The 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 (

Herbert Levine
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.

The 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 12:30.

Tibor Antal, Physics, SFU

" 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 discussed.

The next soft matter / biophysics seminar will be on THURSDAY, 27 February
at 11:30 a.m. in P8445B. Please contact Barbara Frisken ( if
you are interested in meeting with Chi Wu during his visit to SFU.

Chi Wu
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.

There 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"

Research 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.

In view of the CUPE strike, this note is a reminder about tomorrow's
biophysics seminar: 10:30 a.m. in P8445B.

Reza 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.

The 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

Daniel 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.

There will be a soft matter / statistical mechanics seminar on Tuesday, 27
May at 10:30 a.m. in P8445B.

Simulations of Molecules at Solid Surfaces
David Jack
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.

There will be a soft matter seminar on Tuesday, 22 July at 10:30 a.m. in room P8445B.

Speaker: Dr. Olivier Diat
CEA-CNRS-Univ. J. Fournier
Grenoble, France
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.

There will be a second soft matter talk next week, on Thursday, 24 July at 10:30 in P8445B.

Béla Joós
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 of a
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.
The last seminar in this summer's biophysics/soft matter series will be given on Tuesday, August 5 at 10:30 a.m. in P8445B.

Philip 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., no catalysis
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.