University Bulletin (2022-2023)

• Master of Science
• Doctor of Philosophy

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. 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 BS/MS or MS 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 Brandeis 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 MS program requires students 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 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.

Graduate Outcomes

1. Upon graduation, biochemistry students 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 PhD 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 and 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.  For specifics of the program’s requirements, please see the department website.

Dorothee Kern, Program Chair
(Biochemistry)

Michael Hagan
(Physics)

Niels Bradshaw (Biochemistry)
Regulation of Protein Phosphatases and the Evolution of Cellular Signaling.

Irving Epstein (Chemistry; Neuroscience; Volen Center)
Nonlinear chemical dynamics. Mathematical modeling of biochemical kinetics and neural systems.

Seth Fraden (Physics)
Macromolecules in suspension. Physics of protein crystallization. Microfluidics.

Paul Garrity (Biology; Volen Center)
Neural development and behavior.

Jeff Gelles (Biochemistry)
Single-molecular biochemistry and biophysics. Transcription and RNA processing. Cytoskeletal networks and regulation.

Bruce Goode (Biology; Rosenstiel Center)
Cytoskeletal mechanisms controlling cell morphogenesis.

Leslie Griffith (Biology; Neuroscience; Volen Center)
Biochemistry of behavior.

Michael Hagan (Physics) 
Computation and theory in biological physics.

Lizbeth Hedstrom (Biology; Chemistry)
Antimicrobial design; targeted protein degradation; TSC2 activators; enzyme structure-function studies.

Tijana Ivanovic (Biochemistry; Rosenstiel Center)
Molecular mechanisms of virus translocation across biological membranes.

Sebastian Kadener (Biology; Neuroscience; Rosenstiel Center; Volen Center)
Molecular neurobiology and RNA metabolism.

Julia Kardon (Biochemistry)
Mechanisms for control of mitochondrial protein activity, quality, and lifespan.

Dorothee Kern, Biochemistry and Biophysics Graduate Program Chair (Biochemistry; Volen Center)
Dynamics of enzymes. Magnetic resonance methods.

Jane Kondev (Physics)
Biophysics and structural biology

Isaac Krauss (Chemistry)
Organic synthesis.

Susan Lovett (Biology; Rosenstiel Center)
Genetics and molecular biology of bacteria and yeast.

Daniel Oprian (Biochemistry (Biology; Neuroscience; Volen Center)
Structure-function studies of visual pigments and other cell surface receptors.

Maria-Eirini Pandelia (Biochemistry; Rosenstiel Center)
Mapping the functional repertoire of (bio)inorganic systems and protein metallocofactors; paradigms of (bio)catalysts relevant to the human health and environment.

Suzanne Paradis (Biology; Neuroscience; Volen Center)
Molecular mechanisms of synaptic development.

Thomas Pochapsky (Chemistry; Rosenstiel Center)
Biological redox enzymes structure and mechanism.

Avital Rodal (Biology; Rosenstiel Center; Volen Center)
Endosomal membrane traffic in neurons.

Ben Rogers (Physics)
Self-assembly at the colloidal length scale.

Michael Rosbash (Biology; Volen Center)
Circadian rhythms, behavior, and gene expression.

Klaus Schmidt-Rohr (Chemistry)
Solid-state NMR of biological nanocomposites and immobilized proteins; analysis of SAXS proteins.

Timothy Street (Biology; Rosenstiel Center)
Mechanisms of protein folding in the cell.

Douglas Theobald (Biochemistry)
Structural bioinformatics analysis of telomeric complexes, integrating X-ray crystallographic structure determination, molecular evolution, and structure-function studies.

Bing Xu (Chemistry)
Biomaterials and self-assembly.

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:

A. Four one-semester courses, all with a grade of B- or higher:

• BCHM 101a
• BCHM 103b
• BCHM 104b 
• One other advanced level course from the School of Science, approved in advance by the graduate program chair 

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 the Division of Science Responsible Conduct of Research (RCR) workshop, usually offered in the spring.

B. In the first semester, students are required to take two laboratory rotations and enroll in BCBP 296a, b.

C. 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.

D. 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.

E. 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 in-person 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. Students must electronically deposit their thesis to ProQuest ETD. For instructions on how to do this, visit the Thesis and Dissertation Guide.

Summer Registration

Master’s students are required to be on campus engaging in research in the intervening summer and must enroll in BCBP 297a. Registration for Graduate Summer Term does not count toward the residency requirement. The summer registration fee will be waived.

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:

A. 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. 

B. Ordinarily, all students are required to take:

• BCBP 200b (Reading in Macromolecular Structure-Function Analysis).
• The two laboratory rotation courses (BCBP 300a and 300b). 
• All students must also complete the Division of Science Responsible Conduct of Research (RCR) workshop. 

C. All students beyond the first year must register for BCHM 401d. Neither BCBP 300a nor BCBP 300b nor BCHM 401d count toward the seven course requirement.

D. During their second year and beyond, students must also present their own work at least once a year in the QB/MSM Pizza Talk series.

E. 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. Students should also discuss their Individualized Development Plan (IDP) with their advisor or the Graduate Program Advisor. 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.

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.

Teaching Requirement

All PhD students are required to participate in undergraduate teaching during the course of their studies. Every graduate teaching assistant (TA) is supervised by a member of the faculty, who serves as a mentor to improve the quality of the TA's teaching. Please see the GSAS section on Teaching Requirements and the program handbook for more details.

Residence Requirement

The minimum in-person residence requirement is three years.

Language Requirement

There is no language requirement.

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.

Summer Registration

PhD students in the Life Sciences programs are required to be on campus or at a related lab for the full year while engaged in taking classes and/or doing research related to their field of study and will be enrolled in CONT 250b by the Registrar's office. Registration for Graduate Summer Term does not count toward the residency requirement. The summer registration fee will be waived.

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.

Every student, whether or not currently in residence, must register at the beginning of each term. All graduate students will be evaluated by the program each spring. At this evaluation the records of all graduate students will be carefully reviewed with reference to the timely completion of coursework and non-course degree requirements, the quality of the work and research in progress and the student’s overall academic performance in the program. 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.

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.

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.

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.
Emily 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.
Dorothee Kern

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.
Dagmar Ringe

BCBP 230b Advanced Topics in Molecular Virology

Viruses infect all living things and have a role in how life works. They play a direct role in health and disease and even constitute portions of our own genetic material. The course will cover a range of topics focusing on viral mechanisms such as cell entry (membrane fusion and penetration), RNA replication and processing, and virus-particle assembly and budding, and the roles of these basic viral functions in permitting virus evolution. Through in-depth analyses of primary literature, a special emphasis will be placed on understanding experimental approaches and critically evaluating conclusions drawn from experiments. We will build upon various concepts covered in the course to discuss potential strategies for preventing undesired viral adaptations at the root of pandemics or antiviral drug resistance. The course will focus on recent discoveries and the use of modern techniques in virology research. Usually offered every year.
Tijana Ivanovic

BCBP 240a Advanced Topics in Single-molecule Biophysics

Prerequisite: BCHM 102a or the equivalent.

Explores the use of single-molecule biophysics techniques to reveal the kinetics and mechanisms of biochemical reactions. This graduate-level advanced-topics course will cover statistical theory underlying single-molecule fluorescence experiments, computational methods used to analyze data, and practical aspects of experiment design. Usually offered every third year.
Jeff Gelles

BCBP 266a Advanced Topics in Protein Folding

Prerequisite: BCHM 104b or the equivalent.

Explores current research in the field of protein folding. Emphasis will be placed on classic papers that reveal underlying mechanisms of protein folding. Current challenges and questions in the field will also be addressed. Usually offered every third year.
Timothy Street

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

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.
Thomas 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.
Lizbeth 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.
Staff

CHEM 130a Advanced Organic Chemistry: Structure
[ sn ]

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.
Hao 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.

Hao 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.
Chi Ting

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.

Chi Ting

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.

A detailed discussion of modern NMR methods will be presented. The course is designed so as to be accessible to non-specialists, 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.
Thomas 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.
Pengyu Hong

NBIO 136b Computational Neuroscience
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Prerequisites: MATH 10a or MATH 10b or MATH 15a and either NBIO 140b or PHYS 10b or PHYS 11b or COSI 11a.

An introduction to concepts and methods in computer modeling and analysis 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.
Paul 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.
Staff

QBIO 110a Numerical Modeling of Biological Systems
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Prerequisite: MATH 10a and b or equivalent.

Modern scientific computation applied to problems in molecular and cell biology. Covers techniques such as numerical integration of differential equations, molecular dynamics and Monte Carlo simulations. Applications range from enzymes and molecular motors to cells. Usually offered every second year.
Staff

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.

Ben Rogers