s research specialization is required.
Units from APPPHYS 290, APPPHYS 390, and any 1-unit courses do not count towards this requirement.
Teaching Requirement
There is no teaching requirement for the doctoral degree in Applied Physics. However, students may teach as part of their professional training. Numerous applied physics students have held teaching positions in the Physics department.
Research Requirement
Research
Applied Physics offers a rotation program for research assistantships for 1st-year graduate students. The purpose of the rotation program is to acquaint first-year students with research opportunities before they make a final selection of a research group. Each rotation lasts for one quarter. It is not required that students rotate to a different group each quarter, and indeed students often find their research group in their first quarter, without rotating into any subsequent group. Students are expected to coordinate their first rotation prior to the start of their first Autumn quarter (i.e., during the Summer prior to matriculation in the program).
Students are expected to have found a research group (often referred to as a “home lab” or “research home”) for their Ph.D. research by the end of the Spring quarter of their first year. If a student hasn’t found their research home by the end of Summer quarter of their first year, their academic progress may be delayed. One of the requirements of moving to candidacy is having a clear direction for the research that will be the focus of the student’s post-candidacy work towards their Ph.D. This makes finding a home lab by the end of a student’s first academic year a key component of making satisfactory academic progress. (Candidacy is discussed in more detail below.)
Finding a rotation position: Rotations in your first year may be supervised by any member of the Applied Physics faculty, or with faculty in any other science or engineering department at Stanford, including SLAC. Rotation positions are secured by the students through mutual agreement with the rotation supervisor (aka PI aka Research Advisor; these terms are used interchangeably). This is best finalized no later than three weeks before the end of the preceding quarter. (For example, you should secure your Winter quarter rotation 3 weeks before Autumn quarter ends.)
Advancement to Candidacy
PhD Candidacy
Admission to candidacy is a prospective judgement by the faculty of a student's potential to successfully complete the requirements of the degree program. In the Department of Applied Physics, students are reviewed for candidacy by the Graduate Studies and Curriculum (GSC) Committee in the spring quarter of their second-year. The committee’s assessment is based on the student’s performance on the qualifying exam, the student’s research progress as documented by a letter from their advisor, and the student’s performance in coursework.
The GSC will recommend or deny admission to candidacy for each second-year student, noting any unmet course requirements. Although students have until the end of their 3rd year to complete course requirements, it is expected that the vast majority of required courses will be completed by the end of a student’s second year. In a case where admission to candidacy is not recommended, the reason will be stated in writing. Students are able to appeal the committee’s decision to the Director of Graduate Studies.
Failure to advance to candidacy will result in dismissal from the doctoral program.
Oral Exam
Oral Exam
University PhD Oral Examination consists of a public seminar in defense of the dissertation, followed by private questioning of the candidate by the university examining committee. Students consult with their dissertation advisor and reading committee members on the timing of the defense.
Dissertation
Dissertation
The dissertation must be approved and signed by the PhD reading committee. Students are expected to submit the dissertation by the end of their sixth year in the program.

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