A graduate program in Biochemistry and Biophysics

Last updated: September 14, 2017 at 4:09 p.m.

Graduate Program in Biochemistry and Biophysics
The graduate program in Biochemistry/Biophysics leading to the degree of Doctor of Philosophy is designed to provide students with a deep understanding of the mechanisms governing the workings of biological macromolecules. The emphasis in the graduate program is placed upon experimental research work to train students to carry out independent original research. Students are required, however, to complete formal course work in advanced biochemistry and physical biochemistry and biophysics. Additional courses and seminars are available in a wide range of subjects, including enzyme regulation and mechanism, neurobiology, immunology, structural biology including protein crystallography, magnetic resonance spectroscopy and electron microscopy, membrane biology, molecular microscopy, biophysical chemistry, neuroscience, sensory transduction, chemo-mechanical energy transduction and computation.

Applicants are expected to have strong backgrounds in the physical sciences with undergraduate majors in any related field, such as biology, biochemistry, chemistry, engineering, mathematics, or physics. The course requirements for the PhD are formulated individually for each student to complement the student's previous academic work with the goal of providing a broad background in the physics and chemistry of biological processes.

Research for the PhD dissertation is carried out under the personal supervision of a faculty adviser; advisers can be from any department within the Division of Science. Prospective applicants should obtain the complete list of faculty research interests and recent publications from the program or view this information at: www.bio.brandeis.edu.

The graduate program in biochemistry leading to the degree of Master of Science is designed to give students a substantial understanding of the chemical and molecular events in biological processes and experience in research. The program is divided among formal course work, biochemical and biophysical techniques, and a research project. Additional courses and seminars are available in a wide range of subjects.

Graduate Program in Biochemistry and Biophysics

Master of Science in Biochemistry

Knowledge:
All students graduating with a Biochemistry B.S.-M.S. or M.S. degree should have knowledge of the following general areas:
1. Basic principles of cell biology.
2. Firm understanding of general chemistry and organic chemical reaction mechanisms, particularly in the area of carbonyl chemistry.
3. Molecular forces determining protein and nucleic acid folding and membrane assembly.
4. Mechanisms by which enzymes catalyze cellular chemical reactions.
5. Strategies by which cells store and transmit information in DNA and RNA.
6. Mechanisms for communicating changes in the extracellular environment to the cell's interior.
7. Techniques for determining molecular structures of macromolecules.
8. Relation of impairment in macromolecular function to disease.
9. All students are required to carry out an original research project in the laboratory of a Brandies life-science faculty member, including writing a thesis that constitutes a significant research contribution
10. All students participate in full-time summer research

Core Skills:
Our M.S. program requires majors to use a set of basic skills to attack problems particular to biochemistry, some of which should be mastered through prerequisites taken even before encountering our introductory course. The core skills needed for the major are:
1. Facility with familiar mathematical functions, proficiency in univariate calculus, and understanding of basic elements of probability and statistics.
2. Familiarity with the application of calculus to problems in classical physics.
3. Mastery of basic principles of equilibrium thermodynamics and chemical kinetics.
4. Ability to read and analyze primary research literature.
5. Ability to formulate and pursue an increasingly independent research project during the two years of the program. Research projects are usually carried out in small groups of students and postdocs.

Social Justice:
Social justice is not a component of the Biochemistry graduate curricula

Graduate Outcomes:
1. Upon graduation, biochemistry majors electing the BS-MS option will be well- placed for: Graduate and postdoctoral study in preparation for careers in biomedical research. Employment in pharmaceutical and biotech companies. Careers in other biologically related areas, such as patent law, public health policy, etc.
2. Students who entered the MS program will be prepared for careers in biotech and pharma, and some may decide to go on to PhD programs.

Doctor of Philosophy in Biochemistry and Biophysics

Knowledge:
1. The Ph.D. program is designed to provide students with a deep understanding of the mechanisms governing the workings of biological macromolecules in terms of the principles of chemistry and physics
2. The curriculum provides advanced education in the principles and practice of macromolecular chemistry, mechanism, and structure.
3. In-class courses emphasize the arts of navigating the relationships between macromolecular structure and function.
4. Advanced seminar-type classes emphasize analyzing primary literature in specialized topics

Core Skills:
1. Emphasis in the graduate program is placed upon experimental research work to train students to carry out independent original research.
2. Students are also trained to use tools of mathematics and physics to engage with problems arising in the behavior of proteins, nucleic acids, and membrane assemblies.
3. All Ph.D. students are required to assist with the teaching of two one- semester courses.
4. Students are given numerous venues to practice conveying scientific information via expository writing and public speaking
5. Students are encouraged to attend and present research results at professional scientific meetings
6. Trainees are required to propose and defend – orally in in writing – two research projects of their own choice, as models for writing grant proposals.

The general requirements for admission to the Graduate School are given in an earlier section of this Bulletin. Applications should include, in addition to three letters of reference, a personal statement describing the reasons for the applicant's interest in the field and previous research experience, if any. Applicants are required to take the Graduate Record Examination and are encouraged to visit Brandeis for interviews, if possible.

Dorothee Kern, Program Chair
(Biochemistry)

Michael Hagan
(Physics)

Christopher Miller
(Biochemistry)

Program of Study
The MS program in Biochemistry and Biophysics is a two-year program, designed to accommodate students with previous academic majors in a wide range of fields, including biology, biochemistry, physical chemistry, engineering, and physics. The required program of study consists of four one-semester courses (BCHM 101a, BCHM 103b, BCHM 104b and one other advanced level course from the School of Science, approved in advance by the graduate program chair) with a grade of B- or higher. All students are required to take BCHM 101a in the first semester, and both BCHM 103b and BCHM 104b in the second semester All students are required to take Responsible Conduct of Science (CONT 300b), usually offered in the spring.

In the first semester, students are required to take two laboratory rotations and enroll in BCBP 296a,b. Starting in their second semester, students will join a research lab full-time and enroll in BCBP 297a,b, Master's Lab Research, with their research advisor for the three remaining semesters and the intervening summer term. To earn the MS degree, students must also enroll in BCBP 299a in their fourth semester and write and submit a master's thesis deemed satisfactory by a committee of faculty appointed by the Program Chair. In order to earn a degree from this program, the student must complete a minimum of 80 credits unless otherwise specified at the discretion of the graduate committee.

Students may be asked to leave the program at the end of a semester if their progress is found to be unsatisfactory at the discretion of the graduate committee. Satisfactory progress includes receiving grades of B- or higher in all courses, successfully joining a lab after the student’s first semester, and demonstrating adequate research progress thereafter as determined by the graduate committee.

Residence Requirement
The residence requirement is two years.

Language Requirement
There is no language requirement.

Thesis
To qualify for the MS, a student must submit a thesis reporting a substantial piece of original research carried out under the supervision of a research adviser or advisers. The master’s thesis must be deposited electronically to the Robert D. Farber University Archives at Brandeis.

Program of Study
The PhD program in Biochemistry and Biophysics is designed to accommodate students with previous academic majors in a wide range of fields, including biology, biochemistry, physical chemistry, engineering, and physics. Consequently, the course requirements for the PhD are tailored to the needs of the particular student. In consultation with each entering student, the program chair formulates a program of study for the student based on the student's previous academic accomplishments and scientific interests. Successful completion of all the courses listed in the program of study with a grade of B- or higher fulfills the course requirements for the PhD. The required program of study consists of seven one-semester courses, of which four are usually completed in the student’s first year. The program chair will meet with the student to discuss the selection of courses before the student registers for courses; all courses must be approved by the graduate program chair. Ordinarily, all students are required to take BCBP 200b (Reading in Macromolecular Structure-Function Analysis) and the two laboratory rotation courses (BCBP 300a and 300b). All students must also complete the non-credit course CONT 300b (Responsible Conduct of Science). All students beyond the first year must register for BCHM 401d. Neither BCBP 300a nor BCBP 300b nor CONT 300b nor BCHM 401d count toward the seven course requirement. Students in their third and higher years of study will have yearly progress meetings with a faculty committee of three for the purpose of maintaining a satisfactory trajectory toward completion and defense of the thesis. These meetings must be documented with a form signed by the thesis committee members and turned into the Division of Science Graduate Affairs Office by the student.

Teaching Requirement
As part of their PhD training, students are required to assist with the teaching of two one-semester courses.

Residence Requirement
The minimum residence requirement is three years.

Language Requirement
There is no language requirement.

Financial Support
Students receive financial support (tuition and stipend) throughout their participation in the PhD program. This support is provided by a combination of university funds, training grants, and faculty research grants.

Qualifying Examinations
To qualify for the PhD degree, each student must write and defend in oral examinations two propositions related to research in biochemistry and/or biophysics. One of these will be in the general area of the student's thesis research, while the other will be unrelated to this area.

Advancement in the Program
To advance into the second year of graduate studies, students must earn grades of B- or better in all courses including rotations and have gained a position by mutual consent in a laboratory at Brandeis in which the thesis research is to be carried out. To advance into the third year of the program, students must have grades of B- or better in all courses, have performed satisfactorily on research propositions, and be in good standing in the thesis research laboratory. Once thesis work has begun, students meet at least once per year with the Dissertation Committee, which includes the thesis adviser and at least two other professors, to discuss progress toward the completion of the dissertation research.

Progress will be reviewed by the Graduate Committee at the end of each year, and a student may be asked to leave the program if her or his progress is found to be unsatisfactory. At the discretion of the Graduate Committee, students who do not fulfill all of the requirements in a particular year may not be readmitted to the program or may be placed on probation (with stipulations for advancement) for one year. Students who had been placed on probation for the prior year must display significant improvement and meet all stipulations set forth in the probation to be advanced in the program.

Dissertation and Defense
The dissertation must report the results of an original scientific investigation into an approved subject and must demonstrate the competence of the PhD candidate in independent research. The dissertation research must be presented and defended in a final oral examination.

Program of Study
Students wishing to obtain this specialization must first gain approval of the graduate program chair or quantitative biology liaison. This should be done as early as possible; ideally, during the first year of graduate studies. In order to receive the PhD in Biochemistry and Biophysics with additional specialization in quantitative biology, candidates must complete the requirements for the PhD described above and the course requirements for the quantitative biology specialization that are described in the Quantitative Biology section of this Bulletin.

Any alteration to the Quantitative Biology course requirements must be approved by the graduate program chair and by the Quantitative Biology program faculty advisory committee.

In addition to the formal courses listed in the following sections, all graduate students are encouraged to participate in the department's research clubs and colloquia. Colloquia are general meetings of the department in which department and guest speakers present their current investigations. Research clubs are organized by various research groups of the department.

(100-199) For Both Undergraduate and Graduate Students

BCHM 100a Advanced Introductory Biochemistry
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Prerequisite: One year of organic chemistry with laboratory.
Topics include protein and nucleic acid structure; chemical basis of enzyme-catalyzed reaction mechanisms and enzyme kinetics; the chemical logic of metabolic pathways, including glycolysis and oxidative phosphorylation; and regulation of enzymatic pathways through allosteric control. Usually offered every year in multiple sections.
Ms. Westover

BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents.
Describes the principles of biological catalysts and the chemical logic of metabolic pathways. Discusses representative enzymes from each reaction class, with an emphasis on understanding how mechanisms are derived from experimental evidence. Topics include serine proteases, phosphatases, isomerases, carboxylases, and dehydrogenases. Usually offered every year.
Ms. Kern

BCHM 102a Quantitative Approaches to Biochemical Systems
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Prerequisite: BCHM 100a or equivalent and Math 10a and b or equivalent.
Introduces quantitative approaches to analyzing macromolecular structure and function. Emphasizes the use of basic thermodynamics and single-molecule and ensemble kinetics to elucidate biochemical reaction mechanisms. Also discusses the physical bases of spectroscopic and diffraction methods commonly used in the study of proteins and nucleic acids. Usually offered every year.
Ms. Pandelia

BCHM 103b Advanced Biochemistry: Cellular Information Transfer Mechanisms
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Prerequisites: One year of organic chemistry with laboratory and BCHM 100a or equivalents. BIOL 14a or the equivalent is recommended.
Addresses fundamental issues of information transfer in biological systems at a molecular level. Topics may include: DNA recombination and replication; transcription (DNA to RNA); processing/maturation of precursor RNA transcripts; and translation (RNA to protein). An emphasis will be placed on through review of the scientific literature, our understanding of the basics of these events in different biological systems, as well as how they are regulated. Usually offered every year.
Ms. Ivanovic

BCHM 104a Classical and Statistical Thermodynamics
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Prerequisites: MATH 10a,b or equivalent, PHYS 11 or 15.
Covers basics of physical chemistry underpinning applications in BCHM 104b. Focus is placed on quantitative treatments of the probabilistic nature of molecular reality: molecular kinetic theory, basic statistical mechanics, and chemical thermodynamics in aqueous solution. Not offered in 2013-2014.
Mr. Oprian and Mr. Theobald

BCHM 104b Physical Chemistry of Macromolecules II
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Prerequisites: BCHM 100a, and one of the following: BCHM 104a, CHEM 141a, or Phys 40a, and Math 10a and b or equivalent.
Illustrates the basic principles on which biological macromolecules are constructed and by which they function. Describes overall structures of proteins, nucleic acids, and membranes in terms of the underlying molecular forces: electrostatics, hydrophobic interactions, and H-bonding. The energetics of macromolecular folding and of the linkage between ligand binding and conformational changes will also be discussed. Usually offered every year.
Mr. Miller

BCHM 145a How to Decide: Bayesian Inference and Computational Statistics
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Prerequisites: Math 10a and b.
A calculus-based courses that teaches the theory and practice of modern statistical methods used by experimental scientists. Topics include Bayesian inference, maximum likelihood estimation, and computational resampling methods. The course consists of a mixture of small lectures and in-class computational exercises. Usually offered ever year.
Mr. Gelles and Mr. Theobald

BCHM 150a Research for the BS/MS Candidates
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Prerequisites: BCHM 100a, one year of organic chemistry and laboratory, and BCHM 99. A maximum of three course credits may be taken as BCHM 150a and/or 150b.
BCHM 150a and 150b are the final semester(s) of laboratory research under the BS/MS program, to be pursued under the supervision of the faculty adviser. Usually offered every year.
Staff

BCHM 150b Research for the BS/MS Candidates
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See BCHM 150a for special notes and course description. Usually offered every year.
Staff

BCHM 171b Protein X-ray Crystallography
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A practical guide to the determination of three-dimensional structures of proteins and nucleic acids by X-ray diffraction. Students learn the theory behind diffraction from macromolecular crystals and carry out all the calculations necessary to solve a protein structure at high resolution. Usually offered every second year.
Ms. Ringe

BIBC 126b Molecular Mechanisms of Disease
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Prerequisite: BCHM 100a. May not be taken for credit by students who took BIOL 126b in prior years.
Explores biochemical changes—in proteins, enzymes and metabolic pathways—that underlie human diseases. Examines molecular mechanisms for a variety of diseases, with a particular focus on molecular mechanisms for therapies. Draws heavily on current literature. Usually offered every second year.
Ms. Westover

(200 and above) Primarily for Graduate Students

BCBP 200b Reading in Macromolecular Structure-Function Analysis
Introduces students to chemical and physical approaches to biological problems through critical evaluation of the original literature. Students analyze scientific papers on a wide range of topics in the fields of biochemistry and biophysics. Discussion focuses on understanding of the scientific motivation for and experimental design of the studies. Particular emphasis is placed on making an independent determination of whether the author's conclusions are well justified by the experimental results. Students are also introduced to grant-proposal writing by preparing NIH-format mock proposals for critical discussion and evaluation. Usually offered every year.
Staff

BCBP 222a Advanced Topics in Enzyme Mechanism
This graduate-level advanced-topics course will examine, through the primary literature, mechanisms by which enzymes catalyze biochemical reactions. Emphasis will be on diverse chemical strategies used to effect catalysis, and on modern approaches to analyzing enzyme mechanisms. Usually offered every third year.
Ms. Ringe

BCBP 296a Master's Lab Rotation I
Laboratory rotation courses for Master's students in Biochemistry and Biophysics. Enrollment by others requires permission of the Program Chair. Usually offered every year.
Staff

BCBP 296b Master's Lab Rotation I
See description under BCBP 296a. Usually offered every year.
Staff

BCBP 297a Master's Lab Research I
Yields twelve semester-hour credits.
Laboratory research for Master's students in Biochemistry and Biophysics. Enrollment by others requires permission of the Program Chair. Usually offered every year.
Staff

BCBP 297b Master's Lab Research II
See description under BCBP 297a. Usually offered every year.
Staff

BCBP 299a Master's Thesis
Usually offered every year.
Staff

BCBP 300a Introduction to Research in Biochemistry and Biophysics I
BCBP 300a and 300b are laboratory rotation courses in which students gain direct experience conducting research in biochemistry and biophysics. Both courses are intended for Biochemistry and Biophysics graduate students; enrollment by others requires permission of the Program Chair. Usually offered every year.
Staff

BCBP 300b Introduction to Research in Biochemistry and Biophysics II
See description under BCBP 300a. Usually offered every year.
Staff

BCBP 401d Biochemical Research Problems
All graduate students beyond the first year must register for this course each semester.
Independent research for the MS and PhD degrees. Specific sections for individual faculty members as requested.
Staff

BCHM 251b Structure and Function of Membrane Proteins
Considers the molecular properties of membrane transport proteins, including ion channels, aquaporins, solute pumps, and secondary active transporters. Readings focus on primary literature aimed at interpreting the mechanisms of transmembrane solute movements in terms of the structures of these integral membrane proteins. Specific subjects chosen vary depending upon the trajectory of recent advances in this fast-moving research area. Usually offered every third year.
Mr. Miller

Required First-Year Graduate Health-Related Science Programs Course

CONT 300b Responsible Conduct of Science
Required of all graduate students supported on a sponsored project. Not for credit.
Ethics is an essential aspect of scientific research. This course, taught by university faculty from several graduate disciplines, covers major ethical issues germane to the broader scientific enterprise, including areas or applications from a number of fields of study. Usually offered every year.
Staff

Courses of Related Interest

This is a non-exclusive list of courses that may be of interest to Biochemistry and Biophysics graduate students.

CBIO 101a Chemical Biology
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Prerequisites: A satisfactory grade (C- or better) in BIOL 14a, BIOL 15b, and CHEM 25a and b, or the equivalent.
Explores how scientific work in chemistry led to fundamental understanding of and ability to manipulate biological processes. Emphasis is placed on chemical design and synthesis as well as biological evaluation and utility. Content based on scientific literature readings. Usually offered every second year.
Mr. Pochapsky

CBIO 106b Chemical Biology: Medicinal Enzymology
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Prerequisites: Satisfactory grade in BIOL 14a, BIOL 15b, CHEM 25a and 25b, and BCHM 100a or the equivalent.
Introduces students to the conceptual framework and experimental methods in medicinal chemistry. Topics include mechanisms of drug-target interactions, strategies for lead optimization and issues in metabolism, pharmacokinetics and pharmacodynamics. Readings drawn from textbooks and the original scientific literature. Usually offered every second year.
Ms. Hedstrom

CHEM 129b Special Topics in Inorganic Chemistry: Introduction to X-ray Structure Determination
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Prerequisite: A satisfactory grade in CHEM 121a or 122b, or permission of instructor. Knowledge of point groups is essential, but such knowledge may be gained through reading and exercises provided by the instructor.
Topics include basic diffraction and space group theory, practical manipulations of crystals and X-ray diffraction equipment, solving crystal structures, and interpretation of structural chemistry. Course features self-paced exercises on PCs. Usually offered every second year.
Ms. Dickie

CHEM 130a Advanced Organic Chemistry: Structure
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.
Chemical bonding and structure, stereochemical principles and conformational analysis, organic reaction mechanisms, structures and activities of reactive intermediates, and pericyclic reactions. Usually offered every year.
Mr. Xu

CHEM 132b Advanced Organic Chemistry: Spectroscopy
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.
Application of spectroscopy to the elucidation of structure and stereochemistry of organic compounds, with emphasis on modern NMR and MS methods. Usually offered every year.
Mr. Xu

CHEM 134b Advanced Organic Chemistry: Synthesis
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.
Modern synthetic methods are covered, with an emphasis on mechanism and stereochemical control. Discusses the formation of carbon-carbon single and double bonds and carbocycles and procedures for oxidation, reduction, and functional group interchange. Examines selected total syntheses. Usually offered every year.
Mr. Snider

CHEM 137b The Chemistry of Organic Natural Products
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.
Natural products chemistry is surveyed within a biosynthetic framework. Occurrence, isolation, structure elucidation, biosynthesis, and biomimetic synthesis are covered with an emphasis on modern methods of establishing biosynthesis and biomimetic syntheses. Usually offered every second year.
Mr. Snider

CHEM 146b Advanced NMR Spectroscopy
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Prerequisites: A satisfactory grade in PHYS 10a,b, 11a,b, or 15a,b or the equivalent; MATH 10a,10b. Formerly offered as CHEM 246b.
A detailed discussion of modern NMR methods will be presented. The course is designed so as to be accessible to nonspecialists, but still provide a strong background in the theory and practice of modern NMR techniques. Topics include the theory of pulse and multidimensional NMR experiments, chemical shift, scalar and dipolar coupling, NOE, spin-operator formalism, heteronuclear and inverse-detection methods, Hartmann-Hahn and spin-locking experiments. Experimental considerations such as pulse sequence design, phase cycling, and gradient methods will be discussed. Guest lecturers will provide insight into particular topics such as solid-state NMR and NMR instrumental design. Usually offered every second year.
Mr. Pochapsky

COSI 178a Computational Molecular Biology
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Open to advanced undergraduate students and graduate students.
Information and computing technologies are becoming indispensable to modern biological research due to significant advances of high-throughput experimental technologies in recent years. This course presents an overview of the systemic development and application of computing systems and computational algorithms/techniques to the analysis of biological data, such as sequences, gene expression, protein expression, and biological networks. Hands-on training will be provided. Usually offered every other year.
Mr. Hong

NBIO 136b Computational Neuroscience
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Prerequisite: MATH 10a and either NBIO 140b or PHYS 10a or approved equivalents.
An introduction to concepts and methods in computer modeling and review of neural systems. Topics include single and multicompartmental models of neurons, information representation and processing by populations of neurons, synaptic plasticity and models of learning, working memory, decision making and neural oscillations. The course will be based on in-class computer tutorials, assuming no prior coding experience, with reading assignments and preparation as homework. Usually offered every second year.
Mr. Miller

PHYS 105a Biological Physics
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Physical forces in living matter are studied from the perspective offered by statistical mechanics, elasticity theory, and fluid dynamics. Quantitative models for biological structure and function are developed and used to discuss recent experiments in single-molecule biology. Usually offered every second year.
Mr. Hagan

QBIO 120b Quantitative Biology Instrumentation Laboratory
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Focuses on optical and other instruments commonly used in biomedical laboratories to make quantitative measurements in vivo and in vitro. Students disassemble and reconfigure modular instruments in laboratory exercises that critically evaluate instrument reliability and usability and investigate the origins of noise and systematic error in measurements. Usually offered every year.
Staff