first talk on soft matter / biophysics for the spring semester will
be held in room P8445B at 10:30 a.m. on Tuesday, 14 January. Dr. Levine
will be at SFU all day, so if you would like time to meet with him individually,
please let me know. -Dave Boal (email@example.com)
Physics, University of California, San Diego
"The physics of dictyostelium amoeba aggregation"
The amoeba Dictyostelium discoideum undegoes a remarkable series of
developmental steps as it transitions upon starvation from a unitary
lifestyle to a cooperative one. These involve the setting up of a chemical
signaling roadmap so as to guide the cells into aggregates, directed
cell motility in response to these gradients, and ultimately coordinated
motion of the "developed" multicellular organism. Nonequilibrium
physics has an important role to play in understanding these processes;
this talk will describe our past and recent efforts to create a quantitative
understanding of these varied phenomena.
next soft matter / biophysics talk will be on Tuesday, 28 January at
11:30 a.m. in P8445B. Please note that the Open Lab uses this room from
" Width distribution of 1 / f^alpha signals"
The occurrence of signals (time series) in nature with 1 /
f^alpha power spectrum is abundant and usually associated with the presence
of nonequlibrium processes. Thinking of a signal as an interface, the
quantity of primary interest is the width (roughness) of the signal
over a finite period of time T. For self similar surfaces not only the
average value of the width scales with T, but also its whole distribution.
These distributions are characteristic of the type of noise; they have
different shapes for different alpha values. They can be calculated
exactly and can be used for classifying the noise. Experimental evidence
and a mysterious connection to extreme value statistics will also be
next soft matter / biophysics seminar will be on THURSDAY, 27 February
at 11:30 a.m. in P8445B. Please contact Barbara Frisken (firstname.lastname@example.org)
you are interested in meeting with Chi Wu during his visit to SFU.
Chemistry and Physics, Chinese University of Hong Kong
"The folding of single polymer chains in solution"
It has been predicted
in theory that a long linear homopolymer chain can undergo a coil-to-globule
transition when the solvent quality changes from good to poor. However,
it is extremely difficult to observe such a transition; namely, the
intrachain contraction is always spoiled by
interchain aggregation. Our laser light scattering studies of the temperature-induced
folding of narrowly distributed individual poly(N-isopropylacrylamide)
(PNIPAM) linear chains in solution have, for the first time, revealed
such a transition. Moreover, we found a novel molten globular state
between the coil and globular states. The time required for the transition
(~102 sec) was too short to support a previously suggested high chain-knotting
density inside the globule. Our results also showed that even at the
collapsing limit, the globule still contained ~70% of water in their
hydrodynamic volume, which is not as "dry" as we thought.
Recently, our study has been extended to the folding of some PNIPAM
copolymer chains. We have demonstrated that after the introduction of
second hydrophilic or hydrophobic monomer into the PNIPAM chain backbone,
the chain folding could lead to some unique nanostructures, such as
a single-chain micelle and the "ordered-coil" state. More
importantly, the comonomer distribution on the
chain backbone could greatly affect the chain folding in solution. In
this lecture, we also like to emphasize the importance of combining
synthetic chemistry with polymer physics.
will be a biophysics seminar on Tuesday, 11 March at 3:30 pm in
SSB8114. Please note the irregular time and location.
Marcel Bally, BC Cancer Agency
"Liposomes and Lipid-Based Formulation Technology: Optimizing delivery,
targeting and controlled release properties for plasmid expression vectors
and antisense oligonucleotides"
on liposomes as model membrane systems and as drug carriers facilitated
the design of pharmaceutically viable lipid-based drugs. In fact much
of the research and echnology required to prepare liposomal carriers
for testing in clinical trials was well established by 1987. By that
time, four pivotal hurdles were overcome. First, the importance of carefully
assessing structure activity relationships through analysis of physiochemical
characteristics was proven to be essential in product development. Second,
biological barriers previously believed to limit the distribution properties
of systemically administered macromolecular drug carriers, such as liposomes,
proved to be penetrable. Third, manufacturing issues for preparing pharmaceutically
acceptable formulations were resolved and included identification of
sources for inexpensive raw materials, the elucidation of procedures
for storing lipid-based carriers for extended time periods and the development
of methods for reproducibly preparing large batches of liposomes with
attributes that could be characterized according to the rigorous guidelines
of health boards such as the FDA. Fourth, procedures for loading liposomes
with pharmaceutically active agents that
relied on the chemical attributes of the lipids prior to liposome formation
and/or involved loading of pre-formed liposomes were developed. The
latter involves the use of ion gradients to effect drug loading, a procedure
that has proven to be particularly useful and versatile. The most significant
revisions of lipid-based carrier technology that have guided research
efforts during the 1990's involved three breakthroughs made in the late
1980's: 1) the observation that surface associated polymers (i.e.polyethylene
glycol or the ganglioside GM1) cause changes in the liposome surface
properties that contribute to increased circulation lifetimes; 2) the
discovery that positively charged liposomes can be used to transfer
polynucleotides into cells; and 3) the identification of certain lipids
that can act as therapeutic molecules. Given this perspective, it is
useful to consider how this technology may emerge in the next millenium.
Other than the many entrepreneurial interests, we believe that the primary
objective that has driven research focused on development of liposomal
drug carriers concerns improving drug specificity. However, it is believed
that the most important unresolved issue concerns controlling drug release
attributes. This argument must also consider when and where drug release
should occur. For this reason significant advances in the use of liposomes
for therapeutic purposes will have to carefully consider dissociation
of the therapeutic agent from the carrier, a factor that is guiding
our research efforts. We believe that significant advances in the use
of liposomes for delivery of biopharmaceuticals, such as peptides, antisense
oligonucleotides and genes, will require the development of multifunctional
liposomes that contain features specific for stability to biological
fluids (blood, interstitial fluids, lymph), controlled distribution
characteristics, site specific targeting, and controlled content release
attributes. We believe that these liposomes will have to be designed
with the ability to transform their physical characteristics so that
properties required during the liposome delivery phase can be differentiated
from those required for delivery of encapsulated contents. The technical
capabilities for constructing liposomes with such characteristics are
reasonably well established in our laboratory for conventional anticancer
drugs and more recently for gene transfer systems.
of the CUPE strike, this note is a reminder about tomorrow's
biophysics seminar: 10:30 a.m. in P8445B.
Ejtehadi, Physics UBC
"A generic Model for DNA Deformations at Base-pair Level"
We present a model to treat the elasticity of DNA at thebase-pair level.
we use a variant of the Gay-Berne potential to present the stacking
energy between neighboring base-pairs. The Sugar-phosphate backbones
are taken into account by semi-rigid harmonic springs with a non-zero
spring length. The competition of these two interactions and the interaction
of a simple geometrical constraint leads to a stacked right-handed B-DNA-like
conformation. The mapping of the present model to the Marko-Siggia and
the Stack-of-Plates model enables us to optimize
the free model parameters so as to produce the experimentally known
observables such as persistence length, mean and mean squared base-pair
step parameters. For the optimized model parameters we measured the
critical force where the transition from B- to S-DNA occurs to be approximately
160pN. We recover an overstretched S-DNA conformation with highly inclined
bases that enables at least partially a stacking of successive base-pairs.
first soft matter talks for the summer semester will be on May 6 and 13
at 10:30 a.m. in the physics seminar room, P8445B. -DB
Duque, SFU physics
"Dissipative Particle Dynamics, a review"
This is the first of two seminars I will devote to Dissipative Particle
Dynamics (DPD). Since its formulation, about 10 years ago, this has
been one of the most promising numerical simulation techniques to study
the mesoscopic regime. This regime presents time and length scales too
large for molecular simulation but still too small for hydrodynamics.
In this seminar, I will review the standard DPD, its successful applications
and its pitfalls. Recent results have pointed out a way to provide the
theory with a firm theoretical foundation, even if the result is somewhat
different (and more complicated) than the usual DPD. I will leave the
details of how to systematically develop mesoscopic theories (DPD-like
or otherwise) for the next seminar, which will thus be related to this
one but still largely independent.
will be a soft matter / statistical mechanics seminar on Tuesday, 27
May at 10:30 a.m. in P8445B.
of Molecules at Solid Surfaces
Dept. of Chemistry and Biochemistry, Concordia University
Monte Carlo methods
are well suited to the examination of structures formed by molecules
at solid surfaces. These methods can be used to assist in the interpretation
of experimental results, provide details that are experimentally inaccessible,
and predict what structures might be formed in related molecule-substrate
systems. Besides answering direct experimental
questions, one can also address fundamental questions and test theoretical
predictions. In this seminar, work done on the structures formed by
simple molecules (CO & N2) on ionic surfaces (NaCl & MgO) will
be presented. In particular, the values of non-universal critical exponents
of the order-disorder transition in the N2/NaCl system will be presented
and the existence of the Devil’s Staircase phenomenon in the CO/MgO
and the N2/MgO systems will be discussed.
will be a soft matter seminar on Tuesday, 22 July at 10:30 a.m. in room
Speaker: Dr. Olivier Diat
CEA-CNRS-Univ. J. Fournier
Title: New insight into nafion structure
Nafion ? (E.I.
du Pont de Nemours), whose chemical formula is indicated below,
is the most studied
ionomer membrane thanks to its good performance in electrochemical devices
such as chlor-alkali electrolysors and H2O2 fuel cells. Its structure,
characterised by microphase separation, has been widely studied using
small angle scattering with neutrons (SANS) and x-rays (SAXS). The range
of transfer momentum from 0.01 to 0.4 Å -1 has been particularly
investigated because of the occurrence of the so-called “ionomer
peak” at around 0.11Å -1 which is the most striking feature
of these spectra. Other main features are observable at lower and larger
q values and, in spite of numerous studies with different techniques,
Nafion structure is still subject to controversy and several models
have been proposed. The most common is due to Gierke: the polymer is
assumed to form reverse micelles of radius 20Å connected by small
cylindrical pores that are 10Å in length and 5Å in radius.
These pores, which allow ionic conductivity through the hydrophobic
polymeric matrix, have never been observed using scattering techniques.
Other models attempt to describe the structure of the hydrophilic domains
of the Nafion membrane but there is still some debate about the processes
implied during the ionic clusters reorganisation as a function of water
swelling. Our point of view is slightly different; we propose a new
comprehensive structural approach for Nafion membranes taking into account
elongated polymer aggregates, correlated in orientation, as the basic
scattering entity. This consideration is based mainly on SANS experiments
made using a contrast variation method. Other observations using different
microscopy techniques (TEM and AFM and OpticalM) reinforce our insight
into Nafion’s structure. From ion and water dynamics (impedencemetry,
PFG NMR, QNES) as well as deformation (creep) analysis, large scale
characteristic lengths can be extracted, relevant for the transport
and mechanical properties of this type of material.
will be a second soft matter talk next week, on Thursday, 24 July at 10:30
University of Ottawa
Title: A lattice gas model for the rupture kinetics of lipid bilayers
The cylindrical shape of the lipid molecules and their amphiphilic nature
(a water loving head, and water hating tail) are responsible for their
self-assembly into bilayers. The lipid bilayer, the universal basis of
all biomembrane structures, forms the main barrier between the contents
living cell and the surrounding medium. Since this bilayer
is a liquid, rupture is expected to occur via the nucleation and growth
of pores. We developed a lattice gas model for the nucleation, growth,
and coalescence of pores for membranes under expansion. The model
has been extended to discuss the effect on the rupture kinetics of the
absorption and eventual insertion of peptides, many of whom are known
to be effective antimicrobial agents.
last seminar in this summer's biophysics/soft matter series will be given
on Tuesday, August 5 at 10:30 a.m. in P8445B.
Patty, SFU physics
Vesicle Aggregation Induced by Cytidine 5’-triphosphate:phosphocholine
The enzyme Cytidine
5’-triphosphate :phosphocholine cytidylyl-transferase (CT) catalyzes
the formation of cytidine 5’-diphosphate choline, the headgroup
donor in the synthesis of phosphatidylcholine lipids. This enzyme binds
to negatively-charged membranes and membranes with negative curvature
and is activated by those membranes. It is found as a dimer both in
soluble and membrane-bound forms. The soluble form is inactive (i.e.,
occurs) while the bound form is active. Whether the dimer binds to one
membrane or connects two membranes together is not clear. If two membranes
bind together, this should be observable as an increase in vesicle aggregation.
In this talk I will describe dynamic light scattering (DLS) measurements
designed to investigate the possible CT-induced-aggregation of
large unilamellar lipid vesicles. Aggregation is observed in membranes
that include negatively-charged lipids and lipids that tend to form
membranes with negative curvature. The results of DLS measurements are
compared to results for CT activation and to images of CT-vesicles observed
by transmission electron microscope.