BIOEN 599m Spring 2007 Syllabus and Home

In this class, you will learn how active nanostructures work - that is, how molecular machines such as motor proteins, nanoscale smart adhesives, and mechanosensors perform their duties. That is, you will learn how biological macromolecules convert chemical to mechanical signals or energy and vice-versa. The goals of this course are both to understand biology and to learn the principles needed to engineer biologically inspired devices or devices that interface with biology. Mechanics at the nanoscale can be conceptually quite different than mechanics at the macroscale, so the first unit of this course presents a quantitative engineering, physicalm, and biological principles for molecular biomechanics.

The second unit focuses on applications. The applications are chosen from list according to the interest of the students each time the class is taught. Topics can include: (1) motor proteins and other molecules (natural and synthetic) that convert chemical energy to mechanical forces, (2) mechanically regulated smart adhesion, and (3) mechanosensory proteins that convert mechanical signals to chemical or electrical cues, (4) technological applications of these active nanosystems. In all cases, examples will be taken from a broad range of research areas that may include muscle, other eukaryotic cells, and bacteria.

You should be familiar with most of the following topics. Courses in paranthesis cover these topics, but are not prerequisites.

However, this is an interdisciplinary field and I will often review material and can recommend background reading if necessary. If you are not sure if you have sufficient background for this course, you should contact me.

Required Readings: This course will be loosely based around Jonathon Howard’s “Mechanics of Motor Proteins and the Cytoskeleton”. If you do not have a strong background in protein structure and chemical kinetics, you may want to get the supplemental text by Meyer B. Jackson: "Molecular and Cellular Biophysics." You will also be assigned articles from the current literature, for understanding applications.

Homework: Homework will include quantitative problems for the basic principles during the first four or five weeks of the course.

Exams: The first unit on basic principles will be followed by an open-book mid-term designed to test your ability to understand and utilize the basic principles of molecular biomechanics.

Project/Presentation: In the second half of the class, you will have the opportunity to study one or two systems in great depth in a mentored project where I will help you find and understand the original papers by leading groups in your area of interest. Students can chose to present one advanced topic alone or two topics with a fellow student. You will turn in a written report and give an oral presentation on your topic to the rest of the class. During this second half of the class, you will be hearing and discussing presentations by the professor and by other students that provide a broad survey of the field.

All assignments must be handed in before class starts on the due date. All exams must be completed on the specific date unless prior arrangements are made with the course instructor.
You may discuss projects and homework with your fellow students, and even collaborate on the solution, but you may not copy or take credit for another person’s work and you must write your homework, lab or term reports independently. You also must acknowledge the person(s) that collaborated with you on the solution. Please quote any material that you copy directly, and acknowledge the source of material that you rewrite in your own words. Cheating/plagiarism is not tolerated.
Class attendance and participation is strongly encouraged. Feedback and suggestions about the class will be highly appreciated.
To request academic accommodations due to a disability, please contact Disabled Student Services, 448 Schmitz, (206) 543-8925 (V/TTY). If you have a letter from Disabled Student Services (DSS) documenting that you have a disability that requires academic accommodations, please present the letter to the instructor so we can discuss the accommodations you might need for the class.