Chemistry Ph.D.

Introduction

The Department of Chemistry and Biochemistry offers admitted graduate students access to world-class research while in the pursuit of their Ph.D.s. While the department offers Ph.D.s in two separate tracks, it is important to note that both tracks confer a Ph.D. in chemistry.

CHEM Track:

The Ph.D. in the Department of Chemistry and Biochemistry (CHEM), typically involves internal faculty/labs. Within this Ph.D. program, students have the flexibility to design a course of study focused on personal research interests, and at the same time are expected to maintain the high intellectual standards associated with the doctoral degree. Research options include biochemistry, physical chemistry, biophysical chemistry, inorganic chemistry, bioinorganic chemistry, materials chemistry, physical-organic chemistry, and bioorganic chemistry. Some research groups are interdisciplinary and are involved in two or more of these areas. After successful completion of all of the Ph.D. requirements, students in this track will be awarded a Ph.D. degree in chemistry from the Department of Chemistry and Biochemistry.

CB3 Track:

The Department of Chemistry and Biochemistry also participates in the graduate Program in Biomedical Science and Engineering (PBSE) through its administration of the Chemical Biology, Biochemistry and Biophysics (CB3) training track. Sixty-one faculty members, who come primarily from the Departments of Molecular, Cell, and Developmental Biology; Biomolecular Engineering; Chemistry and Biochemistry; and Microbiology and Environmental Toxicology offer an unusual breadth of expertise and exceptional opportunities in interdisciplinary graduate research training. When students apply to the PBSE they indicate interest in one of four training tracks:

• Biomolecular Engineering and Bioinformatics (BMEB)
• Chemical Biology, Biochemistry, and Biophysics (CB3)
• Microbiology and Environmental Toxicology (METX)
• Molecular, Cell, and Developmental Biology (MCD)

The Ph.D. track in chemical biology, biochemistry and biophysics (CB3) provides students with the opportunity to carry out cutting-edge research at the interface between biology and chemistry. The training program emphasizes analysis of molecular structure and mechanism as well as chemical biology and the use of organic chemistry to address biological questions. Interdisciplinary research is encouraged and supported by a diverse group of faculty.

Students in both tracks will be required to complete their coursework and other milestones to advance to candidacy, after which, they will write and defend their dissertations. After successful completion of all of the Ph.D. requirements, students in both tracks will be awarded a Ph.D. degree in chemistry from the Department of Chemistry and Biochemistry.

Progression and Milestones

Course Requirements

Both CHEM and CB3 tracks prepare students with an in-depth understanding of their area of specialization through a core curriculum that prepares them for advanced study and research. Students are also exposed to areas outside of their specialization with elective courses. Below are the course requirements specific to each track. All students are required to take CHEM 292 and CHEM 296 in their first year. Additionally, all Ph.D. students are required to enroll in CHEM 291 (weekly research seminars) until they advance to candidacy.

CHEM Track

Students in the CHEM track are expected to complete 15 credits of core courses (three courses) and 10 credits (two courses) of electives. Electives may be either at the graduate level (200 series) or at the advanced undergraduate level (100 series). Twenty of the 25 credits (four 5-credit courses) must be chemistry and biochemistry courses. The remaining 5 credits may be in chemistry and biochemistry or in a related discipline such as molecular, cell, and developmental (MCD) biology; microbiology and environmental toxicology; physics; math; biomolecular engineering; electrical engineering; etc. Eligible electives do not include CHEM 163A/CHEM 163B/CHEM 163C, CHEM 109, CHEM 110, CHEM 110L, CHEM 143 or CHEM 151A, but can include CHEM 124, 151B, and CHEM 169. Completing these 25 lecture course credits is a requirement that must be met before advancing to candidacy. In consultation with their research advisor, students may take more than the required five courses at any time depending on their interests or research.

Please refer to the Graduate Student Handbook for the current core and elective curriculum by area of specialization.

CB3 Track

Students in the CB3 track complete the courses listed below, as well as at least three additional graduate-level lecture courses by the end of the third year. A list of approved elective courses is available on the PBSE-CB3 website

Teaching Requirement

The focus on high quality undergraduate education is one of the most outstanding features of the UC Santa Cruz campus. Teaching is a job that is taken very seriously and many graduate students and faculty come to UCSC because they want to be in an atmosphere where both teaching and research are important.

Students in the CB3 track are required to serve as a teaching assistant for a minimum of two quarters.

Students in the CHEM track are required to serve as a teaching assistant for a minimum of three quarters.

Committee Requirements

Broadly speaking, all graduate students will interact with three different committees in the pursuit of the degree as listed below.

Dissertation Advising Committee (DAC) - a committee which meets with the student annually to review the student’s progress and to advise on thesis research by providing outside viewpoints. The student’s research advisor is on the committee as well as a committee chair who must be a tenured faculty member from the Department of Chemistry and Biochemistry, as well as a third faculty member from the department. The committee members help decide when sufficient work has been completed for submission of a thesis. In certain cases, students in the CB3 track may nominate a fourth member to join the committee.

Qualifying Exam Committee - committee that assesses a student’s qualifying exam in the second (CHEM track) or third year (CB3 track). Students in both tracks nominate a four-person Qualifying Exam committee.

Members 1 - 3 are track dependent:

• Students in the CB3 track nominate three CB3 faculty members (not to include the research advisor)
• Students in the CHEM track nominate the members of their DAC (chair of DAC and QE committee will not be the research advisor)

The fourth committee member of both tracks is an "outside" member, selected in consultation with the student and the research advisor. This member must be a tenured faculty member in an external department at Santa Cruz, a tenured faculty member at a different university, or a scientist at a different institution with a research record comparable to a faculty member with tenure. The nomination of the committee is due to the graduate student advisor no later than 35 days before the scheduled Qualifying Exam and is subject to the approval by the Graduate Division.

Dissertation Reading Committee (DRC) - committee that is responsible for reading, providing critical feedback on, and ultimately approving the written dissertation. The DRC is chaired by the research advisor, and is typically joined by two other faculty members from the Department of Chemistry and Biochemistry. The composition of the DAC and the DRC may be the same, with the important distinction of which faculty member is chair of which committee as stipulated above. In certain cases, students in the CB3 track may nominate a fourth member to join the committee.

Laboratory Rotations

Students in the CHEM track do two, nine-week rotations during fall and winter quarters in the laboratory of two Chemistry and Biochemistry faculty members. Performance in each rotation is graded as satisfactory/unsatisfactory. At the end of each rotation period, students are required to present their project as a short talk to the department.

Students in the CB3 track students do three, seven-week rotations during fall and winter quarters in the laboratory of three PBSE-affiliated faculty members. Performance in each rotation is graded as satisfactory/unsatisfactory. At the end of each rotation period, students are required to present on their project either with a short talk or poster presentation.

Laboratory Placement

Graduate students in both tracks are required to choose their research advisor and join a lab in the spring quarter (by May 1) of their first year. A research advisor is necessary to make progress toward completing dissertation research.

Commitee Formation

Students in the CHEM track need to nominate names for their Dissertation Advising Committee (DAC). All committee names must be nominated by the end of the first spring quarter.

Students in the CB3 track nominate names in the second year.

Second-Year Requirements

Students in the CHEM track are required to pass a 25-minute literature seminar in their fourth or fifth quarter. Students present a second-year seminar on a topic of current interest in published research. The oral presentation is accompanied by a detailed three-page written document that describes the contents of the presentation, and is delivered to the student’s DAC.

Students in the CB3 track are required to pass their Ph.D. oral qualifying examination before their Qualifying Exam Committee by the end of the student’s sixth quarter. The members of the Qualifying Exam Committee are nominated by the student, subject to approval. Students must demonstrate an expertise in their area of research and include a six-page NIH-style research strategy and specific aims page on their planned dissertation research. Upon passing that examination, the Dissertation Reading Committee (DRC) is formed. The committee comprises the research advisor plus two other members of the Chemistry and Biochemistry faculty. An outside member from the broader community of PBSE faculty can be requested as an additional member of the DRC. The Dissertation Advising Committee is formalized at the same time, and both committees’ memberships will be the same, with differing chairs.

Third-Year Requirements

Students in the CHEM track are required to pass their Ph.D. oral qualifying examination (QE) by the end of their seventh quarter (typically the fall of the third year). The oral QE is given before the Qualifying Exam Committee. The Ph.D. candidate presents (a) a summary of current research results and future directions, and (b) an original research proposal on a chemistry or biochemistry topic. This proposal may either be partially related or unrelated to the candidate's current thesis research. This proposal must be approved by the student’s DAC prior to the oral examination. In addition, a detailed six-page research strategy and specific aims page on their written research proposal will be submitted for evaluation to the QE committee. Upon successful completion of the QE and satisfaction of course requirements, the students advance to candidacy.

By the end of their ninth quarter (typically the spring of the third year), students in the CB3 track must: (a) present an hour-long public seminar that is based on their dissertation research; and (b) answer questions posed by their DAC. Upon successful completion of the seminar and satisfaction of course requirements, the students advance to candidacy.

Advancement to Candidacy

Students in both tracks will have advanced to candidacy when they have completed all progression requirements and other milestones other than defending a dissertation. Both tracks include similar milestones (each detailed in the above ections and distinguished by track):

• Course requirements
• Teaching requirements
• 1st-year requirements
• 2nd-year requirements
• 3rd-year requirements

Note: Students in both tracks are required to be enrolled in at least one quarter between advancing to candidacy and applying to graduate.

Academic Progress Meetings

Students in both tracks will have their academic progress reviewed annually by the graduate program administration each spring term. Progress summaries will be sent to each student and their principal investigator (PI) by the following fall. The summaries will include details of expected requirements for the following year.

Concurrently, students who have advanced to candidacy must meet with their DAC at least once a year, typically during the fall quarter, to report research progress and present an updated prospectus and get advice and guidance for the coming year.

The fourth-year review gives the student an opportunity to focus and plan their research and to begin shaping the final product—the research dissertation. With this goal in mind, the student presents their research progress to the DAC, obtains feedback, and receives guidance on future directions.

Progress discussions and reviews with the DAC are held in the fall quarter of the fifth year and the sixth year, if necessary, until the dissertation is submitted. These meetings’ format is the same as described above for the fourth-year review.

Normative Time to Degree

In alignment with Graduate Division guidelines, the department has established six years of normative time to degree. Ph.D. students from both tracks are expected to complete research and write the dissertation within nine quarters after advancing to candidacy following a successful Ph.D. oral QE. Financial support is not available after 18 quarters in the graduate program.

Dissertation and Graduation

Dissertation

As the final requirement for the Ph.D., students from both tracks will write and defend the dissertation, which must be accepted under the rules of the Academic Senate. When the DRC agrees that the research is ready to be submitted, the student writes the dissertation according to the guidelines prescribed by the University Library and the Graduate Division.

Students must submit the doctoral thesis to the DRC for tentative approval at least one month before presenting a defense seminar.

The dissertation, completed in the format specified by the Graduate Council and approved by the DRC, must be submitted to the Graduate Division no later than the last day of the term in which the degree is to be awarded.

Dissertation Defense

In addition to the research and writing, the dissertation must be defended. The defense takes the form of a public seminar, where the student presents the principal results of their research to their DRC, as well as any members of the public in attendance. Following the presentation, the committee and other attendees will ask questions of the work. The dissertation defense should be scheduled at least one week prior to submitting the dissertation to the Graduate Division for final processing and graduation (per the above section, this means the dissertation defense should be scheduled no later than one week before the end of the term in which the degree is to be awarded).

The DRC makes the final departmental decision regarding the awarding of the Ph.D. degree. The decision is subject to the approval of the graduate dean.

Applying for Graduation

Students close to completing their degree must file an application for the Ph.D. degree by the end of the second week of the quarter in which they wish to graduate (see the Academic and Administrative Calendar for deadline). The application is the student’s official notification to the graduate dean of their intent to graduate. This form is available on the Graduate Division’s website.