AS.250 (Biophysics)

From the origins of cinema to the present, science and technology have remained the most reliably popular subjects for filmmakers and audiences alike. This course will address that enduring fascination, exploring the meanings and uses of science and technology in film through guest lectures and discussion of cinematic examples both recent and historic. Lectures and discussion will focus on a range of questions: How does film both reflect and shape our understanding of scientific concepts and technologies, from artificial intelligence to genetic engineering? How does science fiction reveal contemporary cultural anxieties and address ethical questions? How “fictional” is the science in science fiction film, and how have science fiction films inspired science and technology? What can we learn about “real” science from the movies? In addition to exploring science through film, students will learn the tools of film analysis through lecture, close viewing, and completion of a series of short written responses. In lieu of a short written response, student may choose to work in a team to create a short (1-3 minute) video response. Possible scientific topics: Genetics and Bioethics, Psychological and Brain Sciences, Artificial Intelligence and Robotics, Climate Change and Public Health and Astrophysical and Planetary Sciences. Possible films to be discussed: 2001: A Space Odyssey, Eternal Sunshine of the Spotless Mind, Blade Runner, GATTACA, The Martian, Interstellar, WALL-E, Children of Men and more. Attendance at weekly screenings at the Parkway Theater is required.

Prerequisite(s): Students who have taken AS.250.207 may not take AS.250.105.

Distribution Area: Humanities

AS Foundational Abilities: Science and Data (FA2), Culture and Aesthetics (FA3)

EN Foundational Abilities: Creative Expression (FA3)

This course is helpful for many disciplines, not only the life sciences. It will introduce students to basic computing concepts and tools useful in many applications. Students will learn to work in the Unix environment and write bash shell scripts. They will learn to program using Python and explore graphing, numerical analysis, and statistical computing libraries, such as NumPy, SciPy, pandas, and Matplotlib. The course will also include an introduction to Machine Learning and will conclude with a Python project focused on data analysis. No previous programming knowledge is required. This course is designed for beginners.

Prerequisite(s): You cannot take AS.250.205 if you have already taken AS.250.206.

Distribution Area: Natural Sciences, Quantitative and Mathematical Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5), Projects and Methods (FA6)

As scientists, we make careful but often indirect, incomplete, or noisy experimental measurements and use these to model the world around us. Mathematics gives us the foundation to quantitatively compare experiments, assess and model error, describe large datasets, abstract complex processes, and build predictive models. In essence, mathematics is a language for critical thought. In this course we will study and integrate key concepts from differential equations, linear algebra, probability theory, and transform theory. We will apply the ideas learned in the context of key problems in biophysics.

Prerequisite(s): (AS.110.106 OR AS.110.108) AND (AS.110.107 OR AS.110.109)

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

Explore science through the lens of cinema. This course examines how Hollywood films portray science and scientific discovery and teaches students how to both analyze and create science on film. Students will evaluate how films represent scientific ideas, comparing them with empirical evidence and concepts introduced by scientists, while also exploring the cultural and aesthetic dimensions of films and considering the broader societal impact of science on screen.Film screenings are paired with scientist lectures, structured film discussions, and a recurring media lab where students work in teams to develop skills in film language and production. Step-by-step filmmaking assignments throughout the semester culminate in a final project: a collaborative 3–5 minute short film on a science topic of their choice, integrating scientific reasoning with cinematic storytelling.

Prerequisite(s): Students who have taken AS.250.105 may not take AS.250.207.

Distribution Area: Natural Sciences, Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2), Culture and Aesthetics (FA3), Projects and Methods (FA6)

EN Foundational Abilities: Creative Expression (FA3)

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.

Prerequisite(s): You cannot take AS.250.253 if you have already taken AS.250.254.;Students must have completed Lab Safety training prior to registering for this class. To access the tutorial, login to myLearning and enter Laboratory Safety Introductory Course in the Search Box to access the proper course. Click here to access the Laboratory Safety Introductory Course

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Ethics and Foundations (FA5), Projects and Methods (FA6)

Writing Intensive

From the molecular to the cellular scale, quantitative modeling forces us to formalize how the laws of physics constrain the behavior of atoms, macromolecules, and cells as they interact in complex, multi-component environments. We will learn how models obeying Newtonian Mechanics at the atomic scale can be mapped to coarse-grained or continuum models that predict the dynamics of protein populations, membrane surfaces, and fibers and filaments at the whole-cell scale. We will study equilibrium and non-equilibrium systems, with connections to experimental measurements. Students will implement and validate modern algorithms used at different resolutions in molecular and cellular biophysics, including ML methods for training and analyzing models. Students design their own final projects.

Prerequisite(s): Click here to access the Laboratory Safety Introductory Course;AS.110.202

Distribution Area: Engineering, Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

NMR is a powerful spectroscopic technique which exploits the magnetic properties of atomic nuclei to provide unique, atomistic level resolution and insights into molecular properties such as structure, dynamics and structure-function relationships, both in solution and solid state. In this course, we will learn about the basics of solution state NMR spectroscopy, acquire 1D and 2D NMR spectra and use various NMR experiments to characterize and probe properties of biomolecular systems ranging from small metabolites to large proteins and nucleic acids as well as functionally relevant interactions, at atomic level resolution. The format will include lectures and hands-on data collection sessions in the JHU Biomolecular NMR Center.

Prerequisite(s): Students must have completed Lab Safety training prior to registering for this class. To access the tutorial, login to myLearning and enter ASEN in the Search Box to access the proper course. Click here to access the Laboratory Safety Introductory Course;(AS.030.101 AND AS.030.105) OR AS.020.305 OR Permission of Instructor.

Distribution Area: Natural Sciences, Quantitative and Mathematical Sciences

AS Foundational Abilities: Science and Data (FA2)

Foundation for advanced classes in Biophysics and other quantitative biological disciplines. 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.

Prerequisite(s): If you have completed AS.250.307 you may not register for AS.250.315.;Students must have completed the following courses to enroll in AS.250.315: AS.030.206 OR AS.030.212

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2)

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.

Prerequisite(s): Students who have taken AS.030.316 are not eligible to take AS.250.316.;( AS.250.315 OR AS.030.315 OR AS.020.305 ) AND ( AS.030.206 OR AS.030.212 ) or permission of the instructor.

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2), Ethics and Foundations (FA5)

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.

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.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

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, partition functions, 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 Pythonand will use it for data fitting and for statistical and mathematical analysis. Background: Calculus and Introductory Physics.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

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.

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2), Ethics and Foundations (FA5)

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.

Prerequisite(s): Students must have completed Lab Safety training prior to registering for this class. To access the tutorial, login to myLearning and enter ASEN in the Search Box to access the proper course. Click here to access the Laboratory Safety Introductory Course;AS.250.372 AND AS.250.205

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2), Projects and Methods (FA6)

Writing Intensive

Systems Genome Biology uses predictive mathematical models to describe the physical principles behind biological function in the cell’s genome, including the nucleus and cellular and nuclear organelles, the chromatin and its folding structures, biomolecular complexes, and the individual molecules. Students will learn our current understanding at the systems level of biomolecular condensates, how omics data is analyzed and how it is used to understand cellular regulation and cell fate transitions, how epigenetics is coded in the genome, how DNA repairs its damages, and how all these phenomena are altered in cancer and neurodegenerative diseases as well as in rare diseases. The course will include guest lectures by leading scientists in these areas.

Prerequisite(s): AS.250.372 AND AS.250.302

Distribution Area: Natural Sciences

AS Foundational Abilities: Science and Data (FA2)

The goal of this course is to develop a physical understanding of cellular signaling through quantitative analysis. The lectures focus on introducing techniques from nonlinear and stochastic kinetics to analyze signaling dynamics at the levels of reaction networks and single molecules. Students will also engage with contemporary literature to gain broader exposure to signal transduction systems, experimental observations, and the corresponding quantitative analyses.

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

This advanced seminar course offers an introduction to modern single-molecule biophysical methods. We will explore single-molecule fluorescence imaging (both in vitro and in live cells), force measurements, and single-channel electrical recordings. Students will gain experience discussing primary research papers and crafting a research proposal.

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2), Projects and Methods (FA6)

Writing Intensive

Advanced seminar for biophysics undergraduates. We focus on topics of genome maintenance via telomere regulation and genome engineering by CRISPR-Cas systems. The course will have lecture, scientific article reading, small and large group discussion.

Focus is on structural and physical aspects of DNA processes in cells, such as nucleosomal packaging, DNA helicases, RNA polymerase, and CRISPR. 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)

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

This advanced seminar course will focus on understanding cell-scale biophysics with computational and experimental tools. Covered topics will include cell motility, the origin of multicellularity, the physical limits of cells' ability to sense their environment. This course will involve extensive interaction with the scientific literature, as well as writing to analyze and explain the relevant questions.

Prerequisite(s): AS.250.372 OR AS.171.312.

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

This course introduces students to widely used biophysical techniques, combining theoretical foundations with practical applications. Students will gain familiarity with key experimental methods in biophysics and develop skills to critically read and interpret primary scientific literature. The course format includes lectures, analysis of scientific articles, and group discussions.

Prerequisite(s): AS.250.315 OR AS.020.305

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

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 is a literature and skills-based course that 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. Simulation and analysis of binding scenarios will be used to analyze illustrate binding schemes, and examples from the scientific literature will be reviewed and discussed. Basic working knowledge of Python is helpful. The writing component will be in one of the common formats employed in the professional biophysics field.Recommended Course Background: AS.250.372 Biophysical Chemistry

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

Topics are meant to illustrate the physical basis of membranes and membrane proteins towards understanding their functions and pharmacological importance including aspects of drug design as it relates to membranes. Contemporary issues in the field will be covered using primary literature articles, structural manipulations in pymol, and computational binding simulations.Recommended Course Background: AS.030.205, AS.250.307, and AS.250.372

Distribution Area: Natural Sciences

AS Foundational Abilities: Writing and Communication (FA1), Science and Data (FA2)

Writing Intensive

Topics include protein therapeutics (antibodies and antibody-based as well as non-antibody proteins) and vaccines. Analysis of current markets for these technologies, the underlying science and technologies for creating candidate therapeutics, product development, including formulation, methods to improve shelf-life, and delivery, complications including aggregation, viscosity, and immunogenicity, clinical trials and FDA approval.

AS Foundational Abilities: Science and Data (FA2)

This course is taken S/U (i.e. it does not get letter grades). The course will be offered in Fall, Spring and Summer, with the same number. It is repeatable; students can take it twice, even in the same year. Students are expected to take this course twice (2 semesters) to satisfy the research requirement of the Biophysics major.

Prerequisite(s): You must request Customized Academic Learning using the Customized Academic Learning form found in Student Self-Service: Registration > Online Forms.

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

This course is for Biophysics students who have already satisfied their the research requirement by having taken 2 semesters (6 units) of AS.250.520 - Introduction to Biophysics Research. Students who decide to continue doing research can do so by enrolling in this course. The course is 3 credits and is graded. This course will be offered in Fall, Spring and Summer, with the same number, and is repeatable.

Prerequisite(s): You must request Customized Academic Learning using the Customized Academic Learning form found in Student Self-Service: Registration > Online Forms.;In order to register for this course, you must first take TWO semesters of AS.250.520 - Introduction to Biophysics Research

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

This course is used for students who are completing an internship for credit. A section is created as-needed for advisors who have students who are engaged in such work.

Prerequisite(s): You must request Customized Academic Learning using the Customized Academic Learning form found in Student Self-Service: Registration > Online Forms.

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

Graduate students only. Students and invited speakers present current topics in the field.

Oral presentations are one of the main forms by which scientists communicate their results. Whether in the context of the classroom, the relatively informal lab meeting or as an invited speaker at an international colloquium, the ability to effectively present scientific results is an important skill to master. This course will cover the planning and execution steps necessary to produce an engaging oral presentation. Students will learn to articulate the big biological questions, tell a story that stimulates interest in their chosen subject, and effectively convey their experimental findings. Key methodological steps in planning will guide students on how to create slides with compelling visuals, and how to use technology to their advantage. Students will each prepare, present, and receive feedback on a 15-minute talk on their thesis project in the style of the Biophysical Society short talks. In addition, each student will receive and evaluate a video of their presentation so they can see themselves through the eyes of others.

Oral presentations are one of the main forms by which scientists communicate their results. Whether in the context of the classroom, the relatively informal lab meeting or as an invited speaker at an international colloquium, the ability to effectively present scientific results is an important skill to master. This course will cover the planning and execution steps necessary to produce an engaging oral presentation. Students will learn to articulate the big biological questions, tell a story that stimulates interest in their chosen subject, and effectively convey their experimental findings. Key methodological steps in planning will guide students on how to create slides with compelling visuals, and how to use technology to their advantage. Students will each prepare, present, and receive feedback on a 15-minute talk on their thesis project in the style of the Biophysical Society short talks. In addition, each student will receive and evaluate a video of their presentation so they can see themselves through the eyes of others.

A series of writing workshops designed to help Biophysics Graduate Students develop a proposal of thesis work. Each student will write a specific aims page and a full (6 page) proposal.

Basics of absorbance, CD, and fluorescence spectroscopy; calorimetric methods.

In this module students will learn the basic theory behind Cryo-EM, including sample preparation, data collection, data processing, and map/model interpretation with an emphasis on hands on experience. As such, students will collect data on a JHU electron microscope, process this data themselves and perform several exercises interpreting maps and building models.

Basics of statistics and data analysis

This five-day, hands-on course introduces students to molecular dynamics (MD) simulations of macromolecular systems. Students will learn how to set up and carry out MD simulations and analyze the data.

Basics of NMR spectroscopy

Basic Principles of Single Molecule Measurements

This hands-on laboratory course will be research driven, focusing on the process of conducting research. Students will engage in designing experiments, collecting data, analyzing results, and troubleshooting experimental problems as they arise. The experimental focus will be to characterize proteins that students have designed in the Computational Macromolecular Design course, as well as proteins that have been engineered previously.

Prerequisite(s): AS.250.676 AND AS.250.686

AS Foundational Abilities: Science and Data (FA2)

Students will read, review, and discuss the social psychology literature on bias in science practices. Topics to be discussed include gender and racial biases in faculty and students, imposter syndrome, how stereotypes influence the demographics of scientists, consequences of emotion in the workplace, bystander intervention skills, and the importance of diversity and inclusion. Students will complete a capstone project in the area of improving graduate climate in the STEM fields.

Distribution Area: Social and Behavioral Sciences

In this four week, intensive introductory course, students will gain a practical working knowledge of UNIX and Python programming languages and packages for analyzing data from biochemical and biophysical experiments. Brief daily lectures are followed by extensive hands-on experience in the computer laboratory.

In-depth exploration of biophysical methods used to study structure, thermodynamic stability, and biomolecular interactions of macromolecules. Techniques include Circular Dichroism, Fluorescence Spectroscopy, Differential Scanning Calorimetry, Isothermal Titration Calorimetry, Surface Plasmon Resonance, Analytical Ultracentrifugation, and robotics. Through both lectures and hands-on labs, students will gain an understanding of the theoretical principles and practical applications of these methods, analyzing real data to interpret biomolecular phenomena.

This course introduces students to protein and nucleic acid databases, alignment algorithms, and search tools; data analysis and visualization using R and RStudio; machine learning; and protein structure analysis and prediction.

The structure of proteins, DNA and RNA, and their functions in living systems. Students are required to participate in class discussions based on readings from the primary scientific literature. Co-requisite: AS 250.649 Introduction to Computing in Biology. Instructor permission for undergraduates.

Prerequisite(s): Prerequisite: AS.250.649,may be taken concurrently.

This course introduces students to modern concepts and approaches in AI-based computational macromolecular design and their applications.

Introduction to the principles of thermodynamics and kinetics as applied to the study of the relationship between structure, energy dynamics, and biological function of proteins and nucleic acids. Topics include of classical, chemical, and statistical thermodynamics, kinetics, theory of ligand binding, and conformational equilibria.

Short-term, faculty-supervised research experience tailored to complement a student’s curriculum and career goals. Students engage in a focused project that may involve laboratory experiments and computational modeling. Designed for students who seek research experience without committing to a full thesis, the course emphasizes project design, data collection and analysis, research ethics, and communication of results. Prerequisite: faculty supervisor approval; prior coursework or skills relevant to the project as specified by the supervising faculty member. May be taken for credit more than once with different projects.

Distribution Area: Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

Independent, original research under the guidance of a faculty advisor leading to the preparation of a master’s thesis. Students will design and execute experiments or scholarship, analyze and interpret results, and present findings in written and oral form. Coursework includes regular meetings with the advisor and research group, literature review, methodology development, data collection and analysis, troubleshooting and iteration, and thesis writing. Repeatable for credit only as part of degree program until the thesis is completed. Prerequisite: approval of faculty advisor and department; enrollment typically reserved for students in their second year their degree program.

Distribution Area: Social and Behavioral Sciences

AS Foundational Abilities: Science and Data (FA2), Projects and Methods (FA6)

This course is used for PhD Students conducting research with a Principal Investigator (PI) who has an appointment with the Jenkins or PMB Program. Research is conducted under the supervision of this faculty member and often in conjunction with other members of the research group.

Graduate Independent Academic Work

A full immersion into a potential thesis lab. By the end of the rotation period, students should expect to understand the primary questions and techniques used in the lab and have gained some expertise in acquiring and analyzing data. At the end of the rotation period, students give a 10 min rotation talk to the biophysics community.

As TAs, students provide key support by helping students with course concepts and techniques, holding office hours, and grading assignments.