BM4040: Mechanobiology
Course Details
Credits: 3
Segment: 1-6 of Jan-Apr '2023-24
Schedule and venue: Slot-F (Tue 11:00-11:55, Wed 14:30-15:25, Fri 10:00-10:55) in BT010
Discussion hour: Wednesday after the class
Evaluation:
6 quizzes (24%)
6 assignments (24%)
1 mid term exam (22%)
1 final exam (30%)
Books
Introduction to Cell Mechanics and Mechanobiology by Jacobs, Jacobs and Kwon
Physical Biology of the Cell by Rob Phillips
Some research papers which will be give in in the class
This course is intended for UG students with some background in mechanics or condensed matter physics. It will be helpful if the students have undertaken introductory courses in solid and fluid mechanics or biomechanics. This course will deal with the description of the mechanical properties of the biological systems at the microscopic scales. We will study some specific biological mechanisms of interaction of biological cells with the extracellular matrix and how it gets affected in disease conditions. The tentative contents for the course are
Structure of extracellular matrix (ECM), emergence of mechanical properties of ECM from its constituents, constitutive models of ECM
Mechanical properties of biological cells, how do we study those properties, mechanism of AFM measurements
Interactions of cell and ECM, focal adhesion dynamics, adhesion dependent and independent mechanisms of cell motility
Transport at microscopic scales in biological systems
Force/mechanics sensing by the cells and its response in terms of protein expression
Role of mechanics in diseases- cancer, hypertension etc.
Resources
Marantan and Mahadevan, Mechanics and statistics of the worm-like chain. Am. J. Phys, 2018. (PDF)
Bustamante et al., Entropic Elasticity of lambda-Phage DNA. Science, 1994 (PDF)
Theriot, The Polymerization Motor. Traffic 2000 (PDF)
Tessier et al., Networks with fourfold connectivity in two dimensions. PRE, 2003 (PDF)
Boal et al., Negative Poisson ratio in two-dimensional networks under tension. PRE 1993 (PDF)
Derivation of microscopic free energy for 6 fold network under tension (PDF)
Structure of cytoskeletal networks (PDF)
Introduction to cell junctions (PDF)
Bell, Models for the specific adhesion of cells to cells. Science, 1978 (PDF)
Dembo et al., The reaction-limited kinetics of membrane-to-surface adhesion and detachment. PRS-B, 1988 (PDF)
Mechanics and gene regulation (2012 JCS, 2019 Nat Rev, 2021 Trends Cell Bio)
Cell adhesion (PDF)
Cell migration (PDF)
Mechanotranduction in health and disease (PDF, Di et al, Lui et al.)
Cancer mechanobiology (PDF, Chen et al)
Python scripts
Cell detachment (slip bonds)
Cell detachment (oscillatory forcing)
force velocity cell-substrate adhesion (slip bonds)
General policies
Assignments have to be submitted in soft copy before the class on the deadline day. Delays are allowed only for one assignment for each student for only medical reasons with the submission of medical certificate from the institute clinic.
There will not be any make up for the class quizzes. The students missing the quiz will be awarded the average class marks (in maximum of one quiz) only after the submission of medical certificate from the institute clinic.
There can be a make up exam for any student missing the final exam due to health emergency.
All the quizzes and exams are open notes where you can bring any handwritten material on paper or your body. Any photocopies, printed or electronic materials are not allowed,
Plagiarism/copying of any sort is unacceptable in the course. Any sign of it will result in severe penalty.
Some suggestions
The best way to follow the course is to work out the details of the topics discussed in each class by yourself after the class.
You have to take the assignments seriously and solve all the problems on your own. It is also advised that you solve the practise problems from the reference books.
There will be one discussion hour each week for clarification of doubts and practice problems. Take advantage of that.