An interdepartmental program in Biological Physics

Last updated: August 27, 2014 at 3:49 p.m.

Objectives

The undergraduate major in biological physics is designed to provide the quantitative skills and background in chemistry and biology for students interested in the study of the physics of biological systems, especially on the molecular scale. This program provides a strong foundation in the physical sciences that underpin much of the modern revolution in biology. It should be of particular interest to students wishing to pursue careers in fundamental or applied research in biophysics, quantitative biology, and biotechnology.

For a related graduate program, please see the Biophysics and Structural Biology Program elsewhere in this Bulletin.

Learning Goals

The Biological Physics major offers students the unique opportunity to prepare for graduate school, medical school, or employment in biotechnology. This is an interdisciplinary major that brings together the disciplines of physics, chemistry and biology, with a particular emphasis on physics. Our undergraduate program is firmly based on a first‐rate research program in biophysics, an area of science for which Brandeis is world renowned. A particular strength of the program is that it offers numerous opportunities for cutting‐edge research in biophysics in a number of different labs on campus. In many instances students have published papers in prestigious journals while completing the major.

Core Skills
After completing this major, students will:
Given an observation about the living world, be able to formulate a hypothesis about the physical and chemical principles that give rise to it, produce a mathematical model that embodies these principles, and propose new experiments to test the hypothesis. Evaluate measurement errors in scientific data sets, the effects of these errors on interpretation of the data, and calculate levels of confidence in conclusions drawn from the data. Explain to an interdisciplinary audience the physical and chemical principles that underlie our understanding of the living world. Know how to design experiments, computer simulations, and/or theory to test a scientific hypothesis. They will also have developed their skills in applied mathematics, laboratory techniques, and in oral and written presentation.

Knowledge goals
After completing this major, students will have learned at an advanced undergraduate level the principles and practice of physics, chemistry and biology, as well as statistics and error analysis applied to experimental data. The goal is to become conversant in all three disciplines of science, with a particular emphasis on the mastery of physics as it applies to problems in the biomedical fields.

Upon Graduation
Most of our graduates go on to graduate school in biophysics, bioengineering and related interdisciplinary fields, while others go into high‐tech employment, medical school, or other professional studies.

Social Justice
One of the great challenges facing our society is the need for new sources of clean energy, better medicines, and new breakthroughs in basic science that will fuel the technologies of the future. These challenges will require the concerted effort of scientists from different disciplines working together toward a common goal. One of the key goals of the Biological Physics major is to produce a cadre of scientists that will be able to successfully work in interdisciplinary teams of tomorrow.

How to Become a Major

The major requires a large number of science courses, some of which are prerequisites for more advanced courses. Therefore, it is important to start taking these courses in the first year. Students are advised to meet with the biological physics chair as soon as possible to plan their schedule. It is most advantageous to take physics and math in the first year, but starting with chemistry and math in the first year is also adequate.

In the years it is offered FYS 11a (Nature's Nanotechnology) is recommended for first-year students as an introduction to the major. Students interested in the honors program, involving a senior research thesis, should begin to seek a faculty mentor by the end of their second year, with the prospect of starting research as early as possible.

Committee

Seth Fraden, Chair (fall 2014)
(Physics, Volen National Center for Complex Systems)

Michael Hagan, Chair (spring 2015) (on leave fall 2014)
(Physics)

Bulbul Chakraborty
(Physics)

Zvonimir Dogic (on leave fall 2014)
(Physics)

Jeff Gelles
(Biochemistry)

Dorothee Kern (on leave academic year 2014-2015)
(Biochemistry, Volen National Center for Complex Systems)

Jané Kondev
(Physics)

Gregory Petsko, Emeritus
(Biochemistry and Chemistry; and Director, Rosenstiel Center)

Dagmar Ringe (on leave spring 2015)
(Biochemistry and Chemistry; and Rosenstiel Center)

Avital Rodal
(Biology)

Azadeh Samadani
(Physics)

Timothy Street
(Biochemistry)

Requirements for the Major

Degree of Bachelor of Science
To satisfy the requirements for the major in biological physics leading to the degree of Bachelor of Science, students must successfully complete the foundation of this program, which is a set of required courses in the physical and life sciences. The core courses, divided by fields, are:

Physics: PHYS 11a,b or PHYS 15a,b; PHYS 19a,b; PHYS 20a; PHYS 31a (formerly PHYS 30b); PHYS 39; PHYS 40

Mathematics: MATH 10a,b

Chemistry: CHEM 11a,b and CHEM 18a,b or equivalents

Biology: BIOL 14a, BIOL 15b (or BIOL 22a,b) and BIOL 18a,b

Biological Physics: FYS 11a or PHYS 105a

FYS 11a (Nature's Nanotechnology) should be taken in the first year, if it is offered. Students who enter the program after their first year may find it convenient to replace FYS 11a with PHYS 105a (Biological Physics), which covers the same material at a higher level of both mathematics and physics.

Students with high enough Advanced Placement Examination scores may place out of some of the elementary courses. See the Advanced Placement Credit chart in an earlier section of this Bulletin for details concerning the equivalent Brandeis courses for sufficient scores in the tests in Mathematics (AB or BC), Physics (C), and Chemistry. Credit toward the major is given for all these tests except for Physics C: Electrical. Students who take advanced placement credit for PHYS 15b will be required to take PHYS 30a, the intermediate-level course in this subject.

Beyond the core curriculum, students are expected to explore areas of further inquiry by taking at least two elective courses. Possible topics and related courses are listed in the following sections. Other courses can be taken as electives with approval of the program advisor.

Molecular structure: The use of physical techniques including X-ray diffraction, electron microscopy, and nuclear magnetic resonance to elucidate the structure of bio-molecules. Electives: BIOL 102b, BCHM 171b*, BIBC 126b, BCHM 104b*.

Single molecule biophysics: The study of biological processes on the single molecule scale, such as enzyme function, ion transport through membranes, protein folding, molecular motors. Electives: BCHM 101a*.

Modeling of biological structure and function: The development and analysis of mathematical models for elucidating biological structure and function. Electives: BIOL 135b, PHYS 105a, NBIO 136b, QBIO 110a.

Systems and networks: Study of topics including bioinformatics, neural networks, and networks of genes and proteins. Electives: COSI 178a, NBIO 140b.

*Required prerequisites for this course are not included in the core curriculum.

A student starting the biological physics major in the first year, with no advanced placement, should follow the recommended sequence:

Year 1: FYS 11a; MATH 10a,b; PHYS 15a,b; PHYS 19a,b
Year 2: CHEM 11a,b; CHEM 18a,b; PHYS 20a, PHYS 40a
Year 3: BIOL 18a,b; BIOL 22a,b; PHYS 39a
Year 4: PHYS 31a (formerly PHYS 30b); two electives

A student with advanced preparation in math, physics, and chemistry who wants to emphasize biochemistry might take the following program:

Year 1: FYS 11a; MATH 15a; MATH 20b; PHYS 19b; PHYS 20a; PHYS 40a
Year 2: BIOL 18a,b; BIOL 22a,b; CHEM 25a,b; CHEM 29a,b
Year 3: BCHM 100a; PHYS 39a, one elective
Year 4: PHYS 30a; PHYS 31a (formerly PHYS 30b); one elective

Students with advanced preparation might choose additional courses in other areas rather than organic chemistry and biochemistry. A student who has started as a premed and switched to biological physics (not completing the premed program) might have the following program:

Year 1: CHEM 11a,b; CHEM 18a,b; MATH 10a,b
Year 2: BIOL 18a; BIOL 22a; FYS 11a; PHYS 11a,b or PHYS 15a,b; PHYS 19a,b
Year 3: BIOL 18b; BIOL 22b; PHYS 20a; PHYS 40a; one elective
Year 4: PHYS 31a (formerly PHYS 30b); PHYS 39a; one elective

In addition to the required courses, students are urged to learn the necessary topics in organic chemistry as preparation for biochemistry. This opens up additional options for undergraduate research and graduate programs in the life sciences. For medical school, a year of organic chemistry with laboratory, in addition to the required courses for biological physics, will complete the premed program requirements.

An important component of the program is the opportunity for students to participate in research. Opportunities exist for research in the laboratories of physics, chemistry, neuroscience, biochemistry, and biology faculty.

No course with a final grade below C- can count toward fulfilling the major requirements in Biological Physics.

No course taken pass/fail may count toward the major requirements.

Honors Program
Graduation with honors requires completion of a senior research thesis. Students must enroll in BIPH 99d in their senior year to carry out a research project. Students wishing to join the honors program should apply to the honors advisor in the program in the spring of their junior year.

Special Notes Relating to Undergraduates

Students majoring in biological physics may not count required courses toward a minor in physics. By completing other required courses, they can complete a second major in physics. However, for the preparation for a career in biological physics, it might be more valuable to devote extra science courses to deeper preparation in chemistry and biochemistry.

Courses of Instruction

(1-99) Primarily for Undergraduate Students

BIPH 98a Reading in Biological Physics
Open to students wishing to study a subject not available in the curriculum.
Staff

BIPH 98b Reading in Biological Physics
See BIPH 98a for course description.
Staff

BIPH 99d Senior Research
Permission of the program chair required. Original research under the direction of a faculty member. A written thesis and oral defense are required. The complete set of rules is available from the physics department office. Usually offered every year.
Staff

Core Courses

BIOL 14a Genetics and Genomics
[ qr1 sn ]
May not be taken for credit by students who took BIOL 22a in prior years.
Studies fundamentals of genetics, genomics, molecular biology and biological problem-solving. Topics include heredity, meiosis, molecular basis of phenotypic variations in individuals and populations, as well as an introduction to the tools and techniques used by past and current researchers in genetics and genomics. Usually offered every year.
Ms. Woodruff

BIOL 15b Cells and Organisms
[ sn ]
May not be taken for credit by students who took BIOL 22b in prior years.
Introduces contemporary biology with an emphasis on cells, organs, and organ systems. Topics include the forms and functions of macromolecules, organelles, and cells, the integration of cells into tissues, and the physiology of fundamental life processes. The course is intended to prepare students to understand the biology of everyday life, and to provide a strong foundation for those who continue to study the life sciences. Usually offered every year.
Mr. Simister

BIOL 18a General Biology Laboratory
[ sn wi ]
Prerequisite: BIOL 14a. The prerequisite is waived if students have successfully completed BIOL 22a in a prior semester. Prerequisites: Sophomore standing or permission of the instructor. Yields full-course credit. Laboratory fee: $150 per semester. This lab is time-intensive and students will be expected to come in to lab between regular scheduled lab sessions. In order to accommodate students with time conflicts it may be necessary to re-assign students without conflicts to another section of the course. Students' section choice will be honored if possible.
Provides firsthand experience with a wide array of organisms and illustrates basic approaches to experimental design and problem solving in genetics and genomics. Usually offered every year.
Ms. Kosinski-Collins

BIOL 18b General Biology Laboratory
Prerequisite: BIOL 15b. The prerequisite is waived if students have successfully completed BIOL 22b in a prior semester. Prerequisites: Sophomore standing. Yields half-course credit. Laboratory fee: $150 per semester. This lab is time-intensive and students will be expected to come to lab between regular scheduled lab sessions. In order to accommodate students with time conflicts it may be necessary to re-assign students without conflicts to another section of the course. Students' section choice will be honored if possible. This course offers a 2-credit optional practicum.
Provides firsthand experience with modern molecular biology techniques and illustrates basic approaches to experimental design and problem solving in molecular and cellular biology including applications of biochemical techniques. Usually offered every year.
Mr. Baade

BIOL 135b The Principles of Biological Modeling
[ qr sn ]
Prerequisite: MATH 10a or 10b.
With examples from neuroscience, cell biology, ecology, evolution, and physiology, dynamical concepts of significance throughout the biological world are discussed. Simple computational and mathematical models are used to demonstrate important roles of the exponential function, feedback, stability, oscillations, and randomness. Usually offered every second year.
Mr. Miller

CHEM 11a General Chemistry I
[ qr sn ]
This course may not be taken for credit by students who have passed CHEM 15a in previous years. Four class hours and one sixty-minute structured study group session per week. The corresponding lab is CHEM 18a.
Covers a wide array of topics, embracing aspects of descriptive, as well as quantitative, chemistry. No prior study of chemistry is assumed, as the course begins by looking at the atomic foundation of matter, the elements, and the organization of the periodic table, working its way up to studying how atoms are bonded together to form larger units of matter. Students who complete this course will have an understanding of the three major phases of matter—solids, liquids, and gases—and how they behave, as well as a knowledge of the major types of chemical reactions and how to represent them. A strong focus is put on learning methods of creative problem-solving—using the material as a way to develop creative approaches to solving unfamiliar problems—a skill that carries students far beyond the confines of the classroom. Usually offered every year.
Ms. Novack

CHEM 11b General Chemistry II
[ qr sn ]
Prerequisite: A satisfactory grade (C- or better) in CHEM 11a or an approved equivalent. This course may not be taken for credit by students who have passed CHEM 15b in previous years. Four class hours and one sixty-minute structured study group session per week. The corresponding lab is CHEM 18b.
Picks up where Chemistry 11a left off, advancing students’ understanding of bonding models and molecular structure and exploring the basics of coordination chemistry. Three major quantitative topics are covered in the second half of General Chemistry—chemical equilibrium (including acid-base chemistry, solubility, and complex-ion formation), chemical kinetics, and thermodynamics. Other topics explored are electrochemistry and nuclear chemistry. Usually offered every year.
Ms. Novack

CHEM 18a General Chemistry Laboratory I
Corequisite: CHEM 11a. Dropping CHEM 11a necessitates written permission from the lab instructor to continue with this course. Two semester-hour credits; yields half-course credit. Laboratory fee: $100 per semester. This course may not be taken for credit by students who have passed CHEM 19a in previous years.
Introduction to basic laboratory methods and methods of qualitative and quantitative analyses. Included in the analytical methods are gas chromatography and infrared measurements. A synthesis project that includes analyzing the product by titration. Calorimetric experiment using probes interfaced with computers. Identification of unknowns based on physical and chemical properties. Analysis of the metal content of substances by atomic absorption. One laboratory lecture per week. One afternoon of laboratory per week. Usually offered every year.
Mr. Dolnik

CHEM 18b General Chemistry Laboratory II
Prerequisites: A satisfactory grade (C- or better) in CHEM 18a and CHEM 11a. Corequisite: CHEM 11b. Dropping CHEM 11b necessitates written permission from the lab instructor to continue with this course. May yield half-course credit toward rate of work and graduation. Two semester-hour credits. Laboratory fee: $100 per semester. This course may not be taken for credit by students who have passed CHEM 19b in previous years.
The second semester of the general chemistry laboratory program. Continued use of probes interfaced with computers to monitor pH and electrical conductivity changes in titrating weak monoprotic and polyprotic amino acids, to monitor pressure changes as part of a kinetics study, and to monitor voltage changes of electrochemical cells with temperature so as to establish thermodynamic parameters for redox reactions. Also included is identification of unknowns based on selective precipitation. Usually offered every year.
Mr. Dolnik

COSI 178a Computational Molecular Biology
[ sn ]
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

FYS 11a Nature's Nanotechnology
[ sn ]
Familiarity with high school math, physics, chemistry and biology is expected.
Imagine a world occupied by machines whose size is 10,000 times smaller than the width of a human hair. Some of them produce fuel by harnessing solar energy, while others transport cargo on tracks only 10 atoms across, or assemble other machines following molecular blueprints. This is the bustling world inside a living cell, which we will explore using high school level math, physics and biology. Usually offered every year.
Mr. Kondev (Physics)

MATH 10a Techniques of Calculus (a)
[ sn ]
Prerequisite: A satisfactory grade of C- or higher in MATH 5a or placement by examination. Students may not take MATH 10a if they have received a satisfactory grade in MATH 10b or MATH 20a.
Introduction to differential (and some integral) calculus of one variable, with emphasis on techniques and applications. Usually offered every semester in multiple sections.
Ms. Parker (fall) Ms. Torrey (spring)

MATH 10b Techniques of Calculus (b)
[ sn ]
Prerequisite: A satisfactory grade of C- or higher in MATH 10a or placement by examination. Continuation of 10a. Students may not take MATH 10a and MATH 10b simultaneously. Students may not take MATH 10b if they have received a satisfactory grade in MATH 20a.
Introduction to integral calculus of one variable with emphasis on techniques and applications. Usually offered every semester in multiple sections.
Ms. Torrey (fall) Ms. Parker (spring)

PHYS 11a Introductory Physics I
[ qr sn ]
Corequisite: MATH 10b or the equivalent. Usually taken with PHYS 19a.
An introduction to Newtonian mechanics with applications to several topics. Usually offered every year.
Mr. Fell

PHYS 11b Introductory Physics II
[ qr sn ]
Corequisite: MATH 10b or the equivalent. Usually taken with PHYS 19b. Prerequisite: PHYS 11a or equivalent.
An introduction to electricity and magnetism and the special theory of relativity. Usually offered every year.
Mr. Fell

PHYS 15a Advanced Introductory Physics I
[ qr sn ]
Corequisite: MATH 10a or b or the equivalent, or permission of instructor. Usually taken with PHYS 19a.
An advanced version of PHYS 11a for students with advanced preparation in physics and mathematics. An introduction to Newtonian mechanics with special applications to several topics. Usually offered every year.
Mr. Roberts

PHYS 15b Advanced Introductory Physics II
[ qr sn ]
Prerequisite: PHYS 15a or the equivalent and MATH 10a or b or equivalent, or permission of instructor. Usually taken with PHYS 19b.
An advanced version of PHYS 11b for students with good preparation in physics and mathematics. An introduction to electricity and magnetism and the special theory of relativity for students with advanced preparation. Usually offered every year.
Ms. Sciolla

PHYS 19a Physics Laboratory I
May yield half-course credit toward rate-of-work and graduation. Two semester-hour credits.
Laboratory course designed to accompany PHYS 11a and 15a. Introductory statistics and data analysis including use of microcomputers and basic experiments in mechanics. One afternoon or evening of laboratory per week. One one-and-a-half-hour lecture per week. Usually offered every year.
Mr. Fell

PHYS 19b Physics Laboratory II
May yield half-course credit toward rate-of-work and graduation. Two semester-hour credits.
Laboratory course designed to accompany PHYS 11b and 15b. Basic experiments in electricity, magnetism, and optics. Basic electrical measurements. Determination of several fundamental physical constants. One afternoon or evening of laboratory per week. One one-and-a-half-hour lecture per week. Usually offered every year.
Mr. Fell

PHYS 20a Modern Physics I
[ sn ]
Prerequisites: PHYS 11a, PHYS 11b or PHYS 15a, PHYS 15b or permission of the instructor.
A survey of phenomena, ideas, and mathematics underlying modern physics-special relativity, waves and oscillations, and foundations of wave mechanics. Usually offered every year.
Mr. Blocker

PHYS 31a Quantum Theory I
[ sn ]
Prerequisites: PHYS 15a and b and PHYS 20a or permission of the instructor. This course may not be repeated for credit by students who have taken PHYS 30b in previous years.
Introduction to quantum mechanics: atomic models, Schrödinger equation, angular momentum, and hydrogen atom. Multielectron atoms and interaction of atoms with the electromagnetic field. Usually offered every year.
Ms. Baskaran

PHYS 39a Advanced Physics Laboratory
[ qr sn wi ]
Prerequisite: PHYS 20a. This course may be repeated once for credit with permission of the instructor. This course is co-taught with PHYS 169b.
Experiments in a range of topics in physics, possibly including selections from the following: wave optics, light scattering, Nuclear Magnetic Resonance, numerical simulation and modeling, phase transitions, laser tweezers, chaotic dynamics, and optical microscopy. Students work in depth on three experiments during the term. Usually offered every year.
Mr. Fraden

PHYS 40a Introduction to Thermodynamics and Statistical Mechanics
[ sn ]
Prerequisite: PHYS 20a or permission of the instructor.
Studies the properties of physical systems as predicted by the statistical behavior of their constituent particles. Statistical mechanics provides a molecular-level interpretation of macroscopic thermodynamic quantities such as work, heat, free energy, and entropy. Topics studied will include; the laws of Thermodynamics, semi-classical and quantumstatistical mechanics, ensembles (microcanonical, canonical, and grand canonical), thermodynamic potentials and applications to a number of different systems. Usually offered every year.
Ms Baskaran

Elective Courses

The following courses are approved for the program. Not all are given in any one year. Please consult the Schedule of Classes each semester.

BCHM 101a Advanced Biochemistry: Enzyme Mechanisms
[ sn ]
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. Oprian

BCHM 104b Physical Chemistry of Macromolecules II
[ sn ]
Prerequisites: BCHM 100a, and one of the following: BCHM 104a, CHEM 141a, or Phys 40a.
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

BIBC 126b Molecular Mechanisms of Disease
[ sn ]
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.
Ms. Westover

BIOL 102b Structural Molecular Biology
[ sn ]
Prerequisites: BIOL 14a or BIOL 22a and BIOL 15b or BIOL 22b, or permission of the instructor.
Cells are filled with machines that carry materials about the cell, that chemically transform molecules, that transduce energy, and much more. Our understanding of how these machines work depends on understanding their structures. This introduction to the structural basis of molecular biology examines the designs of proteins, their folding and assembly, and the means whereby we visualize these structures. Usually offered every second year.
Ms. Kosinski-Collins

NBIO 136b Computational Neuroscience
[ sn ]
Prerequisite: NBIO 140b 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

NBIO 140b Principles of Neuroscience
[ sn ]
Prerequisite: Sophomore standing, BIOL 15b or BIOL 22b, and one of the following. One year of college-level chemistry with lab, one year of college-level physics with lab, or any math course above 10a,b. AP scores are not accepted to meet the prerequisite.
Examines the basic principles of neuroscience. Topics include resting potentials, action potentials, synaptic transmission, sensory systems, motor systems, learning, neural circuits underlying behavior, neurological diseases, and mental illness. Usually offered every year.
Ms. Turrigiano

PHYS 105a Biological Physics
[ sn ]
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
[ sn ]
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.
Mr. Hagan

QBIO 120b Quantitative Biology Instrumentation Laboratory
[ sn ]
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