Courses

To see a complete list of courses offered and their descriptions, visit the online course catalog. Please see the right toolbar for individual course websites.

The courses listed below are provided by Student Information Services (SIS). This listing provides a snapshot of immediately available courses within this department and may not be complete. Course registration information can be found at https://sis.jhu.edu/classes.

AS.250.253 - Protein Engineering and Biochemistry Lab

This laboratory examines the relationship between genes and proteins in the context of disease and evolution. It is a research project lab in which the structural and functional consequences of mutations are determined for a model protein. Students will learn basic protein science and standard biochemical techniques and methods in protein engineering. They will perform experiments in site-directed mutagenesis, protein purification, and structural, functional and physical characterization of proteins. No prerequisites. Courses offered in Fall and Spring semesters.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Fall 2018
Meetings: M 1:30PM - 5:30PM
Status: Open

AS.250.253 - Protein Engineering and Biochemistry Lab

This laboratory examines the relationship between genes and proteins in the context of disease and evolution. It is a research project lab in which the structural and functional consequences of mutations are determined for a model protein. Students will learn basic protein science and standard biochemical techniques and methods in protein engineering. They will perform experiments in site-directed mutagenesis, protein purification, and structural, functional and physical characterization of proteins. No prerequisites. Courses offered in Fall and Spring semesters.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Fall 2018
Meetings: T 1:30PM - 5:30PM
Status: Open

AS.250.315 - Biochemistry I

Foundation for advanced classes in Biophysics and other quantitative biological disciplines. Lecture and computer laboratory. This class is the first semester of a two semester course in biochemistry. Topics in Biochemistry I include chemical and physical properties of biomolecules and energetic principles of catabolic pathways. Computer labs include extensive use of molecular graphics and modelling of reaction kinetics and pathway flux. Co-listed with AS.030.315

Credits: 4.00
Instructor: Fleming, Patrick
Term: Fall 2018
Meetings: TTh 12:00PM - 12:50PM, MW 12:00PM - 12:50PM
Status: Open

AS.250.335 - Single Molecule & Cell Biophysics

This (elective) course offers an introduction to the field of single molecule and single cell biophysics to second and third year undergraduate students in biophysics. We will examine technologies such as single molecule fluorescence, force measurements and single cell fluorescence detections that enable high precision molecular visualizations in vitro and in cells. In addition, we will cover topics of genome engineering, cell mechanics and optogenetics toward the end of the semester. Each student is expected to read two articles assigned for each week and submit a written summary. All students will take turns presenting the assigned articles to class.

Credits: 3.00
Instructor: Ha, Taekjip, Myong, Sua
Term: Fall 2018
Meetings: T 3:00PM - 5:30PM
Status: Open

AS.250.351 - Reproductive Physiology

Focuses on reproductive physiology and biochemical and molecular regulation of the female and male reproductive tracts. Topics include the hypothalamus and pituitary, peptide and steroid hormone action, epididymis and male accessory sex organs, female reproductive tract, menstrual cycle, ovulation and gamete transport, fertilization and fertility enhancement, sexually transmitted diseases, and male and female contraceptive methods. Introductory lectures on each topic followed by research-oriented lectures and readings from current literature.

Credits: 2.00
Instructor: Zirkin, Barry R
Term: Fall 2018
Meetings: W 3:00PM - 4:45PM
Status: Open

AS.250.372 - Biophysical Chemistry

Course covers classical and statistical thermodynamics, spanning from simple to complex systems. Major topics include the first and second law, gases, liquids, chemical mixtures and reactions, conformational transitions in peptides and proteins, ligand binding, and allostery. Methods for thermodynamic analysis will be discussed, including calorimetry and spectroscopy. Students will develop and apply different thermodynamic potentials, learn about different types of ensembles and partition functions. Students will learn to use Mathematica and will use it for data fitting and for statistical and mathematical analysis. Background: Calculus, Organic Chemistry, and Introductory Physics.

Credits: 4.00
Instructor: Barrick, Doug
Term: Fall 2018
Meetings: MWF 10:00AM - 10:50AM, F 12:00PM - 12:50PM
Status: Open

AS.250.205 - Introduction to Computing

This course is useful for many disciplines not only the life sciences. It will introduce students to basic computing concepts and tools useful in many applications. Students learn to work in the Unix environment, to write shells scripts, and to make use of powerful Unix commands (e.g grep, awk, and sed). They will learn to program using the Python programming language, graphing software, and a package for numerical and statistical computing, such as Mathematica or MATLAB. At the end of the semester students will complete a project coupling all components of the semester together. Brief lectures followed by extensive hands-on computer laboratories with examples from many disciplines. No prerequisites. Course offered every semester.

Credits: 3.00
Instructor:
Term: Fall 2018
Meetings: MWF 10:00AM - 10:50AM
Status: Open

AS.250.313 - Molecular and Cellular System Biology

This course covers the principles of biological networks, with an emphasis on computational analysis. Networks ranging from simple biochemical pathways to genome-scale metabolic, regulatory, and signaling networks will be studied. Topics include dynamic modeling of biochemical pathways, steady-state analysis of cellular metabolic networks, inference of gene regulatory networks using –omics data, and systems biology approaches to studying signal transduction. Recommended Course Background: Calculus (AS.110.106 and AS.110.107), Biochemistry (AS.250.315 or AS.020.305 or equivalent). Computational Biology (AS.250.353) or Introduction to Bioinformatics (AS.250.265) or prior exposure to programming.

Credits: 4.00
Instructor: Roberts, Elijah
Term: Fall 2018
Meetings: TTh 1:30PM - 2:45PM, M 2:00PM - 3:00PM
Status: Open

AS.250.205 - Introduction to Computing

This course is useful for many disciplines not only the life sciences. It will introduce students to basic computing concepts and tools useful in many applications. Students learn to work in the Unix environment, to write shells scripts, and to make use of powerful Unix commands (e.g grep, awk, and sed). They will learn to program using the Python programming language, graphing software, and a package for numerical and statistical computing, such as Mathematica or MATLAB. At the end of the semester students will complete a project coupling all components of the semester together. Brief lectures followed by extensive hands-on computer laboratories with examples from many disciplines. No prerequisites. Course offered every semester.

Credits: 3.00
Instructor: Damjanovic, Ana
Term: Fall 2018
Meetings: MWF 11:00AM - 11:50AM
Status: Open

AS.250.353 - Computational Biology

This course introduces several computational approaches to the study of biological macromolecules. Students will learn to use computational tools to carry out and analyze molecular simulations and how to work in a UNIX networked environment. A major goal is to understand molecular systems as ensembles. No programming experience is required. A previous biochemistry course is strongly recommended.

Credits: 3.00
Instructor: Fleming, Patrick
Term: Fall 2018
Meetings: TTh 10:30AM - 11:45AM
Status: Open

AS.250.372 - Biophysical Chemistry

Course covers classical and statistical thermodynamics, spanning from simple to complex systems. Major topics include the first and second law, gases, liquids, chemical mixtures and reactions, conformational transitions in peptides and proteins, ligand binding, and allostery. Methods for thermodynamic analysis will be discussed, including calorimetry and spectroscopy. Students will develop and apply different thermodynamic potentials, learn about different types of ensembles and partition functions. Students will learn to use Mathematica and will use it for data fitting and for statistical and mathematical analysis. Background: Calculus, Organic Chemistry, and Introductory Physics.

Credits: 4.00
Instructor: Barrick, Doug
Term: Fall 2018
Meetings: MWF 10:00AM - 10:50AM, F 2:00PM - 2:50PM
Status: Open

AS.250.383 - Molecular Biophysics Laboratory

An advanced inquiry based laboratory course covering experimental biophysical techniques to introduce fundamental physical principles governing the structure/function relationship of biological macromolecules. Students will investigate a “model protein”, staphylococcal nuclease, the “hydrogen atom” of biophysics. Using a vast library of variants, the effect of small changes in protein sequence will be explored. A variety of techniques will be used to probe the equilibrium thermodynamics and kinetics of this system; chromatography, spectroscopy (UV-Vis, fluorescence, circular dichroism, nuclear magnetic resonance), calorimetry, analytical centrifugation, X-ray crystallography and computational methods as needed for analysis. These methods coupled with perturbations to the molecular environment (ligands, co-solvents, and temperature) will help to elucidate protein function. Prerequisite: Introduction to Scientific Computing (250.205) or equivalent. Biophysical Chemistry (250.372 or 020.370) or equivalent. Course taught in Fall and Spring.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Fall 2018
Meetings: Th 1:30PM - 5:30PM
Status: Open

AS.250.403 - Bioenergetics: Origins, Evolution and Logic of Living Systems

The trait shared by all living systems is the capacity to perform energy transduction. This biophysics/biochemistry course examines the physico-chemical and structural basis of biological energy transduction.Emphasis is on understanding the molecular and cellular logic of the flow of energy in living systems. The course explores the connection between fundamental physical requirements for energy transduction and the organization, evolution and possibly even the origins of biological molecules, cells, and organisms. Implications for planet earth¹s energy balance and for the design of synthetic organisms and of artificial energy transducing machines will be discussed, time permitting. Recommended Course Background: One semester of Biochemistry. Recommended Course Background: One semester of Biochemistry

Credits: 3.00
Instructor: Garcia-Moreno, Bertrand
Term: Fall 2018
Meetings: TTh 9:00AM - 10:15AM
Status: Waitlist Only

AS.250.514 - Research in Protein Design and Evolution

Credits: 3.00
Instructor: Garcia-Moreno, Bertrand, Lecomte, Juliette
Term: Fall 2018
Meetings:
Status: Closed

AS.250.520 - Introduction to Research in Biophysics

Credits: 3.00
Instructor: Fleming, Karen G
Term: Fall 2018
Meetings:
Status: Closed

AS.250.521 - Research Problems

Credits: 3.00
Instructor: Ha, Taekjip
Term: Fall 2018
Meetings:
Status: Closed

AS.250.520 - Introduction to Research in Biophysics

Credits: 3.00
Instructor: Ha, Taekjip
Term: Fall 2018
Meetings:
Status: Closed

AS.250.521 - Research Problems

Credits: 3.00
Instructor: Roberts, Elijah
Term: Fall 2018
Meetings:
Status: Closed

AS.250.521 - Research Problems

Credits: 3.00
Instructor: Fleming, Karen G
Term: Fall 2018
Meetings:
Status: Closed

AS.250.520 - Introduction to Research in Biophysics

Credits: 3.00
Instructor: Roberts, Elijah
Term: Fall 2018
Meetings:
Status: Closed

AS.250.205 - Introduction to Computing

This course is useful for many disciplines not only the life sciences. It will introduce students to basic computing concepts and tools useful in many applications. Students learn to work in the Unix environment, to write shells scripts, and to make use of powerful Unix commands (e.g grep, awk, and sed). They will learn to program using the Python programming language, graphing software, and a package for numerical and statistical computing, such as Mathematica or MATLAB. At the end of the semester students will complete a project coupling all components of the semester together. Brief lectures followed by extensive hands-on computer laboratories with examples from many disciplines. No prerequisites. Course offered every semester.

Credits: 3.00
Instructor: Damjanovic, Ana
Term: Spring 2019
Meetings: MWF 10:00AM - 10:50AM
Status: Waitlist Only

AS.250.106 - Introduction to Biomedical Research and Careers I

Lecture Series designed for those curious about a career in life sciences, medicine and public health. A novel format combining presentation with didactic interviews gives a broad view of a range of research topics, experimental approaches and logistics, and practical applications as well as career paths. Emphasis is on the excitement of scientific explorations not an abundance of the technical facts and figures. Freshmen and non-science majors. Co-listed with AS.250.300 and AS.250.306.

Credits: 1.00
Instructor: Huang, P C
Term: Spring 2019
Meetings: T 7:30PM - 8:50PM
Status: Open

AS.250.265 - Introduction to Bioinformatics

Algorithms and databases for biological information. A mostly computer lab course covering basic programming; algorithms for comparison of sequence, protein structure and gene expression; protein structure prediction and an introduction to major databases. Students will complete a genomics database project and will prepare and discuss on-line presentations on topics related to the use of genomic information. No programming experience necessary. Preference to Biophysics majors.

Credits: 3.00
Instructor: Fleming, Patrick
Term: Spring 2019
Meetings: TTh 10:30AM - 11:45AM
Status: Waitlist Only

AS.250.205 - Introduction to Computing

This course is useful for many disciplines not only the life sciences. It will introduce students to basic computing concepts and tools useful in many applications. Students learn to work in the Unix environment, to write shells scripts, and to make use of powerful Unix commands (e.g grep, awk, and sed). They will learn to program using the Python programming language, graphing software, and a package for numerical and statistical computing, such as Mathematica or MATLAB. At the end of the semester students will complete a project coupling all components of the semester together. Brief lectures followed by extensive hands-on computer laboratories with examples from many disciplines. No prerequisites. Course offered every semester.

Credits: 3.00
Instructor: Damjanovic, Ana
Term: Spring 2019
Meetings: MWF 11:00AM - 11:50AM
Status: Waitlist Only

AS.250.253 - Protein Engineering and Biochemistry Lab

This laboratory examines the relationship between genes and proteins in the context of disease and evolution. It is a research project lab in which the structural and functional consequences of mutations are determined for a model protein. Students will learn basic protein science and standard biochemical techniques and methods in protein engineering. They will perform experiments in site-directed mutagenesis, protein purification, and structural, functional and physical characterization of proteins. No prerequisites. Courses offered in Fall and Spring semesters.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Spring 2019
Meetings: Th 1:30PM - 5:30PM
Status: Waitlist Only

AS.250.306 - Introduction to Biomedical Research and Careers III

Lecture Series designed for those curious about a career in life sciences, medicine and public health. A novel format combining presentation with didactic interviews gives a broad view of a range of research topics, experimental approaches and logistics, and practical applications as well as career paths. Emphasis is on the excitement of scientific explorations not an abundance of the technical facts and figures. Freshmen and non-science majors. Co-listed with AS.250.106 and AS.250.300

Credits: 1.00
Instructor: Huang, P C
Term: Spring 2019
Meetings: T 7:30PM - 8:50PM
Status: Open

AS.250.302 - Modeling the Living Cell

Previously titled "Models and Algorithms in Biophysics." Introduction to physical and mathematical models used to represent biophysical systems and phenomena. Students will learn algorithms for implementing models computationally and perform basic implementations. We will discuss the types of approximations made to develop useful models of complex biological systems, and the comparison of model predictions with experiment.

Credits: 4.00
Instructor: Johnson, Margaret E
Term: Spring 2019
Meetings: TTh 1:30PM - 2:45PM, M 5:00PM - 6:00PM
Status: Open

AS.250.131 - Freshman Seminar in Biophysics

Introduction of contemporary biophysics research topics through presentations, discussion and hands-on exercise. Freshmen and sophomores only. S/U grading only.

Credits: 1.00
Instructor: Fleming, Karen G, Roberts, Elijah
Term: Spring 2019
Meetings: W 1:30PM - 2:50PM
Status: Open

AS.250.300 - Introduction to Biomedical Research and Careers II

Lecture Series designed for those curious about a career in life sciences, medicine and public health. A novel format combining presentation with didactic interviews gives a broad view of a range of research topics, experimental approaches and logistics, and practical applications as well as career paths. Emphasis is on the excitement of scientific explorations not an abundance of the technical facts and figures. Freshmen and non-science majors. Co-listed with AS.250.106 and AS.250.306

Credits: 1.00
Instructor: Huang, P C
Term: Spring 2019
Meetings: T 7:30PM - 8:50PM
Status: Open

AS.250.253 - Protein Engineering and Biochemistry Lab

This laboratory examines the relationship between genes and proteins in the context of disease and evolution. It is a research project lab in which the structural and functional consequences of mutations are determined for a model protein. Students will learn basic protein science and standard biochemical techniques and methods in protein engineering. They will perform experiments in site-directed mutagenesis, protein purification, and structural, functional and physical characterization of proteins. No prerequisites. Courses offered in Fall and Spring semesters.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Spring 2019
Meetings: T 1:30PM - 5:30PM
Status: Waitlist Only

AS.250.316 - Biochemistry II

Biochemical anabolism, nucleic acid structure, molecular basis of transcription, translation and regulation, signal transduction with an emphasis on physical concepts and chemical mechanisms. Format will include lectures and class discussion of readings from the literature.

Credits: 3.00
Instructor: Rokita, Steven, Woodson, Sarah
Term: Spring 2019
Meetings: TTh 9:00AM - 10:15AM
Status: Open

AS.250.310 - Exploring Protein Biophysics using Nuclear Magnetic Resonance (NMR) Spectroscopy

NMR is a spectroscopic technique which provides unique, atomic level insights into the inner workings of biomolecules in aqueous solution. A wide variety of biophysical properties can be studied by NMR. For example, we can use the technique to determine three dimensional structure of biological macromolecules such as proteins and nucleic acids, probe their dynamical properties in solution, study their interaction with other molecules and understand how physico-chemical properties (such electrostatics and redox chemistry) affects and modulates structure-function relationships. NMR exploits the exquisite sensitivity of magnetic properties of atomic nuclei to their local electronic (and therefore, chemical) environment. As a result, biophysical properties can be studied at atomic resolution. That is to say, we can deconstruct global properties of a molecule in terms of detailed, atomic level information. In addition, interactions between nuclei can be exploited to enhance the information content of NMR spectra via multi-dimensional (2D and 3D) spectroscopy. Since these properties can be studied in solution, NMR methods serve as an effective complement to X-Ray crystallography, which also provides detailed, atomic level information in the solid state. In this course, we will learn about the basics of NMR spectroscopy, acquire 1D and 2D NMR spectra and use various NMR experiments to characterize and probe biophysical properties of proteins at an atomic level. Juniors and Seniors Only.

Credits: 3.00
Instructor: Majumdar, Ananya
Term: Spring 2019
Meetings: TTh 12:00PM - 1:15PM
Status: Waitlist Only

AS.250.381 - Spectroscopy and Its Application in Biophysical Reactions

Continues Biophysical Chemistry (AS.250.372). Fundamentals of quantum mechanics underlying various spectroscopies (absorbance, circular dichroism, fluorescence, NMR); application to characterization of enzymes and nucleic acids.

Credits: 3.00
Instructor: Lecomte, Juliette
Term: Spring 2019
Meetings: MWF 9:00AM - 9:50AM
Status: Waitlist Only

AS.250.383 - Molecular Biophysics Laboratory

An advanced inquiry based laboratory course covering experimental biophysical techniques to introduce fundamental physical principles governing the structure/function relationship of biological macromolecules. Students will investigate a “model protein”, staphylococcal nuclease, the “hydrogen atom” of biophysics. Using a vast library of variants, the effect of small changes in protein sequence will be explored. A variety of techniques will be used to probe the equilibrium thermodynamics and kinetic properties of this system; chromatography, spectroscopy (UV-Vis, fluorescence, circular dichroism, nuclear magnetic resonance), calorimetry, analytical centrifugation, X-ray crystallography, mass spectroscopy, and computational methods as needed for analysis. These methods coupled with perturbations to the molecular environment (ligands, co-solvents, and temperature) will help to elucidate protein function. Prerequisite: Introduction to Scientific Computing (250.205) or equivalent. Biophysical Chemistry (250.372 or 020.370) or equivalent. Course taught in Fall and Spring.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Spring 2019
Meetings: W 1:30PM - 5:30PM
Status: Waitlist Only

AS.250.320 - Macromolecular Binding

All biological processes require the interactions of macromolecules with each other or with ligands that activate or inhibit their activities in a controlled manner. This course will discuss theoretical principles, logic, approaches and practical considerations used to study these binding processes from a quantitative perspective. Topics will include thermodynamics, single and multiple binding equilibria, linkage relationships, cooperativity, allostery, and macromolecular assembly. Some biophysical methods used in the study of binding reactions will be discussed. Computer simulation and analysis of binding curves will be used to analyze binding data, and binding schemes and examples from the scientific literature will be reviewed and discussed. Recommended Course Background: AS.250.372 Biophysical Chemistry

Credits: 3.00
Instructor: Fleming, Karen G
Term: Spring 2019
Meetings: TTh 10:30AM - 11:45AM
Status: Open

AS.250.522 - Research Problems

Credits: 0.00 - 3.00
Instructor: Barrick, Doug
Term: Spring 2019
Meetings:
Status: Canceled

AS.250.522 - Research Problems

Credits: 0.00 - 3.00
Instructor: Fleming, Karen G
Term: Spring 2019
Meetings:
Status: Canceled

AS.250.522 - Research Problems

Credits: 0.00 - 3.00
Instructor: Bowman, Gregory D
Term: Spring 2019
Meetings:
Status: Canceled

AS.250.383 - Molecular Biophysics Laboratory

An advanced inquiry based laboratory course covering experimental biophysical techniques to introduce fundamental physical principles governing the structure/function relationship of biological macromolecules. Students will investigate a “model protein”, staphylococcal nuclease, the “hydrogen atom” of biophysics. Using a vast library of variants, the effect of small changes in protein sequence will be explored. A variety of techniques will be used to probe the equilibrium thermodynamics and kinetic properties of this system; chromatography, spectroscopy (UV-Vis, fluorescence, circular dichroism, nuclear magnetic resonance), calorimetry, analytical centrifugation, X-ray crystallography, mass spectroscopy, and computational methods as needed for analysis. These methods coupled with perturbations to the molecular environment (ligands, co-solvents, and temperature) will help to elucidate protein function. Prerequisite: Introduction to Scientific Computing (250.205) or equivalent. Biophysical Chemistry (250.372 or 020.370) or equivalent. Course taught in Fall and Spring.

Credits: 3.00
Instructor: Fitch, Carolyn A
Term: Spring 2019
Meetings: W 1:30PM - 5:30PM
Status: Canceled

AS.250.522 - Research Problems

Credits: 0.00 - 3.00
Instructor: Ha, Taekjip
Term: Spring 2019
Meetings:
Status: Canceled

AS.250.411 - Advanced Seminar in Structural Biology of Chromatin

Focus is on structural and physical aspects of DNA processes in cells, such as nucleosomal packaging, DNA helicases, RNA polymerase, and RNA inhibition machinery. Topics are meant to illustrate how the structural and chemical aspects of how proteins and nucleic acids are studied to understand current biological questions. Recommended Course Background: Biochemistry I (AS.250.315) and Biochemistry II (AS.250.316) or Biochemistry (AS.020.305) and Intro to Biophys Chem (AS.250.372)

Credits: 3.00
Instructor: Bowman, Gregory D
Term: Spring 2019
Meetings: T 2:00PM - 4:30PM
Status: Open

AS.250.514 - Research in Protein Design and Evolution

Credits: 3.00
Instructor: Garcia-Moreno, Bertrand, Lecomte, Juliette
Term: Spring 2019
Meetings:
Status: Approval Required