NEUROSCIENCES GRADUATE PROGRAM December 8, 2015 To

NEUROSCIENCES GRADUATE PROGRAM

December 8, 2015

To: Graduate Council

CC:

Benjamin Grinstein, Chair, Physics

Geert Schmid-Schoenbein, Chair, Bioengineering

Thomas Murphy, Vice-chair of Education, Physics

Marcos Intaglietta, Director of Graduate Studies, Bioengineering

Erin Gilbert, Program Administrator, Neurosciences Graduate Program

SUBJECT: Proposed expansion of the Specialization in Computational Neuroscience

Dear Council,

On behalf of the Neurosciences Graduate Program, I am submitting to you a proposal to

expand the Specialization in Computational Neuroscience.

The UCSD Neurosciences Graduate Program is one of the very top programs in

the nation, and a flagship interdisciplinary effort that unites neuroscience research from

over 150 laboratories and multiple institutes across the Torrey Pines Mesa. We currently

offer Neurosciences Graduate students the opportunity to specialize in Computational

Neuroscience. Here we seek to expand the pool of UCSD graduate students with access

to this growing research field, by opening the computational neuroscience specialization

to well-prepared PhD students from Physics and Bioengineering.

We believe that this expansion offers immediate and long-term benefits to

graduate students, to all three participating departments/programs, and to the broader

neuroscience effort across our campus. Our motivations for this expansion, along with

the justification and rationales for all proposed changes are detailed in the following

sections. The proposal was approved by unanimous vote of the Neurosciences Graduate

Program Executive Committee, at its fall 2015 meeting, and endorsed by the graduate

committees in the Departments of Physics and Bioengineering.

Sincerely,

Timothy Gentner, PhD

Director Neurosciences Graduate Program

PROPOSAL TO EXPAND THE SPECIALIZATION IN COMPUTATIONAL

NEUROSCIENCE

2. Executive Summary:

The goal of the existing Specialization in Computational Neuroscience at UCSD is to

train researchers that are equally at home measuring large-scale brain activity, analyzing

neural data with advanced computational techniques, and developing new models for

brain development and function. The specialization is currently open to students in the

Neurosciences Graduate Program (NGP). We propose to expand the specialization so that

students pursuing their PhD in Physics and Bioengineering graduate programs can also

join the specialization.

Academic Rationale and Justification:

The current Specialization in Computational Neuroscience (SCN) grew out of the

Computational Neurobiology Program (CNP), a degree-granting graduate program within

the Biology Department established in 1999. The CNP was a highly interdisciplinary

program, with faculty in the Departments of Biology, Physics, Electrical Engineering,

Mathematics, Cognitive Science and the School of Medicine. For administrative and

academic reasons, the CNP was merged in the NGP in 2008, giving rise to the current

SCN. At present, any student admitted into the NGP can elect to pursue the SCN, and

provided all the requirements are met, receive a designation on their Neurosciences PhD

diploma noting their Specialization in Computational Neuroscience. The CNP-NGP

merger has been very successful. The SCN is now drawing a steady stream of

outstanding students through the NGP who are attracted to computational neuroscience.

As the size and scope of neurobiological data increase, we foresee tremendous

need in the broader neuroscience field for PhDs that combine biological and quantitative

expertise from the physical sciences and engineering. The NGP is in theory open to

applicants with non-traditional undergraduate neuroscience majors, such as physics,

engineering and mathematics. In practice, however, the highly competitive nature of our

applicant pool places students without substantial neuroscience experience at a

disadvantage. As a result, the current SCN now trains mostly neuroscientists seeking to

strengthen their computational skills. Expanding the SCN so that it is open to students in

the Physics and Bioengineering PhD Programs will broaden the scope of our training to

include physical scientists seeking to develop their quantitative and theoretical skills in a

neuroscience framework.

Expansion of the SCN to include Physics and Bioengineering students will have

several benefits to current and future students, and to each department/program. For

Physics and Bioengineering, the specialization will offer the opportunity for students to

focus (and formally denote) their current interests in biological physics or bioengineering

thesis projects that have clear ties to neuroscience theory and/or application. This formal

designation and training should benefit individual graduate program recruitment and open

additional opportunities for post-graduation placement. The expanded specialization will

also offer a core set of courses in Computational Neuroscience that will bring together

students from Physics, Bioengineering and the NGP. This will create a highly

interdisciplinary training environment that enhances the core curriculum within each

department by offering a fuller and more complete education in Computational

Neuroscience than is currently available in any one department or program.

The expanded specialization will also enrich the overall neuroscience community

at UC San Diego. Its interdisciplinary nature will help to harness the collective strength

of Computational Neuroscience efforts across the roughly 150-member strong

neurosciences faculty in the La Jolla Mesa community (UC San Diego, UC San Diego

School of Medicine, The Salk Institute, The Scripps Research Institute, Sanford-

Burnham). By acting as an informal bridge between Neurosciences, Physics, and

Bioengineering graduate students, the specialization will further develop collaborative

networks that span divisions and institutions.

Proposed effective date: We propose to offer the expanded SCN to all current students

in Physics and Bioengineering, including those matriculating in the fall 2015, and

thereafter.

2. Requested Changes

2.a. Student composition: We propose to expand the SCN so that it is open to students

in the Physics and Bioengineering PhD programs as well as those in the Neurosciences

Graduate Program. The SCN currently has 34 students enrolled (or expected to enroll)

out of a total of 85 students in the NGP. Based on discussions with faculty in each

department, we estimate approximately 10 current graduate students in Physics and 8

current graduate students in Bioengineering will wish to pursue the Specialization in

Computational Neuroscience. A steady state enrollment of 50-55 students is expected in

the expanded SCN, with roughly 12-15 entering and graduating each year, distributed

evenly between the three contributing programs.

Justification and rationale: In a sense, the proposed expansion is simply an effort

to formalize and build an enabling infrastructure around a scholarly trajectory that

many students have already chosen. Many faculty in Physics and Bioengineering

already participate in the NGP, and PhD students in their laboratories already

weight their coursework and thesis projects to emphasize computational

neuroscience. Expanding the SCN offers a mechanism to standardize basic

scholarly components of this de facto trend and build on its ubiquitous nature to

strengthen a nascent portion of the broader UCSD neuroscience community.

2.b. Administration of Specialization: Oversight of the current SCN is maintained by a

Computational Neuroscience Committee, appointed by the Neurosciences Program

Executive Committee that also oversees the NGP. We propose that this committee

oversight remain in place, with the stipulation that the Computational Neuroscience

Committee have one member whose primary appointment is in Physics, one member

whose primary appointment is in Bioengineering, and at least two members of the

Neuroscience Graduate Program Faculty who do not hold primary appointments in Physics

or Bioengineering. All members will be faculty in the NGP. In addition to the four

stipulated faculty members, the committee will have at least one graduate student

member selected from all those in the specialization. The NGP Executive committee will

select a chair from among the 4 faculty members on the SCN Oversight Committee. This

chair will serve on the NGP Executive Committee, and act as the

point of contact for

coordinating the specialization within the graduate programs. The SCN Oversight

Committee will be responsible for developing all policies for the SCN, and for developing

and implementing the required coursework and curriculum for the

specialization.

Justification and rationale: It is crucial to the success of the expanded SCN that

all interested departments and programs as well as those of the participating

students be represented in the oversight. In addition, it is vital that the program

maintain its strong focus on neuroscience. The proposed representation on the

oversight committee, under the aegis of the Neurosciences Program Executive

Committee achieves these goals.

2.c. Admission Requirements: Currently, all students admitted to the NGP are eligible

to pursue the SCN. We propose adopting a more formal admissions process requiring (1)

acceptance and matriculation into the PhD program in Physics, Bioengineering, or the

NGP, and (2) approval by SCN Oversight Committee. Eligible students can apply by

submitting a copy of their C.V., undergraduate and graduate transcripts, and a short

description of their research interests to the committee. The committee can either admit

or reject an application, or provisionally approve an applicant contingent on completion

of additional coursework. All admitted students are expected to pursue PhD thesis research

that falls with the domain of Computational Neuroscience as construed by the Oversight

Committee. All students admitted to the specialization who complete the requirements

will have Specialization in Computational Neuroscience

designated on their diploma.

Justification and rationale: Students interested in the Computational

Neurosciences Specialization will have to meet the same general admission

requirements as all other PhD students applying to the Neurosciences Graduate

Program, Physics or Bioengineering. The Computational Neuroscience

Committee ensures a minimum level of preparedness and a relevant scope of

research interests among all PhD students wishing to pursue the specialization.

When appropriate the committee can recommend specific coursework in

neuroscience or mathematics as a condition of admission to the specialization.

2.d. Plans for Evaluation: The expanded Specialization in Computational Neuroscience

will continue to be closely monitored by the Neurosciences Program Executive

Committee. The SCN will be part of the Neurosciences Graduate Program external

review

on a 7-year cycle. Input from Physics and Bioengineering will be encouraged as a

part of this review.

Justification and rationale: The current SCN is overseen by the Neurosciences

Graduate program, and given the proposed content of the expanded SCN we think

maintaining this oversight, and all concomitant evaluation, is appropriate.

4. Rationale and Justification

See section 2

5. Curricular Requirements:

5.a. Required courses: The SCN curriculum will be selected and overseen by the

Computational Neuroscience Committee. In addition to any requirements set forth by

their home departments/programs, all SCN students must complete a common sequence

of courses (12-18 units) as follows:

1. Fall: BGGN 260 (Neurodynamics); cross-listed as BENG 260 and approved to be

cross-listed through physics as PHYS 279. This course deals with fundamental

aspects of excitable membranes and analytically tractable models of single cells

and synapses. It was created by Henry Abarbanel (Physics) and in recent years

has been taught by faculty in Bioengineering. This is a long-standing requirement

of the SCN.

2. Winter: PHYS 278 (Biophysical Basis of Neuronal Computation); Plans

are in

progress to cross-list it through BGGN and ECE. This is a core course on network

models of neuronal computations. It was created by David Kleinfeld

(Physics)

and has been taught as well by Tatyana Sharpee (adjunct through Salk). PHYS

278 course will replace the current PHYS 271 course requirement. A proposed

catalogue copy is included at the end of this proposal.

3. Spring: COG 260 (Algorithms for the Analysis of Neural Data); this is a new

course that we plan to cross list through BGGN. It deals with the use of modern

statistical tools to analyze point processes and continuous data streams. It was

created by Eran Mukamel (PhD in Physics). This is an existing requirement of

the SCN.

N.B.: We are proposing to replace PHYS 271 with PHYS 278 as a SCN course

requirement. The subject matter between the two is very similar but the overlapping

content between PHYS 271 and BGGN 260 is now eliminated, and the entire sequence

is now coordinated and sequenced more efficiently.

Additional course requirements: In addition to those courses in the SCN course series

described above, Physics and Bioengineering graduate students will be required to take BENG

234: Introduction to Neurophysiology: Molecules to Systems. This course was

specifically designed by Prof. Gabriel Silva for students with physical

sciences or

engineering background. It is already being offered in the spring quarter and

thus could

be taken by a SCN student at the end of their

first (or second) year. A Physics or

Bioengineering student can waive the BENG234 requirement by petition to the SCN

Oversight Committee giving evidence

of sufficient background neuroscience knowledge.

Final determination of this sufficiency is at the discretion of the Oversight Committee.

Thesis research: All SCN students are expected to complete a PhD dissertation

connected with an issue in contemporary computational neuroscience. Either the

student’s primary advisor or a close co-advisor (approved by the Computational

Neuroscience Committee) must be a member of the NGP faculty. Their thesis committee

must continue to meet all the requirements of their home department.

Professional Development: The SCN currently offers graduate students a number of

opportunities to interact professionally outside of classes. These include a vibrant journal

club, impromptu workshops on specific techniques and/or theories, and special lectures

and chalk talks with prominent computational neuroscientists visiting campus. These

opportunities would, of course, be made available to all students in the expanded

specialization.

5.b. Foreign language requirement: The SCN has no foreign language requirement.

5.c. Sample programs of study:

Physics: A first year Physics student, assumed to be preparing for the Qualifying Exam,

would take existing course sequences in Mechanics (Physics 200), Quantum Mechanics

(Physics 212), and Electricity and Magnetism (Physics 203). S/he would also take BENG

234 in Spring of year one. In the student’s second year, s/he would complete BGGN 260,

PHYS 278, and COG 260, and other courses beyond the core “Qualifying Exam" course

sequence to complete course requirements. All other requirements for a Physics PhD

(teaching, dissertation, advancement to candidacy, etc.) remain in place.

Bioengineering: All

bioengineering students in their first year will be expected to enroll

in the seven required

core courses in the Engineering Physics and Life Science tracks.

First-year students are

also required to take: two quarters of laboratory research rotation

(BENG 298L); both

one-credit seminars (BENG 281 and BENG 282); and one quarter

(W or S) of Teaching

Experience (BENG 501). Bioengineering PhD students will

continue to be required to pass the

Departmental Qualifying Examination, which must be

taken during the spring quarter of the first year of study. The exam is designed to ensure

that all successful candidates

possess a firm command of the engineering and life science

subjects that form the

foundations of bioengineering research and their integration at a

level appropriate for the

doctorate. The scope of the oral examination includes the two

broad areas that form the

core first-year PhD curriculum, namely Engineering Physics

and Life Science.

Neurosciences Graduate Program: A first year NGP student will take the core 200

series (NEU 200A, B, C), Statistical Methods (NEU 225), Mammalian Neuroanatomy

(NEU 257), and Research Ethics. S/he would then complete the SCN core sequence

(BGGN 260, PHYS 278, and COG 260) in the second year, while also completing the

Minor Prop (NEU 280). The SCN courses count towards the 12 credits of required

electives, as will additional math or other courses suggested by the Computational

Neuroscience Committee. All other requirements for a Neurosciences PhD remain in

place.

5.d. Qualification criteria: In addition to taking the Qualifying Exam

required by their

home department to advance to candidacy, all SCN students will be

required to pass oral

and written examinations for the three core courses listed in section 5.a to demonstrate

their preparation for research in computational neuroscience.

Teaching Requirements: All teaching requirements imposed by the student’s home

department/program will remain in effect. The SCN carries no additional teaching

requirements.

5.e.

Time Limits: Students are generally expected to complete all requirements for the

SCN in the first 2 years; all requirements must be completed before advancement to

candidacy. Students in the SCN will have the same time limits as other graduate students

in their home departments, in accordance with Graduate Division policy.

6. Relationship/Impact on existing academic programs.

6.a. Impact within NGP. For the Neuroscience Graduate Program, the transition to the

expanded specialization should be largely transparent. All current NGP students that

have elected to pursue the specialization will be admitted, and their course requirements

will be remain the same, with the exception of the proposed SCN course requirement to

replace PHYS 271 with PHYS 278. We note that many of the Physics and

Bioengineering students likely

to join the SCN have already taken several of the

proposed core classes, attend the same

lectures and seminars, and many work in the same

labs with NGP students in the current

SCN. Again, we note that this community has

already self-organized to some extent.

6.b. Impact to Physics and Bioengineering. All Physics and Bioengineering students

wishing to obtain the SCN, along with all NGP students admitted for Fall 2015 or later,

would apply to the Computational Neuroscience Committee as described above (section

3.c). Advanced students from Physics and Bioengineering that wished to obtain the SCN

would also apply to the Computational Neuroscience Committee and be considered on an

individual basis, in close consultation with their primary thesis advisor to ensure that the

course requirements could be completed in a timely manner that did not adversely affect

their time to degree. Because many of the students outside NGP that are likely to join the

expanded SCN have already taken (or are taking) several of the proposed core classes, we

expect the negative impact on existing PhD programs to be very low.

6.c. Collective benefits to Physics, Bioengineering, and Neurosciences

•

All three contributing programs would benefit intellectually from the involvement of

a greater number of graduate students and faculty in computational, instrumental, and

theoretical issues pertaining to ongoing experimental work at UCSD. Likewise, the

mixing of students (and faculty) from disciplines with much in common, though

sometimes little interaction, would have synergistic benefits.

•

The expanded SCN would establish a pipeline to new methods of data analysis, of

particular relevance given the growth in high throughput measuring technologies.

7. Academic and Administrative Resources

We anticipate that additional draw on academic and administrative resources will be low.

No additional effort will be required of Bioengineering or Physics (but see suggestions

below). For the Neurosciences program staff the only additional burden will be in

confirming that 5-10 students per year have met the stipulated requirements for the

specialization and filing the appropriate paperwork for the degree annotation. The NGP

staff currently help to organize the SCN course scheduling and will continue to do so.

The NGP allows prospective students to indicate on their application whether they are

interested in the Computational Neuroscience specialization. This indication allows the

admissions committee to take into consideration any potential differences in the

student’s

background. Physics and Bioengineering will consider a similar indication on their

applications. To help with recruitment, a web page will be dedicated to the

Computational Neuroscience specialization, with links made available from each

department/program.

8. Graduate student support.

The proposed expansion of the SCN required no changes to the current methods for

securing graduate student support in each of the participating departments/programs.

Graduate support levels for students within the SCN will be determined by the students’

major department.

Supplementary Proposal Requirements

1. Statements from relevant departments/programs

See attached letters

2. Catalog Copy from each participating department

See attached documents

3. Draft course approval forms: No changes to existing courses or new courses are

required.

GEERT W. SCHMID-SCHÖNBEIN, PH.D. TELEPHONE (858) 534-3852

DISTINGUISHED PROFESSOR OF BIOENGINEERING AND MEDICINE FAX (858) 534-5722

CHAIRMAN E-MAIL: [email protected]sd.edu

DEPARTMENT OF BIOENGINEERING

9500 GILMAN DRIVE

LA JOLLA, CALIFORNIA 92093-0412

July 30, 2015

Timothy Gentner, PhD

Director, Neurosciences Graduate Program

University of California, San Diego

Dear Professor Gentner:

This letter is in support of the proposal for extending the graduate Specialization in Computational

Neuroscience to graduate students in the Department of Bioengineering. An advisory vote on the part

of the faculty was unanimously positive in favor of this.

We have a number of graduate students in the program with strong interests in theoretical and

computational neuroscience and neural engineering who will greatly benefit from this effort.

Furthermore, it will expose them and allow them to interact and integrate with the larger neuroscience

community at UCSD. This specialization is also complimentary to the core mathematics and

engineering curriculum within the bioengineering graduate program. Conversely, there are a number of

relevant courses within bioengineering that could be cross-listed with the specialization, thereby

providing students in the specialization from the neurosciences and physics graduate programs

opportunities to extend the courses available to them. This is already the case with the BENG234

Neurodynamics course, for example.

The department looks forward to working with you on this exciting educational endevour.

Sincerely,

BENJAMIN GRINSTEIN, CHAIR Telephone: (858) 534-6857

DEPARTMENT OF PHYSICS 0354 Email:[email protected]

9500 GILMAN DRIVE

LA JOLLA, CALIFORNIA 92093-0354

August 7, 2015

Professor Timothy Gentner

Department of Psychology

Dear Professor Gentner:

The Department of Physics is pleased to support the proposal for a graduate Specialization in

Computational Neuroscience.

This program opens new outlets for physics graduate students to explore exciting and vibrant research

programs. Our biophysics-interested students also have access to a Biophysics Specialization and to

the Q-Bio program, but we understand the Specialization in Computational Neuroscience to be

complementary to these programs rather than overlapped. Thus it can only be positive for our

students.

The BENG 234, BGGN 260 and COGS 260 courses will count toward the requirements for Physics

graduate students, albeit likely within the same group (they must have a total of five classes spread

across at least three of six groups).

We also support the cross listing of BGGN 260 with PHYS 279, and understand that possible Physics

faculty instructors include Henry Abarbanel, David Kleinfeld, and Massimo Vergassola. While we

support their commitment to the Specialization in Computational Neuroscience track, it is too early

for the Department to guarantee Physics Department teaching credit, contingent on how many

students from the physics community are served.

Congratulations on conceiving this well thought and exciting program.

Sincerely,

Benjamin Grinstein Thomas Murphy

Chair, Department of Physics Vice Chair, Department of Physics

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

oengineeering Graduate Curriculum (June 2015)

Bioengineering

[ undergraduate program | courses | faculty ]

STUDENT AFFAIRS:

141 Powell-Focht Bioengineering Hall

Warren College

http://www.be.ucsd.edu

All courses, faculty listings, and curricular and degree requirements described herein are subject to change or

deletion without notice. Updates may be found on the Academic Senate website:

http://senate.ucsd.edu/catalog-

copy/approved-updates/.

The Graduate Program

Admission to the MEng, MS, and PhD, as well as to the PhD with specializations in bioinformatics, multiscale

biology, and quantitative biology are in accordance with the general requirements of the Graduate Division.

Applicants are required to have completed a BS and/or MS degree by time of admission in a branch of engineering,

natural sciences, mathematics, or quantitative life sciences. MS and PhD applicants must have a GPA of 3.4 or

better in technical courses. MEng applicants should have competitive grades (greater than a 3.2 GPA). All applicants

must submit GRE General Test scores, as well as three letters of recommendation from individuals who can attest to

their academic or professional competence and to the depth of their interest in pursuing graduate study. Attention

will be paid to the background and statement of purpose to ensure that they are consistent with the goals of the

program. For example, whereas undergraduate research experience and the intention to pursue a research career or

advanced studies are qualifications and interests typically well suited to the MS program, industrial experience and

the intention to pursue a professional career are better suited to the MEng program.

A minimum score of 80 (Internet based) on the Test of English as a Foreign Language (TOEFL) or a band 7 on the

IELTS is required of all international applicants whose native language is not English and whose undergraduate

education was conducted in a language other than English. Students who score below 100 on the TOEFL

examination are strongly encouraged to enroll in an English as a Second Language program before beginning

graduate work. (UC San Diego Extension offers an English language program during the summer as well as the

academic year.) Admission to the MS or PhD degree program is designated when the applicants are judged to be

appropriately qualified to pursue the degree requested at the time of application. Applicants are considered for

admission for the fall quarter only.

Nonmatriculated students are welcome to seek enrollment in bioengineering courses via UC San Diego Extension’s

Concurrent Enrollment program. However, such enrollment in a bioengineering graduate course must be approved

by the instructor.

Integrated Bachelor’s/Master’s Program

An integrated program leading to a bachelor of science and a master of science degree in bioengineering is offered

to undergraduate students who are enrolled in any of the major programs offered by the Department of

Bioengineering. Students interested in obtaining the MS within one year following completion of the BS may apply

to the department for admission to the program during spring quarter prior to the receipt of the BS. The program is

open only to UC San Diego undergraduates.

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Bioengineeering Graduate Curriculum (June 2015)

To be eligible, students must have completed the first two quarters of their junior year in residence at UC San Diego

and have an upper-division GPA of 3.5 or better and a 3.0 overall UC GPA. Twelve units of bioengineering

graduate-level courses must be completed during the student’s senior undergraduate year, in addition to the

requirements for the bachelor’s degree; these twelve units will count toward the requirements for the master’s

degree only and must be taken for a letter grade. It is the responsibility of the prospective BS/MS student to select a

bioengineering faculty member who is willing to serve as the student’s adviser. The student will also arrange (with

their faculty adviser’s approval) a schedule of courses for the senior year that will fulfill the requirements for the BS

while also serving the program planned for the MS. Students are expected to meet the requirements for the MS in

one year (three consecutive academic quarters) from the date of the receipt of the BS.

Master of Science Degree Programs

The master of science (MS) program is intended to extend and broaden an undergraduate background and equip

the graduates with fundamental knowledge in bioengineering. It is intended for those students wishing to gain

experience in academic research, especially those considering continuing graduate studies at the doctoral level. The

MS may be terminal or may be obtained while pursuing a doctorate. Doctoral degree students wishing to obtain the

MS should refer to “Obtaining an MS Degree” under the section, “Doctoral Degree Program

.”

An individualized program is agreed upon by the student and a faculty adviser. The plan of study must involve both

course work and research, culminating in the preparation of a thesis.

A total of forty-eight units of credit is required:

• Thirty-six units in course work. Nine courses, of which seven are core courses in Engineering Physics

and Life Science and two are elective courses to be selected from approved graduate level course offerings

in bioengineering, other engineering/science departments, and the School of Medicine. The faculty adviser

must approve the two elective courses. The core courses and the elective courses must be taken for letter

grade.

• Twelve units in research (S/U grading only). Bioengineering Research (BENG 299) under the direction

of the chosen faculty research adviser.

A thesis based on the research is written and subsequently reviewed by the thesis adviser and two other faculty

members appointed by the dean of Graduate Studies. The oral defense of the thesis constitutes the departmental

master’s exam.

Required Courses for MS Program

Core Courses (total of seven required)

All core courses must be taken for letter grade.

Engineering Physics (four required)

• BENG 221. Mathematical Methods for Bioengineering

• BENG 223. Thermodynamics, Statistical Mechanics, Interfacial Phenomena in Living Systems

• BENG 226. Foundations of Biomechanics

• BENG 227. Transport Phenomena in Living Systems

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

oengineeering Graduate Curriculum (June 2015)

Life Science (three required)

• BENG 230A. Biochemistry (required)

• BENG 230B. Cell and Molecular Biology (required)

Plus one of the following courses:

• BENG 231. Foundations of Physiology for Bioengineering

• BENG 230C. Cardiovascular Physiology

• BENG 230D. Respiratory and Renal Physiology

• BENG 232. Musculoskeletal Health, Injury, and Disease

• BENG 260/BGGN 260. Neurodynamics

Elective Courses (two required)

All graduate level courses offered in the Department of Bioengineering may be used to fulfill the elective course

requirement. Students may also take graduate level engineering/science courses offered in other departments (e.g.,

MAE, ECE, SOM) for elective credit with prior faculty adviser approval. Courses taken in fulfillment of the elective

course requirement must be taken for letter grade.

Seminars (required)

• BENG 281. Seminar in Bioengineering (F, W, S)

• BENG 282. Seminar: Faculty Research (F)

Restrictions to course work requirements are as follows:

1. Units obtained in BENG 281, 282, 299, or 501 may not be applied toward the course work requirement.

2. No more than a total of eight units of BENG 296 and 298 may be applied toward the course work

requirement.

Students must maintain at least a B average in the courses taken to fulfill the degree requirements.

Master’s Time Limit Policy

Full-time MS students are permitted seven quarters in which to complete all requirements. While there are no

written time limits for part-time students, the department has the right to set individual deadlines if necessary.

A strong effort is made to schedule MS-level course offerings so that students may obtain their MS in one year of

full-time study or two years of part-time study (see regulations on part-time study under “Graduate Division

”).

Entering students who do not meet the prerequisites of these core courses may have to take some basic courses to

make up the deficiency.

A candidate admitted for the MS who wishes to transfer to the PhD program must consult the Student Affairs Office

concerning the transfer before completion of the MS program.

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

oengineeering Graduate Curriculum (June 2015)

Change of Degree Aim

Upon completion of the requirements for the MS, students are not automatically eligible for admission to the PhD

program.

MS candidates who wish to pursue a doctorate must submit an application for a change in status to the Graduate

Studies Committee. The application is made available each spring by the Student Affairs Office. The application

must be approved and signed by a bioengineering faculty member who expects to serve as the student’s PhD

adviser. Applications will be reviewed by an ad hoc faculty committee. If the committee recommends that the

student has good potential for success in the doctoral program, the student will be given the opportunity to take an

oral examination equivalent to the PhD Departmental Qualifying Examination. At the time of that exam, an

assessment will be made concerning admission to the PhD program.

A change of status from a master’s program to the doctoral program requires that the student meet the minimal grade

point average required by the department of doctoral candidates.

Master of Engineering Degree Program

The department offers a master of engineering (MEng) degree. The purpose of this degree is to prepare design and

project engineers for careers in the medical and biological engineering industries within the framework of the

graduate program of the Department of Bioengineering. It is a terminal professional degree in engineering, which

includes recognition of the importance of breadth in technical knowledge and sufficient electives to address job-

specific interests and professional skills such as economics, management, and business. It is intended for students

who are primarily interested in engineering design, development, manufacturing, and management within an

industrial setting.

Students who may be interested in continuing to the PhD program should apply to the MS program and not the

terminal MEng program.

The MEng program is a flexible, course-intensive terminal professional degree, designed to be completed in one

academic year of full-time study. It does not require a comprehensive exam. However, students must enroll for

technical elective credit in BENG 295, Bioengineering Design Project and Industrial Training, under the direction of

a faculty instructor. This is done by participating in the Graduate Industrial Training Program, which allows students

to work in an industrial setting on bioengineering projects in order to gain practical experience. (See “

Industrial

Internship Program” and “Graduate Industrial Training Program” sections of this catalog.) BENG 295 course

requirements include a written technical report.

In addition to enrolling in one to two quarters (four to eight units) of BENG 295, Bioengineering Design Project and

Industrial Training, students must select six courses from the approved core areas, one to two courses from the

approved technical elective course list, and three courses from the approved general elective course list. Such core

courses and technical and general electives are described below. In selecting breadth courses, students must be

mindful of the prerequisite requirements for some of the courses listed. The lists below are based on the current

graduate course offerings of the bioengineering and other engineering departments. The Graduate Studies

Committee will review the MEng course lists annually and update them as course offerings change. MEng students

are required to complete course requirements with a grade of B or better.

Students must also enroll in BENG 291, Senior Seminar I: Professional Issues in Bioengineering. This course instills

skills for personal and organizational development during lifelong learning. Students prepare portfolios and a model

NIH small business research grant.

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

oengineeering Graduate Curriculum (June 2015)

Required Courses for MEng Program

Core Courses (total of six required)

Engineering Physics

• BENG 221. Mathematical Methods for Bioengineering

• BENG 223. Thermodynamics, Statistical Mechanics, Interfacial Phenomena in Living Systems

• BENG 226. Foundations of Biomechanics

• BENG 227. Transport Phenomena in Living Systems

Life Science

• BENG 230A. Biochemistry

• BENG 230B. Cell and Molecular Biology

• BENG 230C. Cardiovascular Physiology

• BENG 230D. Respiratory and Renal Physiology

• BENG 231. Foundations of Physiology for Bioengineering

• BENG 232. Musculoskeletal Health, Injury, and Disease

• BENG 260/BGGN 260. Neurodynamics

Tissue Engineering

• BENG 241A. Tissue Engineering and Regenerative Medicine: Foundations

• BENG 241B. Tissue Engineering and Regenerative Medicine: Cell Microenvironment

• BENG 242/MATS 257. Polymer Science and Engineering

Imaging

• BENG 247A. Advanced Biophotonics

• BENG 280A. Principles of Biomedical Imaging

• BENG 280B. Comparative Biomedical Imaging

• Other approved core graduate courses taught by bioengineering faculty that satisfy the depth requirement of

the MEng degree as approved by the Graduate Studies Committee.

Technical Elective Courses for the MEng

(three required, one of which must be BENG 295)

• BENG 202/CSE 282. Bioinformatics II: Introduction to Bioinformatics Algorithms

• BENG 203/CSE 283. Genomics, Proteomics, and Network Biology

• BENG 207. Topics in Bioengineering

• BENG 208. Topics in Bioengineering with Lab

• BENG 209/MAE 209. Continuum Mechanics Applied to Medicine/Biology

• BENG 211. Systems Biology and Bioengineering I. Biological Components

• BENG 212. Systems Biology and Bioengineering II. Network Reconstruction

• BENG 213. Systems Biology and Bioengineering III. Building and Simulating Large-Scale in Silico

Models

2015–16 UC SAN DIEGO GENERAL CATALOG

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oengineeering Graduate Curriculum (June 2015)

• BENG 238/MED 238. Molecular Biology of the Cardiovascular System

• BENG 247B/ECE 247B. Bioelectronics

• BENG 247C/ECE 247C. Bionanotechnology

• BENG 250B. Advanced Biomechanics

• BENG 260/BGGN 260. Neurodynamics

• BENG 267. Microcirculation in Health and Disease

• BENG 276/Chem 276/Math 276. Numerical Analysis in Multiscale Biology

• BENG 295. Bioengineering Design Project—required

• MAE 210A/CENG 210A. Fluid Mechanics I

• MAE 210B. Fluid Mechanics II

• MAE 210C. Fluid Mechanics III

• MAE 221/CENG 221AB. Heat and Mass Transfer

• MAE 229A/MATS 211A. Mechanical Properties

• MAE 231A. Solid Mechanics

• MAE 231B. Elasticity

• MAE 231C. Anelasticity

• MAE 280A. Linear Systems Theory

• MAE 293. Advanced Computer Graphics for Engineers and Scientists

• MATS 252/MAE 266. Biomaterials

• MATS 253/MAE 267. Nanomaterials and Properties

• MATS 258/MAE 250. Medical Device Materials and Applications

• CSE 202. Algorithm Design and Analysis

• CSE 210. Principles of Software Engineering

• CSE 250A. Artificial Intelligence: Search and Reasoning

• ECE 235. Nanometer-Scale VLSI Devices

• ECE 251A. Digital Signal Processing I

• ECE 251B. Digital Signal Processing II

Core courses may be taken for technical elective credit.

General Elective Courses (three required)

• BENG 225. BioBusiness: Biotech Company

• ENG 201. Venture Mechanics

• ENG 202. Enterprise Dynamics

• ENG 203. Applied Innovations

• ECE 254. Detection Theory

• IR/PS Management: IRGN 420, 434, 438, 439, 444, IRCO 420, 421

• IR/PS International Issues: IRCO 401, IRGN 407, 411, 413

• MAE 290A. Efficient Numerical Methods for Simulation, Optimization, and Control

• Technical Elective courses may be taken for general elective credit

For other courses that address job-specific interests and professional skills such as economics, management, and

business, consult with the Student Affairs Office.

Seminar (required)

BENG 291. Professional Issues in Bioengineering

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

oengineeering Graduate Curriculum (June 2015)

Sample MEng Schedule

FALL

WINTER

SPRING

Core

BENG 225 (GE)

BENG 295 (TE)

Tech. Elec.

Gen. Elec.

BENG 291 (Seminar)

Doctoral Degree Program

The bioengineering PhD program is intended to prepare students for a variety of careers in research and teaching.

Therefore, depending on the student’s background and ability, research is initiated as soon as possible.

Bioengineering students have specific course requirements and must maintain a minimum grade point average of 3.4

in these courses. Students, in consultation with their advisers, develop course programs that will prepare them for

the Departmental Qualifying Examination and for their dissertation research. These programs of study and research

must be planned to meet the time limits established to advance to candidacy and to complete the requirements for

the degree. Doctoral students who have passed the Departmental Qualifying Examination may take any course for

an S/U grade with the exception of courses required by the Departmental or Senate Qualifying Examination

Committee. It is recommended that all bioengineering graduate students take a minimum of two courses (other than

research) per academic year after passing the Departmental Qualifying Examination. Details can be obtained from

the Student Affairs Office.

Doctoral Examinations

A bioengineering PhD student is required to pass three examinations. The first is a Departmental Qualifying

Examination, which must be taken after spring quarter of the first year of study. The exam is designed to ensure that

all successful candidates possess a firm command of the engineering and life science subjects that form the

foundations of bioengineering research and their integration at a level appropriate for the doctorate. It is

administered by a committee designated by the department, consisting of departmental faculty members and, in

some cases, other faculty members from a related academic department (e.g., MAE, ECE, SOM). The scope of the

oral examination includes the two broad areas that form the core first-year PhD curriculum, namely Engineering

Physics and Life Science. The purpose of the exam is not merely to recapitulate the content of first-year courses, but

rather to establish that students are able to synthesize this knowledge and apply it to solve problems in contemporary

bioengineering research.

Curriculum for PhD Students

Each incoming student will be assigned a bioengineering faculty adviser who will serve as a graduate adviser until

the student chooses a thesis adviser. This assignment is noted in the departmental offer letter.

First-Year Requirements

All bioengineering students in their first year of study are expected to enroll in the seven required core courses in the

Engineering Physics and Life Science tracks listed below. First-year students are also required to take: two quarters

of laboratory research rotation (BENG 298L); both one-credit seminars (BENG 281 and BENG 282); and one

quarter (W or S) of Teaching Experience (BENG 501).

2015–16 UC SAN DIEGO GENERAL CATALOG

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oengineeering Graduate Curriculum (June 2015)

Core Courses (total of seven required)

All core courses must be taken for letter grade.

Engineering Physics (four required)

• BENG 221. Mathematical Methods for Bioengineering

• BENG 223. Thermodynamics, Statistical Mechanics, Interfacial Phenomena in Living Systems

• BENG 226. Foundations of Biomechanics

• BENG 227. Transport Phenomena in Living Systems

Life Science (three required)

• BENG 230A. Biochemistry (required)

• BENG 230B. Cell and Molecular Biology (required)

Plus one of the following courses:

• BENG 231. Foundations of Physiology for Bioengineering

• BENG 230C. Cardiovascular Physiology

• BENG 230D. Respiratory and Renal Physiology

• BENG 232. Musculoskeletal Health, Injury, and Disease

• BENG 260/BGGN 260. Neurodynamics

Laboratory Rotation (two quarters required)

• BENG 298L. Laboratory Research Rotation

Seminars (both required)

• BENG 281. Seminar in Bioengineering (F,W,S)

• BENG 282. Seminar: Faculty Research (F)

Teaching Experience (one quarter required)

• BENG 501. Teaching Experience (W,S)

Elective Courses (five required)

PhD students are required to complete a total of five approved elective courses by the end of their third year of

study. All graduate level courses offered in the Department of Bioengineering (other than the seven core courses)

may be used to fulfill the elective course requirement. Students may also take graduate level engineering/science

courses offered in other departments (e.g., MAE, ECE, SOM) for elective credit with prior faculty adviser approval.

Courses taken in fulfillment of the elective course requirement must be taken for a letter grade.

2015–16 UC SAN DIEGO GENERAL CATALOG

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oengineeering Graduate Curriculum (June 2015)

Courses comprising subject areas as well as subsequent requirements and composition of the examination

committee, must be approved by the Graduate Studies Committee. Students are advised to seek such approval well

in advance of their expected examination date, preferably while planning graduate studies.

Teaching experience is required of all bioengineering PhD students prior to taking the Senate Qualifying Exam

described below. Teaching experience is defined as service as a graduate student instructor in a course designated by

the department. The total teaching requirement for new PhD students is four quarters at 25 percent effort (ten hours

per week). At least one quarter of teaching experience is required during the first year (prior to the departmental

qualifying examination) and at least one quarter in the second year. Students must complete the entire teaching

requirement prior to their Senate Qualifying Exam.

The Senate Qualifying Examination is the second examination required of bioengineering PhD students. In

preparation for this examination, students must have completed the Departmental Qualifying Examination, the

departmental teaching experience requirement, all required course work (seven core and five approved elective

courses), obtained a faculty research adviser, identified a topic for their dissertation research, and made initial

progress. At the time of application for advancement to candidacy, a doctoral committee responsible for the

remainder of the student’s graduate program is appointed by the Graduate Council. The committee conducts the

Senate Qualifying Examination, during which students must demonstrate the ability to engage in thesis research.

This involves the presentation and defense of a plan for the thesis research project. Upon successful completion of

this examination, students are advanced to candidacy and are awarded the Candidate in Philosophy degree (see

“Graduate Division

” section in this catalog).

The Dissertation Defense is the final PhD examination. Upon completion of the dissertation research project, the

student writes a dissertation that must be successfully defended in a public presentation and oral examination

conducted by the doctoral committee. A complete copy of the student’s dissertation must be submitted to each

member of the doctoral committee approximately four weeks before the defense. It is understood that this copy of

the dissertation given to committee members will not be the final copy, and that the committee members may

suggest changes in the text at the time of the defense. This examination must be conducted after completion of at

least three quarters from the date of advancement to doctoral candidacy. Acceptance of the dissertation by the Office

of Graduate Studies and the university librarian represents the final step in completion of all requirements for the

PhD.

There is no formal foreign language requirement for doctoral candidates. Students are expected to master whatever

language is needed for the pursuit of their own research.

Obtaining an MS

PhD students may obtain the MS by completing the course work requirements and by passing the PhD departmental

qualifying examination. Course work requirements include successful completion of a total of forty-eight units of

credit comprising Engineering Physics, Life Science and five approved elective courses (see details on course work

requirements in the section “Doctoral Degree Program

”). Students should consult with the Student Affairs Office in

advance of their second year of study concerning required paperwork and deadlines for conferral of the MS.

PhD Time Limit Policy

Precandidacy status is limited to three years. Doctoral students are eligible for university support for six years. The

defense and submission of the doctoral dissertation must be within seven years.

2015–16 UC SAN DIEGO GENERAL CATALOG

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Bio

engineeering Graduate Curriculum (June 2015)

Evaluations

In the spring of each year, the faculty evaluate each doctoral student’s overall performance in course work, research,

and prospects for financial support for future years. A written assessment is given to the student after the evaluation.

If a student’s work is found to be inadequate, the faculty may determine that the student cannot continue in the

graduate program.

PhD in Bioengineering with Specialization in Bioinformatics

A specialization in Bioinformatics spanning four divisions—Biological Sciences, Physical Sciences, Jacobs School

of Engineering, and Health Sciences. Intended for students who have an interdisciplinary persuasion to work across

computers, biology, medicine, and engineering. Candidates will be admitted into participating graduate programs

(bioengineering, biology, biomedical sciences, chemistry and biochemistry, computer science and engineering,

mathematics, and physics) and work towards degrees in their home departments with a specialization in

Bioinformatics. The specialization will serve to educate future generations of Bioinformatics

researchers. Understanding how genomes work requires sophisticated computer-based information handling tools

(bioinformatics), and new high throughput technologies for understanding the function of genes on a genome-wide

scale (functional genomics).

PhD in Bioengineering with Specialization in Computational

Neuroscience.

The Neurosciences Graduate Program, The Department of Physics, and The Department of Bioengineering offer a

specialization in Computational Neuroscience. Students from these departments/programs that pursue the

Computational Neuroscience specialization are trained in the broad range of scientific and technical skills essential

to understand the computational and theoretical basis of neural systems. Students in this specialization will be

required to fulfill all of the academic requirements for a PhD in their home department/program, and must

successfully complete a set of three core computational courses, any other coursework as directed by the

Computational Neuroscience Committee, and successfully defend a thesis on an approved topic.

PhD in Bioengineering with Specialization in Multiscale Biology

A specialization in Multiscale Biology spanning four divisions—Biological Sciences, Physical Sciences, Jacobs

School of Engineering, and Health Sciences—is available to doctoral candidates in bioengineering. The PhD

specialization is designed to allow students to obtain standard basic training in their chosen field within the

biological sciences, physical sciences, engineering, and health sciences with training in integrative and quantitative

analysis across multiple scales of biological organization from molecule to organism in health and disease into their

graduate studies. For more information students should contact the Student Affairs Office.

PhD in Bioengineering with Specialization in Quantitative Biology

A specialization in Quantitative Biology spanning four divisions—Biological Sciences, Physical Sciences, Jacobs

School of Engineering, and Health Sciences—is available to doctoral candidates in bioengineering. This PhD

specialization is designed to train students to develop and apply quantitative theoretical and experimental

approaches to studying fundamental principles of living systems. The core of this specialization comprises one year

of theory courses and one year of lab courses, most of which can be counted towards satisfying the bioengineering

elective requirement. For more information students should contact the Student Affairs Office.

Formatted:

Heading 4

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

eurosciences Curriculum (June 2015)

Neurosciences

[ courses | faculty ]

Center for Neural Circuits and Behavior

Mail Code 0634

http://neurograd.ucsd.edu

All courses, faculty listings, and curricular and degree requirements described herein are subject to change or

deletion without notice. Updates may be found on the Academic Senate website:

http://senate.ucsd.edu/catalog-

copy/approved-updates/.

The Graduate Program

The Neurosciences Graduate Program accepts candidates for the PhD degree who have undergraduate majors in

such disciplines as biology, chemistry, engineering, microbiology, mathematics, physics, psychology, and zoology.

A desire and competence to understand how the nervous system functions are more important than previous

background and training.

Doctoral Degree Program

The Neurosciences Graduate Program is an interdisciplinary program that provides course work and research

training leading to a degree of doctor of philosophy in all areas related to the development and function of the

nervous system. During the first two years, all students in the program are required to take seven core courses, take

at least one ethics course, fulfill elective requirements, attend research rounds for two years, complete three research

rotations the first year, and serve as a teaching assistant for at least one quarter. Additional course work is required

for the students in the Computational Neuroscience Specialization (see below). Students must advance to candidacy

by the end of their fourth year and complete their dissertation by the end of their sixth year.

Core Courses

Neurosci 200A-B-C

Neurosci 225

Neurosci 241

Neurosci 257

Neurosci 276

Neurosci 280

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Neu

rosciences Curriculum (June 2015)

Specialization in Computational Neuroscience

The Neurosciences Graduate Program, The Department of Physics, and The Department of Bioengineering offer a

specialization in Computational Neuroscience. Students from these departments/programs that pursue the

Computational Neuroscience specialization are trained in the broad range of scientific and technical skills essential

to understand the computational and theoretical basis of neural systems. Students in this specialization will be

required to fulfill all of the academic requirements for a PhD in their home department/program, and must

successfully complete a set of three core computational courses, any other coursework as directed by the

Computational Neuroscience Committee, and successfully defend a thesis on an approved topic.

The Neuroscience Graduate Program offers a specialization in computational neuroscience. Students in the

computational neuroscience specialization are trained in the broad range of scientific and technical skills essential to

understand the computational resources of neural systems. Students in this specialization will be required to fulfill

all of the academic requirements of students in the Neurosciences Graduate Program. In addition to these

requirements, students in the computational neuroscience specialization must successfully complete a set of three

core computational courses, an advanced laboratory, and computational neuroscience journal clubs.

Required neuroscience and computational neurosciences courses include:

Core Courses

Neurosci 200A-B-C

Neurosci 225

Neurosci 241

Neurosci 257

Neurosci 276

Neurosci 280

Computational Neurosciences Specialization Courses

BENG 234

BGGN 246A-B

BGGN 260

BGGN 266

Cog Sci 260

Formatted:

Normal

2015–16 UC SAN DIEGO GENERAL CATALOG

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eurosciences Curriculum (June 2015)

Phys 2781

Course Work

By the end of the second year, students are expected to demonstrate competence in the basics of neuroscience by

taking five quarters of mandatory course work—three quarters of Basic Neuroscience (Neurosci 200 A-B-C), and

one quarter each of Neuroanatomy Lab (Neurosci 257), Statistical Methods and Experimental Design (Neurosci

225), and Minor Proposition (Neurosci 280). In addition, students choose among various core elective courses, such

as Advanced Topics in Neuroscience (Neurosci 221), Developmental Neurobiology (Neurosci 266), Molecular and

Cellular Neurobiology (Neurosci 268), and approved courses from other graduate departments. Students are also

permitted to substitute previous courses that are similar to the neurosciences core courses. Such a substitution would

require approval of the chair of the curriculum committee or the director of the Graduate Program.

Dissertation

During the third year, students are expected to propose and initiate work on a dissertation problem under the

guidance of a faculty adviser. The group in neurosciences faculty at UC San Diego currently conducts animal

research and clinical studies in the fields of neuroanatomy, neurochemistry, neuropharmacology, neurophysiology,

comparative neurology, physiology of excitable membranes, synaptic transmission, neuronal integration and coding,

nervous system tissue culture, neuroimmunology, brain function, sensory physiology, motor mechanism, and

systems analysis as applied to neurological problems.

Qualifying Examination

This examination, a university requirement, focuses on the proposed research that the student will undertake for his

or her dissertation. This examination is conducted by the approved doctoral committee.

Dissertation Examination

The required formalities listed in the Instruction for Preparation and Submission of Doctoral Dissertations issued by

the Graduate Division to students should be followed closely. The final examination includes both a public

presentation followed by a closed defense of the dissertation with members of the committee.

Teaching

All students are required to perform as a teaching assistant for at least one quarter during their graduate career. To

this end, opportunities to lecture and assist in laboratory exercises and demonstrations are available through a

number of departments, including neurosciences, biology, cognitive science, and psychology.

PhD Time Limit Policies

Students must advance to candidacy by the end of four years. Total university support cannot exceed six years. Total

registered time at UC San Diego cannot exceed seven years.

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

Physics

[ undergraduate program | courses | faculty ]

Graduate Student Affairs:

Room 2551 Mayer Hall Addition

All courses, faculty listings, and curricular and degree requirements described herein are subject to change or

deletion without notice. Updates to curricular sections may be found on the Academic Senate website:

http://senate.ucsd.edu/catalog-copy/approved-updates/

The Graduate Program

The Department of Physics offers curricula leading to the following degrees:

MS, Physics

CPhil, Physics

PhD, Physics

PhD, Physics (Biophysics)

PhD, Physics, Specialization in Computational Science

Biophysics students will receive their MS and CPhil degrees in physics. Only their PhD will be in physics

(biophysics).

Entering graduate students are required to have a sound knowledge of undergraduate mechanics, electricity, and

magnetism; to have had senior courses or their equivalent in atomic and quantum physics, nuclear physics, and

thermodynamics; and to have taken upper-division laboratory work. An introductory course in solid-state physics is

desirable.

Requirements for the master of science degree can be met according to Plan II (comprehensive examination). (See

“Graduate Studies: Master’s Degrees

.”) The comprehensive examination is identical to the first-year departmental

examination for PhD students. A list of acceptable courses is available in the Department of Physics Graduate

Student Affairs office.

Contiguous Bachelor’s/Master’s Degree Program in

Materials Physics

The program offers a MS in physics with specialization in materials physics. It is open only to UC San Diego

undergraduates, and is a Plan I program only (thesis). During the first quarter of the senior undergraduate year,

students enrolled in the BS degree program with specialization in materials physics (see above) may apply for

admission to the MS program. To be eligible, students must have completed the first two quarters of their junior year

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

in residence at UC San Diego and have a GPA of at least 3.0 in both their major and overall undergraduate

curriculum. It is strongly recommended that BS students who intend to apply to the MS program take MAE 160,

ECE 103, and ECE 134 as restricted BS electives.

It is the responsibility of the prospective BS/MS student to select a faculty member (from the Department of Physics

or, with Physics department approval, from the MAE, ECE, or Chemistry departments) who would be willing to

serve as the student’s adviser and with whom the student would complete at least twelve units of S/U graded

research. Research could commence as early as the undergraduate senior year; research units taken during the senior

year would count only toward the MS degree and not toward the BS. The student must confirm that the selected

faculty adviser will not be on off-campus sabbatical leave during any quarter of the scheduled BS/MS project.

Students are expected to meet the requirements for the MS in one year (three consecutive academic quarters) from

the date of receipt of the BS. Any deviation from this plan, such as a break in enrollment for one or more quarters,

may result in the student being dropped from the program.

The requirements for the MS are as follows:

1. Completion of at least twelve and no more than twenty-four units of research, which may begin as early as

the first quarter of the senior undergraduate year. Students accumulate units for their research by enrolling

in Physics 295 (MS Thesis Research), which may be taken repeatedly.

2. Completion of MAT SCI 201A-B-C during the fifth (graduate) year.

3. Completion of two restricted electives, to be chosen from Physics 201, 211A-B; MAT SCI 227, 240A-B-C;

ECE 231, 233 (other courses allowed by petition).

4. Completion of additional courses (restricted electives and/or research) so that the total number of units

(research plus required courses plus elective courses) totals no fewer than thirty-six units taken as a

graduate student.

5. Maintenance of a grade-point average of at least 3.0 for all course work, both cumulatively and for each

quarter of enrollment in the BS/MS program.

6. Completion of a thesis, with an oral presentation to, and approval of, a three-member committee from the

Department of Physics including the faculty adviser. If the faculty adviser is from outside the Department

of Physics, the committee shall consist of the adviser and two members from the Department of Physics

faculty.

7. Three consecutive quarters of full-time residency as a graduate student that will commence the quarter

immediately following the quarter in which the BS is awarded (not counting Summer Session).

8. Although students may receive research or teaching assistantships if available, there is no guarantee of

financial support associated with the MS program. Students who obtain a teaching assistantship should

make sure that it does not interfere with completion of the MS degree requirements within the one-year

time frame allotted.

9. Teaching is not a requirement for the MS.

Suggested Schedule - MS requirements completed during the 4

and 5

(graduate)

year:

Year 4:

Fall

Winter

Spring

PHYS 130B

PHYS 124

PHYS 133

PHYS 140A

PHYS 152A

PHYS 152B

PHYS RE (undergrad)

PHYS 295

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

Year 5:

Fall

Winter

Spring

RE/PHYS 295

MAT SCI 201A

MAT SCI 201C

RE/295

MAT SCI 201B

Suggested Schedule - MS requirements completed during the 5

(graduate) year, only:

Fall

Winter

Spring

PHYS 295

MAT SCI 201A

MAT SCI 201C

RE/295

MAT SCI 201B

Doctoral Degree Program

The department has developed a flexible PhD program that provides a broad, advanced education in physics while at

the same time giving students opportunity for emphasizing their special interests. This program consists of graduate

courses, apprenticeship in research, teaching experience, and thesis research.

Entering students are assigned a faculty adviser to guide them in their program. Many students spend their first year

as teaching assistants or fellows and begin apprentice research in their second year. When a student’s association

with a research area and research supervisor is well established, a faculty research progress committee is formed

with the responsibility of conducting an annual review of progress and, at the appropriate time, initiating the

formation of a doctoral committee. After three years of graduate study, or earlier, students complete the

departmental examinations and begin thesis research. Students specializing in biophysics make up deficiencies in

biology and chemistry during the first two years and complete the departmental examinations by the end of their

third year of graduate study. There is no foreign language requirement.

Entrance Testing

An entrance test covering undergraduate physics is given to entering students during the first week of orientation to

give better guidance to students in their graduate program. The results are not entered in the student’s file. Entering

students are encouraged, but not obliged, to bring the results to the first meeting with their academic adviser.

Entering students may elect to take the departmental examination instead of taking the entrance test.

Requirements for the PhD

Students are required to pass a departmental examination, advanced graduate courses, a qualifying examination,

teaching requirement and a final defense of the thesis as described below.

1. Departmental Written Examination

Physics students are required to take the departmental written examination after completing one year of graduate

work at UC San Diego. The examination is on the level of material usually covered in upper-division courses and

the graduate courses listed below:

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

Fall

Physics 200A (Theoretical Mechanics)

Physics 201 (Mathematical Physics)

Physics 212A (Quantum Mechanics)

Winter

Physics 200B (Theoretical Mechanics)

Physics 203A (Adv. Classical Electrodynamics)

Physics 212B (Quantum Mechanics)

Spring

Physics 203B (Adv. Classical Electrodynamics)

Physics 210A (Equilibrium Statistical Mechanics)

Physics 212C (Quantum Mechanics)

The examination is offered twice a year, at the beginning of the fall and spring quarters, and lasts two days, four

hours per day. The examination may be repeated once, the next time it is offered.

Biophysics PhD students are required to take the departmental written examination within two years of graduate

work at UC San Diego and not later than the beginning of the third year.

The university requires an annual evaluation of each graduate student’s progress toward PhD candidacy and thesis

defense. To this end, a Research Progress Committee (RPC) is formed for every student during the spring quarter of

the second year of graduate study. Students must demonstrate proficiency in giving technical talks through an oral

presentation to the RPC.

2. Advanced Graduate Courses

Physics students are required to take five advanced graduate courses from at least three of the groups listed below no

later than the end of the third year of graduate work. A 3.0 average over the five courses is required. (In lieu of the

course requirement, students may petition to take an oral examination covering three areas of physics.)

• Group 1: Physics 218A-B-C (Plasma); 235 (Nonlin. Plas. Th.)

• Group 2: Physics 210B (Nonequil. Stat. Mech.);, 211A, 211B (Solid State); 219 (C.M./Matl. SCI Lab), 230

(Adv. Solid State); 232 (Electronic Materials)

• Group 3: Physics 214 (Elem. Part.); 215A-B-C (Part. & Fields); 217 (Renorm. Field Th.); 222A (Elem.

Particle Phys)

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

• Group 4: Physics 220 (Group Th.); 221A (Nonlinear Dyn.); Physics 241 and 242 (Comp. Phys); Physics

243 (Stochastic Methods) and 244 (Parallel Computing in Science and Engineering); Mathematics 210A-B,

210C (Mathematics Physics); Mathematics 259A-B-C (Geom. Physics)

• Group 5: Physics 225A-B (Relativ.); 271 (Bio. Neurons/Net); 272 (Bio. Molecules)

• Group 6: Physics 223 (Stel. Str.); 224 (Intrstel. Med.); 226 (Gal. & Gal. Dyn.); 227 (Cosmology), 228 (HE

Astro. & Comp. Obj.)

Students enrolled in the Biophysics PhD program select five courses from biology, biochemistry, chemistry, or

physics in consultation with their adviser. At least three courses must be graduate courses. For more information, see

the Biophysics section, below.

3. PhD Candidacy Examination

In order to be advanced to candidacy, students must have met the departmental requirements and obtained a faculty

research supervisor. At the time of application for advancement to candidacy, a doctoral committee responsible for

the remainder of the student’s graduate program is appointed by the Graduate Council. The committee conducts the

PhD candidacy examination during which students must demonstrate the ability to engage in thesis research. This

involves the presentation of a plan for the thesis research project. The committee may ask questions directly or

indirectly related to the project and questions on general physics that it determines to be relevant. Upon successful

completion of this examination, students are advanced to candidacy and are awarded the Candidate of Philosophy

degree.

4. Instruction in Physics Teaching

All graduate students are required to participate in the physics undergraduate teaching program as part of their career

training. The main component of this requirement is an evaluated classroom-based teaching activity. All graduate

student teaching accomplishments are subject to the approval of the Vice Chair for Education. There are several

ways to satisfy the teaching requirement, including: (1) leading discussions as a teaching assistant, (2) practical

classroom teaching, under faculty supervision, (3) participation in an approved teaching development program

offered by the Department of Physics or the campus Center for Teaching Development, or (4) transferred teaching

credit from another institution or department. Students who satisfy the requirement by teaching at UC San Diego

should enroll in Physics 500 during the quarter in which they complete it.

5. Thesis Defense

When students have completed their theses, they are asked to present and defend them before their doctoral

committees.

Time Limits for Progress to the PhD

In accordance with university policy, the Department of Physics has established the following time limits for

progress to the PhD. A student’s research progress committee helps ensure that these time limits are met.

Theorists

Experimentalists

Advancement to Candidacy

4 years

5 years

Total Registered Time and Support

7 years

8 years

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

PhD in Physics (Biophysics)

The Department of Physics offers a graduate program which prepares students for a career in biophysics and that

leads to the following degrees:

CPhil in Physics

PhD in Physics (Biophysics)

Biophysics students will receive their MS and CPhil degrees in physics. Only their PhD will be in physics

(biophysics).

The PhD program consists of graduate courses, apprenticeship in research, teaching experience, and thesis research.

Research in biophysics is being actively pursued in several departments (physics, chemistry/biochemistry, and

biology) that also offer courses in, or courses relevant to, biophysics.

Requirements for the PhD in Physics (Biophysics)

The specialization in biophysics requires that students complete many of the same requirements as for the physics

PhD. Students must pass a departmental written examination, advanced graduate courses, PhD candidacy

examination, teaching requirement, and a final defense of the thesis. However, the requirements for the written

examination and advanced courses differ slightly from those of the PhD.

Biophysics PhD students are required to take the departmental written examination within two years of beginning

graduate studies at UC San Diego, and no later than the beginning of the third year. Biophysics students are required

to pass five courses from biology, chemistry, biochemistry, or physics no later than the end of the third year of

graduate study. The course plan shall be determined in consultation with the adviser. At least three of these courses

must be graduate courses. A 3.0 average over the five courses is required. (In lieu of the course requirement,

students may petition to take an oral examination covering three areas of physics.)

PhD in Physics with Specialization in Computational Neuroscience

The Neurosciences Graduate Program, The Department of Physics, and The Department of Bioengineering offer a

specialization in Computational Neuroscience. Students from these departments/programs that pursue the

Computational Neuroscience specialization are trained in the broad range of scientific and technical skills essential

to understand the computational and theoretical basis of neural systems. Students in this specialization will be

required to fulfill all of the academic requirements for a PhD in their home department/program, and must

successfully complete a set of three core computational courses, any other coursework as directed by the

Computational Neuroscience Committee, and successfully defend a thesis on an approved topic.

Computational Neurosciences Specialization Courses:

BGGN 260/Phys 279/BENG 260 (Neurodynamics) Phys 278 (Biophysical Basis of Neuronal Dynamics) Cog Sci

260 (Algorithms for the Analysis of Neural Data)

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2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

PhD in Physics with Specialization in Computational Science

See “PhD in Mathematics with Specialization in Computational Science” for more information.

The UC San Diego campus is offering a new comprehensive PhD specialization in computational science that will

be available to doctoral candidates in participating academic departments at UC San Diego.

This PhD specialization is designed to allow students to obtain training in their chosen field of science, mathematics,

or engineering with additional training in computational science integrated into their graduate studies. Prospective

students must apply and be admitted into the PhD program in physics, and then be admitted to the CSME program.

Areas of research in the Department of Physics will include computational astrophysics and cosmology (studying

star formation and the large scale structure of the universe), computational condensed matter physics (studying

nanodevices), computational quantum field theory (studying the four basic forces of nature), computational

biological physics (protein folding and other biologically important complex structures), computational nonlinear

dynamics, and computational plasma physics. Each faculty member works with graduate students on the listed

research topics.

The specialization in computational science requires that students complete all home requirements for the physics

PhD degree. Students are required to pass the departmental written examination, advanced course requirements, PhD

candidacy examination, teaching requirement, and a final defense of the thesis. The qualifying and elective courses

for the CSME program (e.g., Physics 241-244) can be used as part of the advanced course requirement, which is the

same as for the physics PhD.

Requirements for the PhD in Physics with Specialization in

Computational Science:

Qualifying Requirements: In addition to the home department qualifying exam requirements, PhD students must

take the final exams in three qualifying exam courses from the list below. Courses taken to satisfy the qualifying

requirements will not count toward the elective requirements.

1. Math 275 or MAE 290B (Numerical PDEs)

2. Phys 244 or CSE 260 (Parallel Computing)

3. One course to be selected from List A

List A: CSME Qualifying Exam Courses

1. Phys 243 (Stochastic Methods)

2. Math 270A, B, or C (Numerical Analysis)

3. Math 272A, B, or C (Advanced Numerical PDEs)

4. MAE 223 (Computational Fluid Dynamics)

5. MAE 232A or B (Computational Solid Mechanics)

6. MAE 280A or B (Linear Systems Theory)

7. To be determined by Executive Committee

Elective Requirements: To encourage PhD students to both broaden themselves in an area of science or engineering

as well as to obtain more specialized training in specific areas of computational science, students will be required to

take and pass three elective courses from the following approved List B (four units per course). The Executive

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

Committee may approve the use of courses not appearing on the following list on a case-by-case basis. Courses

taken to satisfy the elective requirements will not count toward the qualifying requirements.

List B: Relevant Elective Graduate Courses in Mathematics, Science, and Engineering

1. Math 270A-B-C (Numerical Analysis; not permitted for mathematics students)

2. Math 271A-B-C (Optimization)

3. Math 272A-B-C (Advanced Numerical PDEs)

4. Math 273A-B-C (Computational Mathematics Project)

5. Phys 141/241 (Computational Physics I)

6. Phys 142/242 (Computational Physics II)

7. Phys 221A-B (Nonlinear Dynamics)

8. Chem 215 (Modeling Biological Macromolecules)

9. BGGN 260 (Neurodynamics)

10. To be determined by Executive Committee

Program Policies: The following is a list of policies for the PhD specialization with regard to proficiency,

qualifying, and elective requirements:

1. Proficiency in computer engineering must be demonstrated by the end of the first year.

2. The qualifying exams must be passed by the end of the second year, or, on petition, by end of the third

year.

3. The qualifying exams can be attempted repeatedly but no more than once per quarter per subject.

4. The qualifying exams in the home department and the CSME qualifying exams must all be passed before

the student is permitted to take the candidacy (senate) exam.

5. Two electives outside the home department must be taken.

6. The two electives can be taken at any time before defending the thesis.

7. One of the electives may be taken Pass/Fail; the other must be taken for a letter grade.

Recommended schedule for the PhD in physics with specialization in computational

science

YEAR 1: PHYSICS CORE COURSES

Phys 200A

Phys 200B

Phys 203B

Phys 201

Phys 203A

Phys 210A

Phys 212A

Phys 212B

Phys 212C

YEAR 2: CSME QUALIFYING COURSES

Math 275

Non-Phys Elective

Phys 244

Phys 243

Adv Phys Course

YEAR 3: CSME ELECTIVE COURSES

Non-Phys Elective

Phys 241

Phys 242

PhD in Physics with Specialization in Quantitative Biology:

2015–16 UC SAN DIEGO GENERAL CATALOG

June 15, 2015 Catalog of Record

Physics Graduate Curriculum (Revised Nov 2015)

A specialization in Quantitative Biology spanning four divisions—Biological Sciences, Physical Sciences, Jacobs

School of Engineering, and Health Sciences—is available to doctoral candidates in Physics. This PhD specialization

is designed to train students to develop and apply quantitative theoretical and experimental approaches to studying

fundamental principles of living systems. The core of this specialization comprises of one year of theory courses and

one year of lab course, most of which can be counted towards satisfying Physics elective requirements. For more

information students should contact the Student Affairs Office.

Departmental Colloquium

The department offers a weekly colloquium on topics of current interest in physics and on departmental research

programs. Students are expected to register and attend the colloquium.

Supplementary Course Work and Seminars

The department offers regular seminars in several areas of current interest. Students are strongly urged to enroll for

credit in seminars related to their research interests and, when appropriate, to enroll in advanced graduate courses

beyond the departmental requirement. To help beginning students choose a research area and a research supervisor,

the department offers a special seminar (Physics 261) that surveys physics research at UC San Diego.

Course Credit by Examination

Students have an option of obtaining credit for a physics graduate course by taking the final examination without

participating in any class exercises. They must, however, officially register for the course and notify the instructor

and the Department of Physics graduate student affairs office of their intention no later than the first week of the

course.