Department of Biochemistry

Last updated: August 28, 2009 at 11:14 a.m.

Objectives

Undergraduate Major
 The biochemistry major is designed to equip students with a broad understanding of the chemical and molecular events involved in biological processes. The biochemistry major provides a foundation for careers in medicine, biotechnology, or research in all branches of the biological sciences.

The general aim of the major is to ensure that the students first learn the necessary chemical and physical chemical background and then the basic principles and observations of biochemistry and molecular biology. The department also offers a variety of introductory and advanced courses in more specialized subjects such as neurobiology, X-ray crystallography, and physical biochemistry. These courses sample the range of subjects that can be studied by biochemical methods and from a biochemical point of view.

Graduate Program in Biochemistry
 The graduate program in biochemistry leading to the degree of Doctor of Philosophy is designed to provide students with a deep understanding of the chemical principles governing the workings of biological macromolecules. The bioorganic chemistry specialization of this program gives students the option of training in organic chemistry in addition to biochemistry. 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. Students in the bioorganic chemistry specialization supplement this core curriculum with courses in organic synthesis and other topics in organic chemistry. Additional courses and seminars are available in a wide range of subjects, including enzyme regulation and mechanism, neurobiology, immunology, structural biochemistry, membrane biology, and molecular genetics. Students are encouraged to choose advanced courses and seminars according to their particular interests. Doctoral research topics are chosen in areas under investigation by the faculty; these include problems in macromolecular structure and function, enzyme function and regulation, RNA processing, gene regulation, membrane transport and receptor function, molecular pharmacology, mechanisms of cell motility, microbial metabolism, and the biochemistry of cellular electrical excitability. A theme running through this research is the relationship of biochemical functions to underlying molecular structures and mechanisms.

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 techniques, and a research project. Additional courses and seminars are available in a wide range of subjects.

How to Become a Major

Students who are interested in majoring in biochemistry should speak with the department advising head.

How to Be Admitted to the Graduate Program

The general requirements for admission to the Graduate School, given in an earlier section of the Bulletin, apply here. Applicants for admission to the biochemistry PhD program are also required to take the Graduate Record Examination. It is strongly suggested that the applicant take one of the advanced sections of this examination. The applicant's undergraduate curriculum should include fundamental courses in biology and chemistry.

Faculty

Gregory Petsko, Chair
 X-ray crystallographic analysis of protein structure and enzyme mechanisms.

Jeff Gelles
 Mechanisms of mechanoenzymes. Stochastic processes in single-enzyme molecules. Light microscopy as a tool to study enzyme mechanisms.

Nikolaus Grigorieff
 High-resolution electron cryo-microscopy of membrane proteins and channels.

Dorothee Kern
 Dynamics of enzymes. Magnetic resonance methods.

Daniel Pomeranz Krummel
 Structure-function studies of RNA-protein complexes critical to eukaryotic RNA maturation.

Christopher Miller, Graduate Program Chair
 Structure and function of ion channel proteins. Membrane transport and mechanisms of electrical excitation.

Daniel Oprian, Undergraduate Advising Head
 Structure-function studies of visual pigments and other cell surface receptors.

Dagmar Ringe
 Structures of enzymes and enzyme-substrate complexes. X-ray crystallography.

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

Requirements for the Major

Degree of Bachelor of Arts
 One year of general chemistry with laboratory; one year of organic chemistry with laboratory; one year of physics taught using calculus (PHYS 11a,b or PHYS 15a,b) with laboratory; BIOL 22a with laboratory (Genetics and Molecular Biology); BIOL 22b with laboratory (Cell Structure and Function)--the above courses must be taken prior to the senior year; BCHM 100a (Introductory Biochemistry); one year of physical chemistry, CHEM 141a (Thermodynamics and Statistical Thermodynamics), and either BCHM 104b (Physical Chemistry of Macromolecules) or CHEM 143b (Kinetics, Dynamics, and Transport); and one elective consisting of a biochemistry-related 100-level course (excluding research courses) from any science department. The course used to fulfill the elective requirement must be approved in advance by the biochemistry undergraduate advising head.

Degree of Bachelor of Science
 In addition to the degree requirements listed previously for the Bachelor of Arts degree, the Bachelor of Science degree requires one semester each of BCHM 101a and BCHM 103b (Advanced Biochemistry).

Required of all students: No course offered for major requirements may be taken pass/fail. Grades below C- in upper-level courses (any course numbered 100 or higher) cannot be used to fulfill the requirements for the major. Furthermore, no more than one D will be allowed in any other course required for the major.

Senior Honors Program
 In addition to the degree requirements listed previously, departmental honors require completion of two semesters of BCHM 99 (Research for Undergraduates), submission of an acceptable research thesis, and a final GPA 3.00 or better in the sciences and mathematics. Honors candidates are also expected to give a short oral presentation of their thesis research to members of the department at the end of their senior year. BCHM 99 may not exceed three semester credits. Petition the department for participation in this program is made at the beginning of the senior year.

Combined BS/MS Program

In addition to all courses required for the BS degree, the BS/MS degree requires completion of one additional elective (excluding research courses) approved in advance by the biochemistry undergraduate advising head, three semesters of research (one or two semesters of BCHM 99 plus one or two semesters of BCHM 150), a full-time (i.e., no concurrent course work) summer research residency lasting at least ten weeks, submission of an acceptable thesis, a GPA of 3.00 or better in the sciences and mathematics, and grades of B- or better in all 100-level biochemistry and biology courses.

This program requires completion of thirty-eight courses; no more than four semesters of research (BCHM 99 or BCHM 150) can count toward this total. Application to this program is made to the department and Graduate School no later than May 1 preceding the senior year, and all work, including the thesis, must be completed by the time the BS is awarded.

To qualify for the BS/MS degree, the thesis must constitute a significant research contribution; if a thesis is found to be unacceptable under the BS/MS program, it will automatically be considered under the honors program. The master’s thesis must be deposited electronically to the Robert D. Farber University Archives at Brandeis.

In order to complete the honors program or the combined BS/MS program, it is advisable to gain exemption where possible from introductory courses in science and mathematics. This is especially important for the premedical students who must also fulfill the requirements imposed by medical schools.

In order to complete the honors program or the combined BS/MS program, it is advisable to gain exemption where possible from introductory courses in science and mathematics. This is especially important for the premedical students who must also fulfill the requirements imposed by medical schools.

Requirements for the Degree of Master of Science

Program of Study
 Students must successfully complete an approved program of at least six courses. These courses are:

A. BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
BCHM 102a Quantitative Approaches to Biochemical Systems
BIOP 200b Reading in Macromolecular Structure-Function Analysis
BCHM 300a,b Biochemical Techniques (laboratory rotations)
One advanced (100-200 level) course from the School of Science, approved in advance by the graduate program chair.

Residence Requirement
 The minimum residence requirement is one year.

Language Requirement
 There is no language requirement.

Thesis
The student must complete an acceptable MS thesis describing original research. The master’s thesis must be deposited electronically to the Robert D. Farber University Archives at Brandeis.

Requirements for the Degree of Doctor of Philosophy in Biochemistry

Students must successfully complete:

A. The core curriculum consisting of:
 BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
BCHM 102a Quantitative Approaches to Biochemical Systems
BCHM 300a,b Biochemical Techniques (laboratory rotations course)
BIOP 200b Readings in Macromolecular Structure-Function Analysis
CONT 300b Ethical Practices in Health-Related Sciences

B. Elective courses: Electives may be chosen from any 100- or 200- level biochemistry, biology, chemistry, neuroscience, or quantitative biology courses listed in this Bulletin. Other advanced-topics courses may be substituted with the explicit permission of the thesis advisor and notification of the graduate program chair.

C. Students in their second and higher years of study must register for BCHM 401d (Biochemical Research Problems)--a dissertation research course--during every semester in which they are enrolled.

D. 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 of the thesis defense.

Students ordinarily complete the core curriculum plus one elective in the first year and complete the remaining requirements in their subsequent years in the program.

Requirements for the Degree of Doctor of Philosophy in Biochemistry with Specialization in Bioorganic Chemistry

In order to receive a PhD in biochemistry with a specialization in bioorganic chemistry, students must complete the requirements defined for the biochemistry PhD degree, with the following restrictions:

A. As one of their four elective courses, students must complete one course in synthetic organic chemistry, chosen from the following:
CHEM 134b Advanced Organic Chemistry: Synthesis
CHEM 135a Advanced Organic Chemistry: Synthesis II

B. As one of their four elective courses, students must complete one other advanced chemistry course approved in advance by the graduate program chair.

Students wishing to obtain the specialization must first gain approval of the graduate program chair. This should be done as early as possible; ideally, during the first year of graduate studies.

Requirements for the Degree of Doctor of Philosophy in Biochemistry with Specialization in Quantitative Biology

In order to receive a PhD in biochemistry with a specialization in quantitative biology, students must complete the requirements defined for the biochemistry PhD degree, and in addition must satisfy 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 quantitative biology program faculty advisory committee. With the approval of the biochemistry graduate program chair, courses taken to satisfy the quantitative biology specialization requirements can be used to satisfy course requirements of the biochemistry PhD degree.

Students wishing to obtain the 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.

Teaching Requirement
 As a 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 Requirements
 There is no foreign language requirement.

Financial Support
 Students may 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 individual research grants.

Qualifying Examinations
 A qualifying examination must be taken following the first year of course work. In this examination, the student will be asked to present and defend an original proposition put forth by the student. In addition, the student must successfully pass a comprehensive examination administered following the second year of course work.

Dissertation and Defense
 The required dissertation must summarize the results of an original investigation of an approved subject and demonstrates the competence of the candidate in independent research. This dissertation will be presented in a departmental lecture and defended in a final oral examination.

Special Note Relating to Graduate Students

In addition to the formal courses listed in the following sections, all graduate students are expected 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.

Courses of Instruction

(1-99) Primarily for Undergraduate Students

BCHM 93a Research Internship and Analysis
Supervised research experience in a Brandeis University laboratory. In consultation with a Brandeis faculty member, the student will design and execute an individual research project, culminating in an oral and written presentation.
Staff

BCHM 98a Readings in Biochemistry
Prerequisites: BIOL 22a, BCHM 100a, and one year of organic chemistry with laboratory. Does NOT satisfy the requirement for the major in biochemistry.
Directed scholarship on selected topics in biochemistry for outstanding juniors or seniors. Regularly scheduled discussion and written assignments leading to a substantive term paper. The tutorial is arranged only by mutual agreement between a faculty mentor and student. Usually offered every year.
Staff

BCHM 99a Research for Undergraduates
Prerequisites: BIOL 22a, BCHM 100a, and one year of organic chemistry with laboratory. Requirement of BCHM 100a may be waived.
Undergraduate research. A maximum of three course credits may be taken as BCHM 99a and/or 99b. At the discretion of the department, one semester may be taken for double credit (99e). Offered every year.
Staff

BCHM 99b Research for Undergraduates
See BCHM 99a for special notes and course description.
Staff

BCHM 99e Research for Undergraduates
See BCHM 99a for special notes and course description.
Staff

BCSC 1a Designer Genes
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Does NOT satisfy the requirement for the major in biochemistry.
We are living during a far-reaching biological revolution. Information is stored in genes as DNA, the hereditary material of life, and this information is converted into proteins. This course investigates: identifying undesirable mutations; creating desirable mutations; cloning of cells, organs, and animals in agriculture and medicine. Usually offered every second year.
Staff

(100-199) For Both Undergraduate and Graduate Students

BCHM 100a Introductory Biochemistry
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Prerequisite: One year of organic chemistry with laboratory.
Topics include chemistry, reaction, and metabolism of biologically important compounds; formation and utilization of "energy-rich" compounds; introduction to enzyme mechanisms; interrelation and comparison of basic biochemical and chemical processes; and metabolic regulation. Usually offered every year in multiple sections.
Staff

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.
Mr. Petsko

BCHM 102a Quantitative Approaches to Biochemical Systems
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Prerequisite: BCHM 100a 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.
Staff

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.
Address fundamental issues of information transfer in biological systems at a molecular level. Topics may cover: DNA recombination and replication; transcription (DNA to RNA); processing/maturation of precursor RNA transcripts; and translation (RNA to protein). An emphasis will be placed 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.
Mr. Krummel

BCHM 104b Physical Chemistry of Macromolecules
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Prerequisites: CHEM 141a or equivalent and BCHM 100a 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. Theobald

BCHM 107b Advanced Topics in Biochemistry: Research Hoedown
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Prerequisite: BCHM 100a. May not be taken for credit by students who took BCHM 103b in spring 2009.
An eclectic series of lectures taught by members of the faculty in their own area of research, with the intent that the student gain an in-depth appreciation for current research in the field, as well as a first hand exposure to biochemical research at Brandeis. Usually offered every year.
Staff

BCHM 150a Research for the BS/MS Candidates
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Prerequisites: BIOL 22a and BCHM 100a, one year of organic chemistry and laboratory, and BCHM 99.
The final semester(s) of laboratory research under the BS/MS program, to be pursued under the supervision of a 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 150e Research for the BS/MS Candidates
See BCHM 150a for special notes and course description.
Staff

BCHM 153b Methods in High-Resolution Electron Cyro-Microscopy
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Transmission electron microscopy is introduced as a method in structural biology. Instrumentation, data collection, image processing, and interpretation of biological structures visualized by this method are discussed. Usually offered every second year.
Mr. Grigorieff

BCHM 170b Bioinformatics
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Prerequisites: Familiarity with computing is necessary and a basic biochemistry course is recommended. A joint offering between Brandeis University and Wellesley College.
Familiarizes students with the basic tools of bioinformatics and provides a practical guide to biological sequence analysis. Topics covered include an introduction to probability and statistics; sequence alignments; database searches; alignments and phylogenetic trees; sequence pattern discovery; structure determination by secondary structure prediction; and three-dimensional structure prediction by homology modeling. In all cases, the strengths and limitations of the methods will be discussed. Usually offered every third year.
Ms. Ringe

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.
Mr. Miller and Mr. Oprian

(200 and above) Primarily for Graduate Students

BCHM 219b Enzyme Mechanisms
Staff

BCHM 223a Enzymology of Biofuels, Bioplastics, and Bioremediation
Mr. Oprian

BCHM 224a Single-Molecule Biochemistry and Biophysics
Mr. Gelles

BCHM 225b Protein Dynamics
Prerequisite: BCHM 101a.
Introduces the fundamental concept of atomic fluctuations in proteins and their relation to protein function. Protein dynamics on different timescales is discussed, with emphasis on different experimental and computational approaches to this problem. Usually offered every third year.
Ms. Kern

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

BCHM 300a Biochemistry Techniques
Prerequisite: BCHM 101. May be taken concurrently.
Usually offered every year.
Staff

BCHM 300b Biochemistry Techniques
Prerequisite: BCHM 101. May be taken concurrently.
Usually offered every year.
Staff

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

BIOP 200b Reading in Macromolecular Structure-Function Analysis
Required for first-year biochemistry and biophysics and structural biology graduate students.
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. Usually offered every year.
Mr. Petsko

Required First-Year Graduate Health-Related Science Programs Course

CONT 300b Ethical Practice in Health-Related Sciences
Required of all first-year graduate students in health-related science programs. 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.
Mr. Simister

Cross-Listed in Biochemistry

CHEM 123b Bioinorganic Chemistry
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Prerequisite: A satisfactory grade in CHEM 25a and b.
Bioinorganic chemistry involves the study of metal species in biological systems. Nearly one-third of proteins contain a metal cofactor. These cofactors catalyze an enormous breadth of chemical reactions, including many not yet accessible through conventional syntheses. Usually offered every second year.
Mr. Agar

CHEM 129b Special Topics in Inorganic Chemistry: Introduction to X-ray Structure Determination
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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.
Mr. Foxman

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. Deng

CHEM 131a Advanced Organic Chemistry: Topics in Structure and Reactivity
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Prerequisite: A satisfactory grade in CHEM 25a and b, or the equivalent.
Broad coverage of a variety of transformations involving additions, eliminations, substitutions, oxidations, reductions, and rearrangements. Usually offered every year.
Staff

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 143b Kinetics, Dynamics, and Transport
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Macroscopic kinetics: elementary reactions and rate laws. Kinetic study of reaction mechanisms: techniques for kinetic measurements, fast reactions, treatment of kinetic data. Microscopic kinetics: molecular dynamics, transition state theory, reactions in the gas phase and in solution. Catalytic and chain reactions, enzyme kinetics. Nonlinear dynamics: chemical oscillations and waves. Usually offered every other year.
Mr. Jordan

CHEM 144a Computational Chemistry
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or 15a,b or equivalent. Organic chemistry is also recommended.
Topics in computational chemistry: applications of quantum mechanics to structural and spectroscopic analysis of small molecules; molecular dynamics and Monte Carlo simulations of biomacromolecules. Standard computational programs are used by students to perform homework exercises. Usually offered every other year.
Mr. Jordan

CHEM 146a Single Molecule Spectroscopy
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Prerequisites: A satisfactory grade in CHEM 11a, 15a and CHEM 11b, 15b or equivalent; MATH 10a,b or equivalent; PHYS 11a,b or PHYS 15 a,b, or equivalent.
Studies single molecule spectroscopy techniques including fluorescence microscopy experiments, laser tweezers, magnetic tweezers, and atomic force microscopy, along with their applications to chemical and biological systems. Usually offered every second year.
Staff

CHEM 147b Mass Spectrometry
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Prerequisite: A satisfactory grade in CHEM 11b, 15b or equivalent or permission of the instructor. Organic chemistry is also recommended.
The process of ionization, ion separation, and ion detection is taught at the theoretical level, and applied to the understanding of modern mass spectrometry. Usually offered every second year.
Mr. Agar

CHEM 246b Advanced NMR Spectroscopy
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 third 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 the significant advances of high-throughput experimental technologies in recent years. This course presents an overview of the systematic 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. Hand-on training will be provided. Usually offered every other year.
Mr. Hong

COSI 230a Topics in Computational Biology
This course aims to transcend traditional departmental boundaries and facilitate communications between experimental biologists and computational scientists. Through reading literature and small research projects, students will be introduced to problems in computational biology and learn the methods for studying them.
Mr. Hong

NBIO 136b Computational Neuroscience
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Prerequisite: MATH 10a or PHYS 10a or approved equivalents.
An introduction to concepts and methods in computer modeling 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 neuroeconomics. 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. Kondev

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 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.
Mr. Dogic