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Chemistry and Biochemistry

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Chair’s Office 2040 Urey Hall Addition (858) 534-5489 http://chemistry.ucsd.edu

Undergraduate Student Affairs Revelle College, 4010 York Hall (858) 534-4856

Graduate Student Affairs Revelle College, 4010 York Hall (858) 822-6014

All courses, faculty listings, and curricular and degree requirements described herein are subject to change or deletion without notice.

The Graduate Programs

The Chemistry Program in the Department of Chemistry and Biochemistry accepts students for study toward the MS in chemistry, the PhD in chemistry, the PhD in chemistry with specialization in bioinformatics, the PhD with specialization in computational science, the PhD with specialization in multiscale biology, and the PhD with specialization in quantitative biology.

The Biochemistry and Molecular Biophysics Program in the Department of Chemistry and Biochemistry accepts students for study toward the MS in biochemistry and molecular biophysics and the PhD in biochemistry and molecular biophysics with specialization in bioinformatics, the PhD with specialization in computational science, the PhD with specialization in multiscale biology, and the PhD with specialization in quantitative biology.

Chemistry Program (CHEM)

Master of science.

A Plan I (Thesis) MS in chemistry and a Plan II (Comprehensive Examination) MS in chemistry are offered. The former allows specialization in one area as well as research experience. The latter encourages breadth and offers opportunities to broaden one’s scientific background.

Admissions: Students are admitted for fall quarter entrance only. Eligibility requirements for admission include solid training in the chemical sciences as judged by the undergraduate record, a minimum 3.0 GPA in chemistry courses completed, and a minimum 3.0 overall GPA.

Students who attended the University of California San Diego are eligible to apply for either the Plan I (Thesis) or Plan II (Comprehensive Examination) master’s program. Those who wish to apply to the Thesis Plan must have a letter of support from the proposed thesis adviser. All other students are admitted to the Plan II (Comprehensive Examination) master’s program only.

The GRE general test is required of all applicants. Foreign applicants must submit a TOEFL score; TWE scores are strongly recommended.

Residency and Time-to-Degree: Master’s students must register at UC San Diego for a minimum of three quarters, and complete at least twenty units per academic year. Full-time Comprehensive Examination Plan students can complete the degree in three quarters. Thesis Plan students typically take eighteen to twenty-four months to graduate.

Plan I (Thesis)

Purpose: To prepare students for research careers or for doctoral or professional studies.

Advancement to Candidacy: A minimum of thirty-six units with an overall minimum GPA of 3.0 must be completed. Complete a minimum of eighteen units of thesis research (CHEM 299). At least eight units of graduate level chemistry courses must be completed for a letter grade. Four units of teaching apprenticeship (CHEM 500) and two units for the teaching seminar (CHEM 509) may be applied (see “ Doctoral Program ,” “ Teaching ,” and “ Language Requirement ” sections). Additional/elective courses taken to meet the thirty-six-unit requirement must be upper division or graduate chemistry courses. Students must obtain department approval to apply courses from other departments. Contact the Chemistry and Biochemistry Student Affairs Office for full information.

Thesis: Students must give an oral presentation and defense of their thesis project to a thesis committee. A student graduates after the thesis has been defended and the written dissertation approved by his or her committee, the department, and the Graduate Division, and then filed with the university archivist. The thesis committee consists of at least three faculty: (1) the thesis adviser, (2) a faculty member from the Department of Chemistry and Biochemistry familiar with the student’s research area, and (3) a faculty member from either this or another department whose research is in an area different from that of the thesis.

Plan II (Comprehensive Exam)

Purpose: To prepare students for doctoral or professional studies, or for teaching at the community college or high school level, or for career work in industry.

Advancement to Candidacy: A minimum of thirty-six units with an overall minimum GPA of 3.0 must be completed. A minimum of sixteen units must be letter-graded chemistry graduate courses. Four units of teaching apprenticeship (CHEM 500) and two units for the teaching seminar (CHEM 509) may be applied (see “ Doctoral Program ,” “ Teaching, ” and “ Language Requirement ” sections). Four units of non-thesis research (CHEM 297 or CHEM 298), four units of research survival skills (CHEM 250), and two letter-graded units of molecular biophysics (CHEM 291) are allowed (enrollment in CHEM 250 and 291 is only permitted for students who are pursuing a PhD degree). Additional/Elective courses taken to meet the 36-unit requirement must be upper-division or graduate Chemistry courses. Students must obtain department approval to apply courses from other departments. Plan II students may not use CHEM 299 units toward their degree. Contact the Chemistry and Biochemistry Student Affairs Office for full information.

Comprehensive Examination: The purpose of this requirement is to confirm that students have achieved an advanced understanding of, and a comprehensive training in, the chemical sciences. The tests cover a wide range of material, so that students will have a chance to show what they have learned. For master’s students, the department administers exams in biochemistry and in analytical/instrumental, inorganic, organic, and physical chemistry. Students must pass three of the exams in order to graduate. For doctoral students earning a Plan II MS on the way to the PhD, the written and oral Departmental Examination components fulfill this requirement.

Doctoral Program

The goal of the PhD in chemistry is to prepare students for careers in science by expanding their knowledge of chemistry while developing their ability for critical analysis, creativity, and independent study. The program is designed to encourage initiative and to stimulate enjoyment and development of the student’s area of research expertise as well as the broader aspects of scientific inquiry and enlightenment.

Students choose their research concentration from program tracks in Analytical and Atmospheric Chemistry, Physical Chemistry, Inorganic Chemistry, Organic Chemistry, Chemical Biology, Materials Chemistry, Theoretical and Computational Chemistry, and Biochemistry and Biophysics. Opportunities for scientific discovery are also abundant through the department’s extensive collaborations with investigators in other physical, biological, and engineering sciences. This includes on-campus collaborations with faculty in the Materials Science Program, School of Medicine, School of Pharmacy and Pharmaceutical Sciences, and Scripps Institution of Oceanography. There are off-campus interactions with scientists at nearby research facilities such as the Salk Institute and The Scripps Research Institute. State-of-the-art facilities and equipment support all the research programs. The department’s Industrial Relations Program interfaces with national and local chemical, biotechnology, and pharmaceutical industries to encourage technology transfer and to assist postgraduates interested in industrial careers.

Research Adviser

A first-year faculty adviser guides students until a research adviser is chosen. Most of a student’s efforts in graduate school are directed toward research for the doctoral dissertation, and selection of a research adviser is of utmost importance. To assist students with this critical decision, all chemistry and biochemistry faculty describe their current research activities early in the fall quarter. Students then rotate in laboratories or consult with faculty to discuss research opportunities. Although students have until the end of the first year to join a laboratory, most start their research by midyear.

Placement Examinations and Course Work

There will be two required examinations for incoming doctoral students: one general exam and one in-track exam (in the student’s area of research specialization). These examinations will cover undergraduate-level course material in chemistry and biochemistry. The in-track exam will focus on the student’s area of research and the general exam will encompass topics from all subdisciplines of chemistry and biochemistry: biochemistry, inorganic chemistry, organic chemistry, physical chemistry, materials chemistry, and analytical/instrumental analysis. To meet the placement examination requirement, students must show proficiency at the upper-division level on the topics covered in the general exam and the in-track exam by the end of spring quarter of the student’s first year. Students must demonstrate proficiency by passing both placement exams, or by completing prescribed course work with a grade of B or higher if they do not pass one or both exams.

Departmental Examination

In the second year, a student’s progress in research and graduate studies is evaluated through the departmental examination, which includes a written component and oral defense of the student’s research proposal. Students are also evaluated on their general knowledge of their particular field of study and students may be asked about progress on their dissertation.

Qualifying Examination

By the end of the third year, students defend the topic, preliminary findings, and future research plans of their dissertation. Passing this defense qualifies the student to advance to candidacy for the dissertation. A dissertation committee composed of five faculty, one of whom is the research adviser, provides consultation and evaluation for the dissertation project.

Dissertation

The dissertation is normally completed in the fourth or fifth year. This body of research is expected to make an innovative contribution to the field of chemistry. PhD candidates present a seminar summarizing their research accomplishments and defend their thesis in an oral examination before their dissertation committee.

Experience in teaching is a vital and integral part of every graduate student’s training, and all students participate in the instructional activities of the undergraduate curriculum. Course credit for the teaching apprenticeship is earned by enrolling in CHEM 500. Excellence in teaching is stressed, and the department provides a thorough training program covering the fundamentals of teaching as well as other useful information and techniques for effective instruction. Students are required to enroll in the CHEM 509 teaching training seminar in their first quarter as a chemistry/biochemistry graduate TA at UC San Diego. Further training is provided by the campus’s Center for Teaching Development. Faculty and the students taught evaluate the performance of teaching assistants every quarter and awards are bestowed annually for outstanding performance as a teaching assistant.

Language Requirement

Students whose native language is not English must demonstrate a mastery of English adequate to complete the teaching requirement. Deficiencies must be remedied by the end of the first year of academic residency. For native English speakers, there is no foreign language requirement.

Time Limits

In accordance with UC San Diego policy, students must advance to candidacy by the end of four years. Total university support cannot exceed six and one-third years. Total registered time at UC San Diego cannot exceed seven and one-third years.

Seminars by researchers from other universities, national laboratories, and industry are another important aspect of the graduate curriculum. Seminars are presented weekly in biochemistry, inorganic, organic, and physical chemistry. Department colloquia are given on topics of general interest to the department. Seminars are also sponsored by many other departments and institutes, both on the UC San Diego campus and at our neighbor institutions.

Financial Support

The department supports all first-year students in good academic standing from a variety of sources, including teaching and research assistantships, training grants, fellowships, and awards. A stipend is paid in addition to fees and, if applicable, tuition. Continuing students who do not have fellowships or awards are normally supported on training grants or on research assistantships by their thesis advisers.

The department seeks bright, motivated doctoral students and welcomes all such applications. To make admissions decisions, the department considers an applicant’s statement of purpose and research interests, GRE scores on the general test plus either the advanced chemistry or advanced biochemistry test, undergraduate record, quality of the undergraduate university, letters of recommendation, and research experience and publications. Applicants whose native language is not English must also submit TOEFL scores; TWE scores are strongly recommended. Admission to the doctoral program is for fall quarter.

Biochemistry and Molecular Biophysics Program (BIOC)

The goal of the PhD in biochemistry and molecular biophysics is to prepare students for careers in science by expanding their knowledge of biochemistry, molecular biophysics, and structural biology while developing their ability for critical analysis, creativity, and independent study. The program is designed to encourage initiative and to stimulate enjoyment and development of the student’s area of research expertise as well as the broader aspects of scientific inquiry and enlightenment.

Master’s Degree: Plan II (Comprehensive Exam)

For students in the Biochemistry and Molecular Biophysics PhD Program, they may earn a Plan II MS degree in biochemistry and molecular biophysics on the way to the PhD. The departmental examination (written and oral components) fulfill the comprehensive examination requirement for the MS degree. See above under “Chemistry Program” for full degree requirements.

Students choose their research concentration in broad areas of biochemistry, molecular biophysics, and structural biology. Opportunities for scientific discovery are also abundant through the department’s extensive collaborations with investigators in other physical, biological, health, and engineering sciences. This includes on-campus collaborations, for example, with faculty in biological sciences, engineering, the School of Medicine, the School of Pharmacy and Pharmaceutical Sciences, and physics. There are off-campus interactions with scientists at nearby research facilities such as the Salk Institute for Biological Studies and The Scripps Research Institute. State-of-the-art facilities and equipment support all the research programs. The department’s Industrial Relations Program interfaces with national and local chemical, biotechnology, and pharmaceutical industries to encourage technology transfer and to assist postgraduates interested in industrial careers.

A first-year faculty adviser guides students until a research adviser is chosen. Most of a student’s efforts in graduate school are directed toward research for the doctoral dissertation, and selection of a research adviser is of utmost importance. To assist students with this critical decision, all biochemistry and molecular biophysics faculty describe their current research activities early in the fall quarter. Students then rotate in laboratories to explore research opportunities. Although students have until the end of the first year to join a laboratory, most join a lab during winter quarter.

Course Work

First-year students typically take six graduate courses based on their research interests. CHEM 219A, CHEM 250, CHEM 509, and CHEM 500 are required. Undergraduate courses and courses offered through other departments may also be taken, depending on the student’s research area. By the second year, the emphasis is on thesis research and a lighter load of courses is taken, although participation in seminars and informal study groups continues.

See above under “Chemistry Program.”

PhD in Chemistry or Biochemistry and Molecular Biophysics with Specialization in Computational Science

Since fall 2007, the UC San Diego campus has offered a comprehensive PhD specialization in computational science that is available to doctoral candidates in participating science, mathematics, and engineering departments. This PhD specialization is designed to allow students to obtain training in their chosen field of science, mathematics, or engineering along with a specialization in computational science integrated into their graduate studies. Prospective students must apply and be admitted into the PhD program in chemistry/biochemistry described previously.

PhD in Chemistry or Biochemistry and Molecular Biophysics with Specialization in Multiscale Biology

Since fall 2009, the UC San Diego campus has offered a PhD specialization in multiscale biology that is available to doctoral candidates in participating programs that span four schools—Biological Sciences, Physical Sciences, Jacobs School of Engineering, and Health Sciences. This PhD specialization is designed to allow students to obtain training in their chosen field within the biological sciences, physical sciences, engineering, and health sciences along with training in integrative and quantitative analysis across multiple scales of biological organization from molecule to organism to health and disease. It educates a new cadre of PhD scientists to undertake interdisciplinary work at the interfaces between the biological, medical, physical, and engineering sciences.

PhD in Chemistry or Biochemistry and Molecular Biophysics with Specialization in Quantitative Biology

A specialization in quantitative biology spanning four schools—Biological Sciences, Physical Sciences, Jacobs School of Engineering, and Health Sciences—is available to doctoral candidates in the Department of Chemistry and Biochemistry. 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, with most of these courses substitutable for chemistry elective courses. For more information, students should contact the Student Affairs Office.

PhD in Chemistry or Biochemistry and Molecular Biophysics with Specialization in Interdisciplinary Environmental Research

A graduate specialization in interdisciplinary environmental research (PIER) is available for select doctoral students in chemistry. PIER students seek solutions to today’s environmental challenges.

The PhD specialization is designed to allow students to obtain standard training in their chosen field and an opportunity to interact with peers in different disciplines throughout the duration of their PhD projects. Such communication across disciplines is key to fostering a capacity for interdisciplinary “language” skills and conceptual flexibility.

Specialization Requirements

• Complete all course work, dissertation, and other requirements of the chemistry PhD
• Sixteen-unit interdisciplinary boot camp (summer session, SIO 295S-295LS)
• Eight units from a secondary field (outside the home department)
• Six units (three quarters) Interdisciplinary Environmental Research Forum (SIO 296)
• At least one chapter of the dissertation will be broadly related to environmental research and will be interdisciplinary in nature.

Application Requirements

We advise students to begin PIER in their third year upon completion of core chemistry course requirements.

The following items should be combined into a single PDF document and submitted to [email protected] .

• Student’s CV
• Half-page abstract of proposed thesis work
• Up to one-page statement of student’s interest in interdisciplinary environmental research including career goals.
• Nomination letter from adviser acknowledging student’s academic ability and interdisciplinary environmental interest. The letter must include a commitment for summer stipend support.

Admission to the Specialization

Students are admitted into the chemistry doctoral program. Admission to PIER is a competitive process with six to eight students granted admission each year from across ten participating UC San Diego departments. Selected applicants will have the opportunity to enroll in the specialization.

PIER Fellowships

When funding is available, all applicants will be considered for one year of PIER fellowship support.

Joint Doctoral Program with San Diego State University

The Department of Chemistry and Biochemistry at UC San Diego and the Department of Chemistry at San Diego State University offer a joint program of graduate study leading to the PhD in chemistry. More information is available in the current edition of the Bulletin of the Graduate Division of San Diego State University.

Bertrand, Guy

Brydges, Stacey

Budin, Itay

Burkart, Michael

Bussey, Thomas

Cohen, Seth

Continetti, Robert

Debelouchina, Galia

Deshmukh, Lalit

Devaraj, Neal

Donoghue, Daniel

Ferguson, Fleur

Figueroa, Joshua

Galperin, Michael

Ghosh, Gourisankar

Ghosh, Partho

Gilson, Michael

Godula, Kamil

Grassian, Vicki

Griffith, Kent

Guseman, Alex

Hermann, Thomas

Herzik, Mark

Christine Hrycyna

Jennings, Patricia

Jinich, Adrian

Joseph, Simpson

Klosterman, Jeremy

Komives, Elizabeth

Komor, Alexis

Kubiak, Clifford

Kummel, Andrew

Leigh, Brian

Li, Shaowei

McHugh, Colleen

Mishanina, Tatiana

Molinski, Tadeusz

Muller, Ulrich

O'Connor, Joseph

Obara, Christopher

Julia Ortony

Paesani, Francesco

Pomeroy, Robert

Prather, Kimberly

Pun, Andrew

Rinehart, Jeffrey

Romero, Erik

Romero, Nathan

Sailor, Michael

Schimpf, Alina

Schmidt, Valerie

Schoeneberg, Johannes

Schurmeier, Kimberly

Siegel, Dionicio

Sinha, Amitabha

Slade, Jonathan

Stallings, Dontarie

Stauber, Julia

Tauber, Michael

Taylor, Susan

Tezcan, Akif

Theodorakis, Emmanuel

Toor, Navtej

Tor, Yitzhak

Weizman, Haim

Yang, Jerry

Yong, Haiwang

Young, Mark

Yuen-Zhou, Joel

Zhao, Hongbo

Chemistry and Biochemistry

• Alphabetical
• Faculty/Academic Positions
• Faculty by Research Speciality
• Graduate Programs
• Undergraduate Program
• Administration

Our faculty's research is highly interdisciplinary, spanning biochemistry; biophysics; inorganic, organic, physical, analytical, computational, and theoretical chemistry; surface and materials chemistry; and atmospheric and environmental chemistry. Please refer to the faculty pages for full descriptions of the on-going research in our department. State-of-the-art facilities and laboratories support these research programs.

At UCSD, chemists and biochemists are part of a thriving community that stretches across campus and out into research institutions throughout the La Jolla and San Diego area, uniting researchers in substantive interactions and collaborations.

• Graduate Programs
• Chemistry PhD

Research Tracks

• Materials Chemistry

The Materials Chemistry track research is highly interdisciplinary. This track is at the interface of designing and preparing advanced materials, and characterizing their unique physical and chemical properties. The students will develop knowledge of physical principles of materials, skills in modern synthetic technologies, proficiency with state-of-the-art characterization tools, and a broad background in applications of semiconductor, photonic, energy, and biomedical devices. Current research areas include (1) Inorganic, organic, polymer, and hybrid materials for novel electronic, magnetic, mechanical, chemical, and biological properties; (2) Cutting-edge techniques to characterize materials in energy, time, and spatial dimensions, from macroscopic ensembles to the single-atom level; (3) Design and fabrication of devices from the molecular level; (4) First-principles calculation and prediction of material properties; (5) Soft materials from biological molecules. Faculty and students in the Materials Chemistry Track may also benefit from association with the UC San Diego Materials Research Science and Engineering Center (MRSEC), a National Science Foundation funded center for interdisciplinary research in materials science and engineering. Many research programs within the Materials Chemistry track are synergistic with Inorganic, Organic, and Physical Chemistry tracks.

• Analytical and Atmospheric Chemistry
• Chemical Biology
• Inorganic Chemistry
• Organic Chemistry
• Physical Chemistry
• Theoretical and Computational Chemistry