Students entering the University of San Diego and/or declaring a major during 2019-2020, should follow information contained in the printed course catalog (also known as the "catalog of record") published on April 1, 2019. Access the catalog of record at http://catalogs.sandiego.edu.

## The Biophysics Major

### Preparation for the Major (48-50 units)

Preparation for the Biophysics Major is designed to give students a broad background in biology, chemistry, and physics. In order to successfully navigate these diverse fields, a strong background in math is also required.

Code | Title | Units |
---|---|---|

Physics Courses | ||

PHYS 270 & 270L | Introduction to Mechanics and Mechanics Lab | 4 |

PHYS 271 & 271L | Introduction to Electricity and Magnetism and Introduction to Electricity and Magnetism Lab | 4 |

PHYS 281 | Introduction to Optics | 1 |

PHYS 272 & 272L | Introduction to Modern Physics and Introduction to Modern Physics Lab | 4 |

PHYS 282 | Introduction to Methods in Computational Physics | 1 |

Mathematics Courses | ||

MATH 150 | Calculus I | 4 |

MATH 151 | Calculus II | 4 |

MATH 250 | Calculus III | 4 |

Chemistry Courses | ||

CHEM 151 & 151L | General Chemistry I and General Chemistry I Laboratory | 4-5 |

CHEM 152 & 152L | General Chemistry II and General Chemistry II Laboratory | 4 |

CHEM 301 & 301L | Organic Chemistry I and Organic Chemistry I Laboratory | 4 |

CHEM 302 & 302L | Organic Chemistry II and Organic Chemistry II Laboratory | 4 |

Biology Courses | ||

BIOL 240 & 240L | Bioenergetics and Systems and Bioenergetics and Systems Laboratory | 4 |

BIOL 242 & 242L | Genomes and Evolution and Genomes and Evolution Laboratory | 4 |

OR | ||

BIOL 190 | Introduction to Evolution | 3 |

BIOL 225 | Introduction to Cell Processes | 3 |

## Major Requirements (26 units)

Courses required for the Biophysics Major reflect the integration of the sciences, with upper-division courses from each of the sciences, as well as interdisciplinary Biophysics lecture and lab courses. Students are urged to work with their biophysics academic advisor to work out a schedule of courses and electives that best fits their career goals and aspirations. Students are also encouraged to start research (PHYS 400 and PHYS 496) as early as possible.

Code | Title | Units |
---|---|---|

PHYS 319 | Thermal and Statistical Physics | 3 |

PHYS 340 | Biological Physics | 3 |

PHYS 381 | Experimental Biophysics | 4 |

PHYS 400 | Research Forum | 1 |

PHYS 493 | Seminar I: The Craft of Scientific Presentation | 1 |

PHYS 495 | Seminar II: Frontiers of Physics | 1 |

PHYS 496 | Research | 1 |

CHEM 331 | Biochemistry | 3 |

BIOL 300 | Genetics | 3 |

Two Upper-Division Electives from BIOL, PHYS, CHEM or EOSC (subject to advisor approval) | 6 | |

Total Units | 26 |

### Recommended Program of Study, Biophysics

Freshman Year | ||
---|---|---|

Semester I | Units | |

MATH 150 | Calculus I | 4 |

CHEM 151 & 151L | General Chemistry I | 4 |

BIOL 240 & 240L | Bioenergetics and Systems | 4 |

CORE or electives | 0-3 | |

Semester II | Hours | |

PHYS 270 & 270L | Introduction to Mechanics | 4 |

MATH 151 | Calculus II | 4 |

CHEM 152 & 152L | General Chemistry II | 4 |

CORE or electives | 0-3 | |

Sophomore Year | ||

Semester I | Hours | |

PHYS 271 & 271L | Introduction to Electricity and Magnetism | 4 |

PHYS 281 | Introduction to Optics | 1 |

MATH 250 | Calculus III | 4 |

CHEM 301 & 301L | Organic Chemistry I | 4 |

CORE or electives | 0-2 | |

Semester II | Hours | |

PHYS 272 & 272L | Introduction to Modern Physics | 4 |

PHYS 282 | Introduction to Methods in Computational Physics | 1 |

BIOL 242 & 242L | Genomes and Evolution | 4 |

CHEM 302 & 302L | Organic Chemistry II | 4 |

CORE or electives | 0-3 | |

Junior Year | ||

Semester I | Hours | |

PHYS 319 | Thermal and Statistical Physics | 3 |

PHYS 381 | Experimental Biophysics | 4 |

PHYS 400 | Research Forum | 1 |

PHYS 496 | Research | 1 |

CORE or electives | 3-6 | |

Semester II | Hours | |

PHYS 340 | Biological Physics | 3 |

CHEM 331 | Biochemistry | 3 |

PHYS 496 | Research | 1 |

CORE or electives | 5-8 | |

Senior Year | ||

Semester I | Hours | |

PHYS 325 | Introduction to Fluids | 3 |

BIOL 300 | Genetics | 3 |

PHYS 493 | Seminar I: The Craft of Scientific Presentation | 1 |

PHYS 496 | Research | 1 |

CORE or electives | 5 | |

Semester II | Hours | |

PHYS 371 | Computational Physics (suggested elective) | 3 |

PHYS 495 | Seminar II: Frontiers of Physics | 1 |

PHYS 496 | Research | 1 |

CORE or electives | 7-10 |

Students entering the University of San Diego and/or declaring a major during 2019-2020, should follow information contained in the printed course catalog (also known as the "catalog of record") published on April 1, 2019. Access the catalog of record at http://catalogs.sandiego.edu.

PHYS 102, PHYS 102L, PHYS 105, PHYS 136, PHYS 136L, PHYS 137, PHYS 137L, PHYS 270, PHYS 270L, PHYS 271, PHYS 271L, PHYS 272, PHYS 272L, PHYS 281, PHYS 282, PHYS 294, PHYS 300, PHYS 301, PHYS 307, PHYS 314, PHYS 319, PHYS 324, PHYS 325, PHYS 330, PHYS 331, PHYS 340, PHYS 371, PHYS 381, PHYS 400, PHYS 480, PHYS 481W, PHYS 487, PHYS 493, PHYS 494, PHYS 495, PHYS 496, PHYS 499

Core Attributes: Science/Tech Inquiry area

Corequisites: PHYS 102L

An introduction to physics concepts and principles with tangents into related technologies and global issues. Special attention is paid to devices and networks that furnish two necessities of modern life: energy and information. No background in physical science is required.

Core Attributes: Lab

Corequisites: PHYS 102

Laboratory component of PHYS 102. Guided hands-on investigation of physics principles and related technologies.

Core Attributes: Science/Tech Inquiry area, Lab

A laboratory/lecture/discussion class designed to lead students toward an understanding of selected topics in chemistry and physics. The course topics are selected to satisfy the Physical Science specifications of the Science Content Standards for California Public Schools (K-12). Enrollment is limited to liberal studies majors. Two two-hour laboratory sessions per week. This course is cross-listed with Chemistry 105. Fall semester.

Core Attributes: Physical Science-Pre F17 CORE

Prerequisites: (MATH 130 or MATH 150)

Corequisites: PHYS 136L

A study of the fundamental principles of mechanics and wave motion, sound, and heat. Algebra and some calculus are required. Three hours of lecture weekly. Concurrent enrollment in 136L required.

Core Attributes: Lab

Prerequisites: PHYS 136 (Can be taken Concurrently)

A laboratory course introducing the concepts and techniques of experimental physics. Meets weekly.

### PHYS 137 | GENERAL PHYSICS II

Units: 3 Repeatability: No

Prerequisites: PHYS 136 and PHYS 136L and (MATH 130 or MATH 150)

Corequisites: PHYS 137L

A study of the fundamental principles of electricity and magnetism, light, and modern physics. Algebra and some calculus are required. Three hours of lecture weekly. Concurrent enrollment in 137L required.

Core Attributes: Lab

Prerequisites: PHYS 137 (Can be taken Concurrently)

A laboratory course introducing the concepts and techniques of experimental physics. Meets weekly.

Core Attributes: First Yr Integration (LC Only), Science/Tech Inquiry area

Prerequisites: MATH 150 or MATH 151

Corequisites: PHYS 270L

A study of the fundamental principles of Newtonian mechanics, kinematics, and momentum and energy conservation laws. Harmonic oscillations and wave motion will also be discussed. Three hours of lecture weekly. Concurrent enrollment in 270L required.

Core Attributes: Science/Tech Inquiry area, Lab

Prerequisites: PHYS 270 (Can be taken Concurrently)

A laboratory course introducing the concepts and techniques of experimental physics. Meets weekly.

### PHYS 271 | INTRODUCTION TO ELECTRICITY AND MAGNETISM

Units: 3 Repeatability: No

Prerequisites: (PHYS 270 and PHYS 270L) or (PHYS 136 and PHYS 136L) and MATH 151 and PHYS 271L (Can be taken Concurrently)

A study of the fundamental principles of classical electricity and magnetism focusing on electrostatics and magnetic force. Circuits, electromagnetism, and light are also introduced. Three hours of lecture weekly. Concurrent enrollment in 271L required.

Core Attributes: Science/Tech Inquiry area

Prerequisites: PHYS 271 (Can be taken Concurrently)

A laboratory course that introduces the concepts and techniques of experimental physics. Meets weekly.

### PHYS 272 | INTRODUCTION TO MODERN PHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 271 and PHYS 271L and MATH 250 (Can be taken Concurrently)

An introduction to modern physics including principles and applications of quantum mechanics, atomic and nuclear physics, and special relativity. Required for all physics and biophysics majors and physics minors, and is an accepted elective for engineering students. For physics and biophysics majors concurrent enrollment in PHYS 272L and PHYS 282 is required.

Core Attributes: Lab

Corequisites: PHYS 272

Laboratory experiments to illustrate the topics presented in the lecture course: Introduction to Modern Physics (PHYS 272).

Core Attributes: Lab

Prerequisites: (PHYS 270 and PHYS 270L) or (PHYS 136 and PHYS 136L) and MATH 151 and PHYS 271L

This lab course provides a hands-on introduction to the fundamentals of optics. Several guided lab activities will introduce basic concepts in optics including reflection, refraction, image formation, coherence, diffraction and interference. Following these guided labs, students will have the final few weeks to work in teams on a project of their own design. Projects may extend any of the earlier lab activities or explore several other options that will be presented. But students are encouraged to pursue any feasible optics project they find exciting.

Core Attributes: Lab

Prerequisites: PHYS 272

A hands-on introduction to the fundamentals of using computation in physics and biophysics. A combination of in-class guided group practice and at-home individual practice will be employed to introduce, practice and apply fundamental computational techniques including: the declaration and manipulation of variables and arrays, conditional statements, loops, as well as procedural programming through creating functions. These fundamentals will be applied to creating graphical representations and performing calculations to further elucidate topics discussed in PHYS 272. Computational techniques will be introduced to highlight the application of these fundamentals. These techniques may include: solutions to initial value problem ordinary differential equations; solving boundary value problems and the eigenvalue problem; and statistics and stochastic methods.

### PHYS 294 | SPECIAL TOPICS IN PHYSICS AND BIOPHYSICS

Units: 0.5-4 Repeatability: Yes (Can be repeated for Credit)

Topics chosen by the instructor in areas that include but are not limited to: Newtonian mechanics, electricity and magnetism, waves, optics, physics and society, modern physics, astronomy, fluids, and thermodynamics. May be repeated for credit if the course material is different.

### PHYS 300 | MATHEMATICAL METHODS OF THEORETICAL PHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 271 and PHYS 271L and MATH 250 and PHYS 272 (Can be taken Concurrently)

An introduction to the methods of theoretical physics that uses physical applications to introduce mathematical techniques. This course will cover: the eigenvalue problem; Taylor expansions in one and multiple variables; solutions techniques to ordinary differential equations; Fourier analysis; separation of variables in partial differential equations; probability distribution functions and Dirac delta function. Other topics that may be discussed at the instructor’s discretion include: complex variables; Green’s functions and solutions to partial differential equations; vector spaces and group theory; chaos theory; special functions; Monte Carlo methods; and computational applications.

### PHYS 301 | ENERGY AND THE ENVIRONMENT

Units: 3 Repeatability: No

Prerequisites: PHYS 272

Energy is the lifeblood of civilization, but its use entails substantial environmental costs. This course examines the physics and technology of energy production, distribution and use, as well as its environmental and societal consequences. It is suitable for students having completed lower-division physics.

### PHYS 307 | ASTROPHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 272

A study of the fundamental principles of astrophysics including topics such as stellar formation, life and death, galaxy evolution, special and general relativity, and cosmology.

### PHYS 314 | ANALYTICAL MECHANICS

Units: 3 Repeatability: No

Prerequisites: PHYS 272

Statics and dynamics are developed using vector analysis, the Hamiltonian and Lagrangian formulations. Orbit theory and chaos are among the special topics treated.

### PHYS 319 | THERMAL AND STATISTICAL PHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 272

This course develops modern statistical mechanics and its application to thermodynamic principles and phenomena. Topics include ideal gases, phase transitions, stellar systems, chemical equilibrium, kinetic theory, paramagnetism, polymers and biophysics.

### PHYS 324 | ELECTROMAGNETISM

Units: 3 Repeatability: No

Prerequisites: PHYS 272

A development of Maxwell’s equations using vector calculus. The electrical and magnetic properties of matter, solutions of boundary value problems, special relativity and radiation theory are also developed. Three lectures per week.

### PHYS 325 | INTRODUCTION TO FLUIDS

Units: 3 Repeatability: No

Prerequisites: PHYS 272

An introduction to the basic principles of fluids. This course will serve as an introduction to concepts used in physical oceanography, atmospheric science, and other disciplines in which fluids are studied or utilized. Examples of applications to a broad range of disciplines (physics, engineering, earth sciences, astrophysics, and biology) will be developed.

### PHYS 330 | QUANTUM MECHANICS

Units: 3 Repeatability: No

Prerequisites: PHYS 272

Introduction to the fundamental properties of nonrelativistic quantum mechanics, including the Schrödinger equation in 1-3 dimensions, the mathematical formalism (involving linear algebra and partial differential equations) of quantum theory, the solution of the hydrogen atom, and elementary perturbation and scattering theory. Entanglement, Bell’s theorem, exotic states of matter, and history of physics are among the special topics discussed.

### PHYS 331 | ADVANCED TOPICS IN QUANTUM PHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 330

Applications of Quantum Theory in areas such as atomic, nuclear, solid state, and elementary particle physics.

### PHYS 340 | BIOLOGICAL PHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 272

Biological physics introduces the interface between the two classic sciences. Physics principles and techniques are applied to questions and problems in biology with a focus on molecular and cellular biology. Topics will be introduced systematically, building on the fundamentals of thermodynamics up to current cutting edge research topics such as protein folding, molecular machines and brain function. Specific topics may include single-molecule biophysics, optical trapping, molecular and cellular self-assembly, gene regulation, biomaterials and biomedical imaging.

### PHYS 371 | COMPUTATIONAL PHYSICS

Units: 3 Repeatability: No

Prerequisites: PHYS 272 and PHYS 282

A hands-on introduction to the implementation of computational algorithms to solve problems in physics and biophysics and the interpretation of the results. Detailed topics covered will depend on instructor expertise. Topics may include solutions to ordinary and partial differential equations, linear algebra, fast Fourier transforms, numerical integration, differentiation and approximation, statistics and Monte Carlo methods.

Core Attributes: Advanced writing competency, Quantitative reasoning comp

Prerequisites: PHYS 272 and PHYS 272L

A laboratory-based course introducing biophysics majors to interdisciplinary research techniques. Instrumentation development and experimental research explore topics of fluorescence and force spectroscopy, molecular diffusion, fluctuation-dissipation theory and viscoelasticity related to molecular and cellular biophysical systems. Students are trained in wet-lab techniques and computational methods using Matlab and Fiji. This is the primary upper-division laboratory requirement for biophysics majors and fulfills the core advanced writing and quantitative reasoning requirements. Students write and edit research reports on their experimental results at a level suitable for journal publication. The writing process also includes literature search techniques and an introduction to the peer review process.

Core Attributes: Undergraduate Research

Prerequisites: PHYS 496 (Can be taken Concurrently)

PHYS 400 brings together all Physics and Biophysics majors involved in undergraduate research (PHYS 496) to provide a formal platform to: (1) gain skills in abstract writing and poster preparation, (2) engage in the scientific literature, (3) form a community of scholars, (4) develop a sense of ownership of their work, and (5) contextualize how their research fits into the big picture. The course meets weekly for 1 hour. Class time is primarily devoted to: learning about and practicing to write scientific abstracts and prepare posters, and having journal club style discussions on student-chosen papers. Outside of class, students are responsible for completing literature searches, reading assigned research papers, writing abstracts, preparing posters, and writing research summaries. PHYS 496 is a required concurrent prerequisite. Offered in Fall semesters.

Core Attributes: Advanced writing competency

Prerequisites: PHYS 330

A laboratory-based course focused on the introduction to principles of research techniques with an emphasis on modern physics. Experiments illustrate physical phenomena pertaining to core areas of physics: quantum mechanics, atomic and nuclear physics, laser physics and plasma physics. Analog and digital data acquisition instrumentation, high-resolution optical and laser technology, and phase sensitive detection technology will be explored. This course is the required writing-intensive course for physics majors and fulfills the upper-division core writing requirement. Students write papers up to professional standards required of publication in physics research journals, learn to write mathematical prose, engage in the peer review process, and learn to code LaTeX.

Core Attributes: Writing-Pre F17 CORE

Prerequisites: PHYS 272 and PHYS 272L and MATH 250

A laboratory-based course focused on the introduction to principles of biophysics research techniques. Instrumentation development and experimental research will explore topics of fluorescence and force spectroscopy, molecular diffusion, fluctuation-dissipation theory and viscoelasticity related to molecular and cellular biophysical systems. Students will also be trained in general wet-lab techniques and computational data acquisition and analysis using Labview and Matlab. This course is the primary upper division laboratory requirement for the biophysics major and fulfills the upper division core writing requirement. Students will write and edit research reports on their experimental results at a level suitable for journal publication. The writing process will also include literature search techniques and an introduction to the peer review process.

### PHYS 487 | TECHNIQUES IN PHYSICS

Units: 1-3 Repeatability: Yes (Can be repeated for Credit)

Training and practice in those areas of physics of practical importance to the technician, teacher, and researcher. To include, but not limited to, technical methodology, preparation and technique in the teaching laboratory, and routines supportive of research. May be repeated up to a maximum of four units of credit.

Core Attributes: Oral communication competency

Prerequisites: PHYS 496

First semester of the physics and biophysics seminar series devoted to instruction on scientific presentations. Students give short presentations on topics of interest, and prepare a lengthy presentation on their research. Stress is laid on the preparation, execution, and critique of effective scientific presentations. One hour per week. Fall semester.

### PHYS 494 | SPECIAL TOPICS IN PHYSICS AND BIOPHYSICS

Units: 0.5-4 Repeatability: Yes (Can be repeated for Credit)

Prerequisites: PHYS 271 and PHYS 271L

Topics chosen by the instructor in areas that include but are not limited to: condensed matter physics, quantum field theory, general relativity, plasma physics, electronics, soft matter physics, particle physics, neurophysics, and advanced physics and biophysics laboratories. May be repeated for credit if the course material is different.

Core Attributes: Advanced Integration

Prerequisites: PHYS 272

The second semester of the capstone seminar series for the Physics and Biophysics major that fulfills the Advanced Integration component of the Core curriculum. This course focuses on exposure to the breadth of current physics-related research topics, and understanding the impact and context of the research through the lens of other disciplines. Students will learn about a wide range of cutting-edge research topics such as: dark matter, global warming and alternative energy sources, biomechanics, graphene, neutrinos, etc. They will also learn about how the research fits into the “big picture” by considering ethical, political, societal, technological and/or historical issues related to the research. These goals are achieved through attending seminars, meeting with scientists, and completing routine reading and writing assignments. The course culminates with a final project in which students investigate and articulate the connection of one of the covered research topics to another discipline.

### PHYS 496 | RESEARCH

Units: 1-3 Repeatability: Yes (Can be repeated for Credit)

Prerequisites: PHYS 400 (Can be taken Concurrently)

An independent research project supervised by a faculty mentor in the physics department. Each student works closely with a faculty mentor to address a mutually agreed upon research problem in experimental or theoretical physics. A student seeking PHYS 496 credit must take initiative to meet with physics faculty members to learn about their research interests and possible problems to research. PHYS 496 credit requires the consent of the faculty mentor. A written report is required.

Department of Physics and Biophysics

College of Arts and Sciences

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