IITS course on
Statistical Physics in Biology
KU Leuven, Spring 2013
Lecture 6
Cell Motion
Brownian motion
: (
seminar
,
offline
)
Movies of
milk droplets in water
,
beads in water & DNA
,
DNA tethered bead
,
bead capture
Animated simulation
(see also
Applet#2
,
Applet#3
)
Langevin description
Fokker-Planck descrition
Thermal equilibrium and the Einsten relation
Application to molecular motors ala "Einstein force:"
"
The force exerted by a molecular motor
,"
M.E. Fisher & A.B. Kolomeisky, PNAS
96
, 6597 (1999).
Crawling cells
Remodelling of actin cycloskeleton
Crawling Neutrophil Chasing a Bacterium
Actin-based motility
(Listeria)
More from the
Theriot lab movie collection
Latex beads coated with ActA protein
:
motion
Spontaneous symmetry breaking
Swimming cells:
Life at Low Reynolds Number
(E.M. Purcell)
The scallop theorem: impossibility of reciprocal motion
Flagellar rotary motion (efficiency)
Chemotaxis by runs and tumbles- why?
Membranes
Membrane Structure and Function:
Cells are enclosed by membranes
Lipids
(Amphiphylic phosphoglycerids) are the principal component
Self-assemply into micelles and bilayers
The Canham-Helfrich energy of a membrane
Differental geometry: principal, mean, Gaussian
curvature
of a surface
Reparametrization invariant energy
Gauss-Bonnet theorem
Euler characteristic
Vanishing surface tension; why bilayers form vesicles? (
borders
)
Red blood cells
Predicting shapes:
Peterson
,
Syracuse U.
,
shape transitions
Membrane fluctuations and
`flicker' of red blood cells
Persistence length of membranes
Flexibility of
cykoskeleton
, and
aspirated erythrocytes
Transport in and out of cells
Diffusion of small molecules
(
another link
)
Why do oxygen and benzene pass through, but smaller ions do not?
Passive ion channels and active ion pumps
Intracellular and extracellular concentrations
The Nernst equation and membrane potentials
[
Lecture Notes
]
DNA packing
Slides by Anton Goloborodko
In
eukaryotic cell
DNA is confined to the
cell nuclues
Chromatin
DNA organization
Chromosome conformation capture
(
video
)
"
Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
,"
Erez Lieberman-Aiden, Science
326
, 289–93 (2009)
Scaling of contact probability
Fractal globule
Grosberg, Nechaev, and Shakhnovich
,
J. Phys. France
49
, 2095-2100 (1988)
L. Mirny, "
The fractal globule as a model of chromatin architecture in the cell
"
Compact vs crumpled globule
Biological implications
Protein DNA interactions
Regulation of genes by protein-DNA interactions (
L. Mirny slides
)
Lac repressor
CRP activation
Recruitment of polymerase
Structure of protein-DNA complexes
Specificity
Bonds
DNA bending, non-direct readout
Energetics of Protein-DNA binding
Kinetics of binding
Reaction Kinetics
Debye-Smoluchowski theory and equation
Estimated and observed rates
Berg-von Hippel theory of facilitated diffusion
[
Exercises
]
Related links
Membrane Structure
, from
Cell Biology topics
(Gwen V. Childs, U. of Arkansas for Med. Sci.)
On-Line Biology Book
Sparks Notes on Cell Membranes
Test yourself with this
Cell Membranes Tutorial
from the University of Arizona
Biology Project
Membranes from SimScience
The geometry of soft materials: a primer
by R.D. Kamien
Flexibility of Cell Membranes
, from Physics Focus
Transport Across Cell Membranes
, from
Kimball's Biology Pages
IITS
lec6- last update 6/3/13 by M. Kardar