535.750.81 - Biomechanics of the cell: From nano- and micro-mechanics to cell organization and function

Course Structure

The course materials are divided into modules which can be accessed by clicking Course Modules on the course menu. A module will have several sections including the overview, content, discussions, and assignments. You are encouraged to preview all sections of the module before starting. Most modules run for a period of seven (7) days, exceptions are noted in the Course Outline. You should regularly check the Calendar and Announcements for assignment due dates.

Course Topics

1) Introduction to cell mechanics & math/physics review
2) Phase space and equilibrium ensembles
3) Ideal systems, partition function and free energies I
4) Ideal systems II, entropy and free energy of mixing
5) Free energies and thermodynamic force. Mechanics of proteins and protein motors
6) Mechanics of rod-like molecules (DNA and cytoskeleton), flexible chains and random walks
7) Brownian motion, random walks and diffusion. Mean squared displacement
8) Mechanics of lipid bilayers and membranes
9) Cytoskeletal mechanics and how cells responds to forces
10) Biological materials, ECM, cytoskeletal networks and viscoelastic constitutive laws
11) Cell interaction with environment I: Flows, Stokes equation and hydraulic pressure
12) Cell interaction with environment II: Adhesions and molecular-level force response
13) Cell motility and cell shape regulation
14) The role of mechanics in cell dynamics, growth and tissue patterning

Course Goals

This course aims to use mechanical concepts (kinematics, forces, statistical mechanics) to explore cellular function and cell dynamics. We will establish the conceptual framework for rationalizing phenomena at the cell scale. Then we will explore a number of simple models for understanding cell structures and mechanics. Finally, application of our mechanical concepts to modern biological questions such as cell motility, gene regulation, and tissue morphogenesis will be discussed.

Course Learning Outcomes (CLOs)

• Explain theoretical principles in equilibrium statistical mechanics, and the molecular origin of forces in complex many body systems.
• Apply concepts of equilibrium statistical mechanics to simple systems.
• Explain and apply simple models of free energies for rod-like molecules and cell membranes.
• Develop models of flexible and semiflexible chains, and explain their relationship to random walks and Brownian motion.
• Explain biological force generation in protein motors.
• Develop simple constitutive models for biological materials.
• Explain latest understanding of cell mechanical response, and models of cell shape regulation and cell movement.

Textbooks

None

Student Coursework Requirements

Homeworks: 35%
Midterm I and II, 20% each
Discussion and participation, 25%

Grading Policy

EP uses a +/- grading system (see “Grading System”, Graduate Programs catalog, p. 10).

Academic Policies

Deadlines for Adding, Dropping and Withdrawing from Courses

Students may add a course up to one week after the start of the term for that particular course. Students may drop courses according to the drop deadlines outlined in the EP academic calendar (https://ep.jhu.edu/student-services/academic-calendar/). Between the 6th week of the class and prior to the final withdrawal deadline, a student may withdraw from a course with a W on their academic record. A record of the course will remain on the academic record with a W appearing in the grade column to indicate that the student registered and withdrew from the course.

Academic Misconduct Policy

All students are required to read, know, and comply with the Johns Hopkins University Krieger School of Arts and Sciences (KSAS) / Whiting School of Engineering (WSE) Procedures for Handling Allegations of Misconduct by Full-Time and Part-Time Graduate Students.

This policy prohibits academic misconduct, including but not limited to the following: cheating or facilitating cheating; plagiarism; reuse of assignments; unauthorized collaboration; alteration of graded assignments; and unfair competition. Course materials (old assignments, texts, or examinations, etc.) should not be shared unless authorized by the course instructor. Any questions related to this policy should be directed to EP’s academic integrity officer at ep-academic-integrity@jhu.edu.

Students with Disabilities - Accommodations and Accessibility

Johns Hopkins University values diversity and inclusion. We are committed to providing welcoming, equitable, and accessible educational experiences for all students. Students with disabilities (including those with psychological conditions, medical conditions and temporary disabilities) can request accommodations for this course by providing an Accommodation Letter issued by Student Disability Services (SDS). Please request accommodations for this course as early as possible to provide time for effective communication and arrangements.

For further information or to start the process of requesting accommodations, please contact Student Disability Services at Engineering for Professionals, ep-disability-svcs@jhu.edu.

Student Conduct Code

The fundamental purpose of the JHU regulation of student conduct is to promote and to protect the health, safety, welfare, property, and rights of all members of the University community as well as to promote the orderly operation of the University and to safeguard its property and facilities. As members of the University community, students accept certain responsibilities which support the educational mission and create an environment in which all students are afforded the same opportunity to succeed academically. 

For a full description of the code please visit the following website: https://studentaffairs.jhu.edu/policies-guidelines/student-code/

Classroom Climate

JHU is committed to creating a classroom environment that values the diversity of experiences and perspectives that all students bring. Everyone has the right to be treated with dignity and respect. Fostering an inclusive climate is important. Research and experience show that students who interact with peers who are different from themselves learn new things and experience tangible educational outcomes. At no time in this learning process should someone be singled out or treated unequally on the basis of any seen or unseen part of their identity. 
 
If you have concerns in this course about harassment, discrimination, or any unequal treatment, or if you seek accommodations or resources, please reach out to the course instructor directly. Reporting will never impact your course grade. You may also share concerns with your program chair, the Assistant Dean for Diversity and Inclusion, or the Office of Institutional Equity. In handling reports, people will protect your privacy as much as possible, but faculty and staff are required to officially report information for some cases (e.g. sexual harassment).

Course Auditing

When a student enrolls in an EP course with “audit” status, the student must reach an understanding with the instructor as to what is required to earn the “audit.” If the student does not meet those expectations, the instructor must notify the EP Registration Team [EP-Registration@exchange.johnshopkins.edu] in order for the student to be retroactively dropped or withdrawn from the course (depending on when the "audit" was requested and in accordance with EP registration deadlines). All lecture content will remain accessible to auditing students, but access to all other course material is left to the discretion of the instructor.