BIPH 98a Reading in Biological Physics

Open to students wishing to study a subject not available in the curriculum.

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.

BIOL 14a Genetics and Genomics
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Studies fundamentals of genetics, molecular biology and genomics through analytical thinking and problem-solving. Topics include heredity, meiosis, molecular basis of phenotypic variations, and an introduction to tools and techniques used by past and current researchers in genetics and molecular biology. Usually offered every semester.

BIOL 15b Cells and Organisms
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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 semester.

BIOL 18a General Biology Laboratory for Biology Majors
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Prerequisites: BIOL 14a, BIOL 18b, sophomore standing, and a declared biology major. Yields full-course credit. 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.

BIOL 18b General Biology Laboratory for Biology Majors
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Prerequisites: BIOL 15b, sophomore standing, and a declared biology major. Yields full-course credit. 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.

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.

CHEM 11a General Chemistry I
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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 gasses--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.

CHEM 11b General Chemistry II
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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.

CHEM 18a General Chemistry Laboratory I
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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. 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.

CHEM 18b General Chemistry Laboratory II
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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. 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.

MATH 10a Techniques of Calculus (a)
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Prerequisite: 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.

MATH 10b Techniques of Calculus (b)
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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.

PHYS 11a Introductory Physics I
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Corequisite: MATH 10a or the equivalent. Usually taken with PHYS 19a.

An introduction to Newtonian mechanics with applications to several topics. Usually offered every year.

PHYS 11b Introductory Physics II
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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.

PHYS 15a Advanced Introductory Physics I
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Corequisite: MATH 10b or the equivalent. 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.

PHYS 15b Advanced Introductory Physics II
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Prerequisite: PHYS 11a or PHYS 15a or the equivalent, and MATH 10b 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.

PHYS 19a Physics Laboratory I
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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.

PHYS 19b Physics Laboratory II
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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.

PHYS 20a Waves and Oscillations
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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.

PHYS 31a Quantum Theory I
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Prerequisites: PHYS 20a and either PHYS 11a and b or PHYS 15a and b, or permission of the instructor.

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.

PHYS 39a Advanced Physics Laboratory
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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.

PHYS 40a Introduction to Thermodynamics and Statistical Mechanics
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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.

QBIO 11a Nature's Nanotechnology
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Familiarity with high school math, physics, chemistry and biology is expected. Enrollment limited to QBReC Scholars. Formerly offered as FYS 11a.

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.

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.

BCHM 104b Physical Chemistry of Macromolecules II
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Prerequisites: BCHM 100a, and one of the following: BCHM 104a, CHEM 141a, or Phys 40a, and Math 10a and b or equivalent.

Illustrates the basic principles on which biological macromolecules are constructed and by which they function. Describes overall structures of proteins, nucleic acids, and membranes in terms of the underlying molecular forces: electrostatics, hydrophobic interactions, and H-bonding. The energetics of macromolecular folding and of the linkage between ligand binding and conformational changes will also be discussed. Recitation optional. Usually offered every year.

BIBC 126b Molecular Mechanisms of Disease
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Prerequisite: BCHM 88b or BCHM 100a. May not be taken for credit by students who took BIOL 126b in prior years.

Explores biochemical changes in proteins, enzymes and metabolic pathways that underlie human diseases. Examines molecular mechanisms for a variety of diseases, with a particular focus on molecular mechanisms for therapies. Draws heavily on current literature. Usually offered every second year.

BIOL 102b Structural Molecular Biology
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Prerequisites: BIOL 14a and BIOL 15b, or permission of the instructor.
 

This introduction to the structural basis of viral molecular biology examines the designs of proteins, their folding and assembly, and the means whereby we visualize these structures. We will use several recent viral pandemics including SARS-CoV-2, Ebola, and HIV as models of how to understand viral structure and assembly. Usually offered every second year.

BIOL 107a Data Analysis and Statistics Workshop
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Prerequisites: BIOL51a, high school statistics, or similar course.

The interpretation of data is key to making new discoveries, making optimal decisions, and designing experiments. Students will learn skills of data analysis and computer coding through hands-on, computer-based tutorials and exercises that include experimental data from the biological sciences. Usually offered every year.

NBIO 136b Computational Neuroscience
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Prerequisites: MATH 10a or higher and one of the following: NBIO 140b/240b, PHYS 10b/11b/15b, BIOL 107a, or any COSI course.

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 limited prior coding experience, with reading assignments and preparation as homework. Usually offered every second year.

NBIO 140b Principles of Neuroscience
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Prerequisites: Sophomore standing, BIOL 15b, one additional BIOL, BCHM, NBIO or NPSY course 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. Junior standing recommended.

Examines the fundamental 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.

NPHY 115a Dynamical Systems
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Prerequisites: MATH 10a, b or equivalent; MATH 15a and/or some coding experience would be helpful.

An introduction to the theory of nonlinear dynamical systems, including bifurcations, limit cycles, chaos, and coupled oscillators. Covers analytical, computational, and graphical methods of solving sets of nonlinear ordinary differential equations, as well as mathematical modeling of natural phenomena. Examples will be drawn from physics, chemistry, population biology, and neuroscience. Usually offered every third year.

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 analyze systems such as single molecule experiments, transcriptional regulation networks, the forces arising during DNA packaging in a virus, and mechanisms underlying mammalian pattern formation. Usually offered every second year.

QBIO 24b QBReC Lab

Prerequisite: QBIO 11a. Yields half-course credit. Formerly offered as EL 24b.

Students explore the living world through experimental and computational projects conducted in research labs. The emphasis is on interdisciplinary science where techniques from physics, chemistry and biology are used to develop a quantitative understanding of life at the molecular and cellular level. Usually offered every year.

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.

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.

BIOL 18b General Biology Laboratory for Biology Majors
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Prerequisites: BIOL 15b, sophomore standing, and a declared biology major. Yields full-course credit. 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.

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.

BIOL 18a General Biology Laboratory for Biology Majors
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Prerequisites: BIOL 14a, BIOL 18b, sophomore standing, and a declared biology major. Yields full-course credit. 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.

PHYS 39a Advanced Physics Laboratory
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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.