Forces organizing soft matter:
large bio-molecules, colloids, polymers
* Theory and measurement of intermolecular forces
* Single molecule transport driven by molecular interaction
Visiting scientist: Rudi Podgornik (course “Physics of DNA”!)
Grad Students: Selcuk Yasar, Jaime Hopkins, Alphan Aksoyoglu, Brian
Hildebrandt
Undergrads: Adam Cohen, Andrew Clark
Theory of intermolecular forces
(electrostatics, electrodynamics, solvation, steric)
example: single-walled carbon nanotubes
Connection between
dielectric spectra and
van der Waals
torques/forces.
Dept of Energy review: French, Parsegian, Podgornik et al. Rev Mod Phys 82:
1887 2010 “Long Range Interactions”
Now under under study: DNA, Lipids (cell membranes), Proteins
Rudi Podgornik, course, Physics of DNA
Measurement of forces and energies:
example DNA-DNA repulsion
Equation of State: Osmotic pressure vs. DNA density, DNA inside virus
function of salt, temperature
A. Evilevitch
Single-molecule transport: example, ionic channels
Detection
_
+
I(pA)
pA pA
E(mV)
0
10 ms
ms
10
25 µm
1 cm
Current
through
channel
70 µm
Sergey Bezrukov, Philip
Gurnev
100 µm
2 nm
Unified equation of state for
flexible polymers:
Osmotic pressures of many sizes
and concentrations fit with ONE
parameter.
Now measuring pressures
in mixed systems, seeing
polymers push other
polymers through
channels.
Ross Lab: Biophysics of Microtubules and Motors
Cytoskeleton: Rich Biological System of Interest
1. Microtubules shape the cell and remodeling of the
network is important biological and intriguing
physical problem
a. Biology: cell division, cell differentiation,
development
b. Physics: Non-equilibrium processes and selforganization.
2. Mechanics and dynamics are physical parameters
important for cellular activities.
3. Amenable to high-resolution single molecule
microscopy methods
Website: http://people.umass.edu/rossj/Ross_Lab/Home.html
Ross Lab - Biophysics
Current Projects:
1. Biophysics/biochemistry of microtubule severing enzymes
2. Measuring flexural rigidity of microtubules with associated
proteins bound
3. Self-organization and nanoscale traffic of microtubule
motors
4. Building and characterizing the FPALM/STORM microscope
Diaz-Valencia, et al. Biophysical Journal May, 2011
+++
1. My lab is fun and full. Always someone to talk to. Two postdocs
2. You get to learn biology. More job options than physics alone.
3. We are writing papers!
Website: http://people.umass.edu/rossj/Ross_Lab/Home.html
Ross Lab - Biophysics
Methodologies:
1. Biochemistry and Molecular Biology:
Protein Design and Engineering, Purification, and Characterization
2. Biophysical methods:
In vitro Reconstitution Assays, Bottom-up Engineering of Cellular Systems,
3. Microscopy:
Epi-fluorescence, TIRF, electron microscopy, AFM
4. Analysis:
Image analysis, MATLAB analysis, measure velocity, intensity, Fourier modes
Website: http://people.umass.edu/rossj/Ross_Lab/Home.html
Dynamics and mechanics of a range of biomaterials
Kilfoil Lab
Mechanotransduction in cell membranes
Colloids as a model biomaterial
Dynamics of cell division
A bottom-up approach to cell mechanics
κ
17 µ m ≈ l p ≈
k BT
lp ≈ mm
€
Scale bar 10 µm
Force generation and transduction in these cell materials
Prophase
Prometaphase
Metaphase
Anaphase
Telophase
movie: Saccharomyces
cerevisiae
spb separation
12
expressing fluorescent
labels:detection
2nd centromere
L(t) (µm)
Interphase
10
poles of mitotic spindle (spindle pole
8
bodies, or SPB)
6 chromosomes at attachment site
(centromere)
4
2
0
0
20
40
60
t (min)
80
100
Towards more complex in vitro cell mechanics models
!
!+
$!
$
$!
r%,!-.
)
$!
!!"#
!$
!
Drr&r,!(%,!-).
F-actin 1mg/ml
"
Poisson’s ratio
!"#
!*
Composite
$!
MT + F-actin
network
!#
$!
!"#
$
!%&'(
Poisson’s Ratio of
Material
1 mg/ml actin
1.0 µm beads
162 µm
2.4 mg/ml microtubules
Scale bar 10 µm
1.9 µm beads
Close-up:
axes in µm
Random walk of
single bead
$"#
Kilfoil Lab: Dynamics and mechanics of a range of
biomaterials
Methodologies
Microscopy:
3-Dimensional confocal microscopy, multi-point scanner
Analysis:
Develop new image analysis methods, data analysis
in vivo expression of fluorescent proteins and genetic manipulation of
cells:
Microfluidics
Biophysical methods:
In vitro reconstitution of protein networks
Single Biomolecules
in Confining and Crowded Environments
Lori S. Goldner
Graduate students:
Peker Milas
Richard Buckman
Ben Gamari
Sheema Rahmanseresht
Nina Zefroosh (summer 2011)
Overall Objectives:
Understand the physics of biological molecules and
molecular complexes in confining or crowded
environments that mimic the environment of the cell.
Specific Projects or Interests:
Short DNA flexibility
Short RNA/DNA interactions with proteins.
Molecular assembly.
Protein assembly.
Cellulose synthesis.
Approach:
Develop and apply novel optical techniques for
single molecule detection, confinement, and
manipulation.
R.V. Miller, Scientific American 1998
Biomolecules in Nanodroplets
We use nanodroplets both to facilitate measurement of biomolecular interactions, and to enhance
relevance to real biological systems.
Appl. Phys. Lett. 89, 013904 (2006).
2
Antisense Interactions in RNA
One strand of RNA binds to a complementary region of
another strand of RNA in an interaction that can be
regulatory or enzymatic in function.
Often a “kissing” or “loop-loop” interactions such as that
shown on the left is involved.
Kissing interactions are often
the first step in a structural
change such as that shown on
the right.
3
Cellulose synthesis
(with Tobias Baskin, Biology)
Cellulose synthesizing complexes (CSC)
in the membrane of a plant cell.
Image taken from Delmer, D. P Annual
Review of Plant Physiology and Plant
Molecular Biology (1999).
Brownian ratchet model of cellulose
synthesis.
From Diotallevi, F. and Mulder, B. Biophys.
J. (2007).
Image of fluorescently-labeled CESA-3
in living plant cells, portion of three cells
shown.
Image taken by Nina Zefroosh in the
Goldner lab.
4
Bacterial locomotion: swarming
Swarming is high-density motion of bacteria on a surface
The exterior portion of a swarm colony self-organizes into a single-cell-thick layer
This is a naturally occurring biological analog of the Menon group’s system of vibrated rods.
The swarm is naturally modeled as a 2D self-propelled gas
We have measured local short-range correlation functions, on the order of the cell length. We have observed longer-range swirling, but not yet characterized it.
We ultimately want to understand bulk flow rates, local jamming and multiple layer formation.
Swarming E. coli. A typical cell is 6 µm long.
Correlation between cells’ velocities.
Bacterial locomotion: flagellar polymorphism
Bacteria swim by rotating helical flagella
Flagella occasionally change shape during swimming.
The transformation between different polymorphic forms is triggered by changes in the torque being applied by the
flagellar rotary motor.
The shapes themselves are understood but not the energy associated with shape
change.
Each shape corresponds to a different fraction of the flagellin proteins switching to a higher-free-energy state with
more inherent twist.
Swimming E. coli with fluorescently labeled flagella.
Repeatedly pulling on a single flagellum in an optical trap gives a
force-displacement curve.
Smooth portions of the curve are elastic stretching of the helix
A vertical jumps occurs when a section of helix transforms from one polymorphic form to another.
Using the statistics of the transition between forms, we will measure the relative
thermodynamic stability of different forms.
Flagellum stretched in an optical trap.
Thanks