ENGG 199 Mechanics of the biological cell Winter, 2008
Description:
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Cell functions can be considered from a variety of perspectives. Some functions are chemical, such as the protein synthesis. This course concentrates on the physical attributes of cells, addressing questions such as: How does a cell maintain or change its shape (e.g., red blood cells deform significantly without breaking when passing through narrow capillaries)? How do cells move? How do cells transport material internally? (diffusion is not the answer) How do cells stick to surfaces (e.g., leukocyte adhesion in inflammatory response)?
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The course is aimed at upper level undergraduate or beginning graduate students interested in biophysics. The presentation will be self-contained and suitable for students from different backgrounds – engineering, physics, applied math, chemistry, and biology.
Prerequisites: Engs 25 (Thermodynamics) or equivalent
Objective: Students who have taken this course will understand the interrelation between mechanical properties of cells components (e.g., polymers and membranes) and cell biological function.
Professor: Petia M. Vlahovska, Room 119B, Cummings Hall, telephone: 646-9922 or
E-mail: petia.vlahovska@dartmouth.edu.
Office Hours: Open-door policy, except on Tuesdays. If you want to make an appointment at a specific time, please email me. Note that I do not check and respond to email after 7pm.
Classes: Monday and Wednesday, 4-5:50 (subject to change) Room 201, MacLean
no X-hour.
Text: Readings and problem assignments will be taken mainly from the book "Mechanics of the cell" by David Boal, Cambridge University Press.
Blackboard: I will use the course website extensively to distribute information relevant to the course. Please check the site often for updates. Lectures will be posted before the class.
Homework: weekly
Exams: There will be a midterm and a final exam. All exams are take-home. Final exam will be cumulative.
Project: review and present a pertinent journal article
Lab: No labs
Grade: The midterm exam will count 15%, final exam 30%, homework 35% and project 30% towards the final grade.
Approximate grade scale:
A B C D
90 80 70 60
The graded homework will be returned within a week with a copy of the instructor's solution.
Honor Code: The Honor Principle of Dartmouth College and the Thayer School applies (see ORC). Generally this implies that work handed in for credit is your own with all sources acknowledged.
The principles behind homework problems may be discussed but not in any way that bypasses the need to think and learn. Specific assistance must be acknowledged, otherwise we are obliged to investigate whether a violation of the Honor Code occurred.
Examination should not be discussed, nor any other form of assistance sought or given.
There is no penalty for citation of other sources - this is encouraged.
Special
Assistance: I encourage students with disabilities, including invisible disabilities like chronic diseases, learning disabilities, and psychiatric disabilities to discuss with me after class or during my office hours appropriate accommodations that might be helpful to them.
Reserve Books: "Mechanics of the cell" by David Boal, Feldberg Library (2 hour limit)
ENGG199 Mechanics of the Cell
Winter 2008 Tentative schedule
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DATE |
TOPIC |
NOTES |
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Jan |
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1 |
7M |
Introduction |
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2 |
9W |
Intro 1: cells and cell building blocks |
Cell design: shapes, sizes and structures
Fatty acids and phospholipids
Sugars
Amino acids and proteins
Nucleotides and DNA
ADP and ATP |
3 |
14M |
Intro 2 Soft strings and sheets: Elasticity |
Deformations and the strain tensor
Small deformations
Forces and the stress tensor
Hooke’s law and elastic moduli
Fluctuations |
4 |
16W |
Intro 3 statistical mechanics |
Temperature and Entropy
Boltzmann factor (ex. Harmonic oscillator)
Partition function (ex. Entropy of an ideal gas) |
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21M |
No class (Martin Luther King Day) |
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5 |
23W |
polymers |
Filaments in the cell
Flexible rods
sizes of polymer chains
chain configurations and elasticity |
6 |
28M |
Two dimensional networks |
Soft networks in the cell
Elastic moduli in two dimensions
Spring networks with six-fold coordination
Spring networks with four-fold coordination
Membrane-associated networks |
7 |
30W |
Three-dimensional networks |
Networks of biological rods and ropes
Elastic moduli in three dimesions
Rheology of cytoskeletal components |
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Feb |
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8 |
4M |
Biomembranes |
Composition of biomembranes
Self-assembly of amphiphiles
Bilayer compression resistance
Bilayer bending resistance
Edge energy |
9 |
6W |
Membrane- undulations |
Thermal fluctuations in membrane shape
Surface curvature
Membrane bending and persistence length
Scaling of polymers and membranes
Measurement of membrane undulations |
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Week
of Feb 11 |
Take home midterm exam |
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10 |
19M |
. The simplest cells |
Cell shapes
Energetics of thin shells
Pure bilayer systems
Vesicles and red blood cells
Simple bacteria |
11 |
20W |
Intermembrane forces |
Interactions between membranes
Charged plate in an electrolyte
Van der Waals and electrostatic interactions
Entropic repulsion of sheets and polymers
Adhesion |
12 |
25M |
Dynamic filaments |
Cell motility
Polymerization of actin and tubulin
Molecular motors
Forces from filaments |
13 |
27W |
Mechanical designs |
Tension and compression
The largest and smallest cells
Cell division |
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Mar |
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16 |
3M |
Presentations |
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17 |
5W |
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Take home final exam |
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