Date / Place Speaker Title
10:30 AM, Sept 11
@ P8445B
Daniel Duque, SFU The standard model for copolymers and an application to lipids
10:30 AM, Sept 17
@ P8445B
Marcel den Nijs,
Univ. of Washington, Seattle, WA
Scaling of Avalanches in an Unloading Sandbox Model
3:30 PM, Sept 23
@ AQ 5027
Daniel Kandel,
Weizmann Institute
Phospholipid Membranes with Embedded Inclusions
10:30 AM, Nov 6
@ P8445B
David Boal, SFU Mechanical evolution of the cell
10:30 AM, Nov 20
@ P8445B
Hue Sun Chan,
University of Toronto
Generic Protein Properties as Powerful Experimental Constraints on Modeling: The Cases of Thermodynamic and Kinetic Cooperativity
10:30 AM, Nov 26
@ P8445B
Yuekan Jiao, SFU
Dynamic Interactions of p53 with DNA observed by Atomic Force Microscopy
10:30 AM, Dec 10
@ P8445B (TUESDAY)
Evan Evans , UBC
Membrane Rupture: 2-D cavitation


Daniel Duque, Simon Fraser University
"The standard model for copolymers and an application to lipids"

We will review what has been called the standard model for the statistical mechanics of copolymer melts: the so-called self consistent field theory. We will then consider a variation of it, which has been used to describe lipids. We will conclude with a recent expansion of the latter to include proteins, which shows how this approach may be used to address biological questions.

The talk will be held in P8445B at 10:30 a.m. on Wednesday, Sept. 11.

TUESDAY, 17 September at 10:30 a.m. in room P8445B.

Marcel den Nijs, University of Washington
"Scaling of Avalanches in an Unloading Sandbox Model"

We introduce a directed avalanche model; a slowly unloading sandbox driven by lowering a retaining wall. The directness of the dynamics allows an interpretation of the stable sand surfaces as world sheets of fluctuating interfaces in one lower dimension. In our specific case, the interface growth dynamics belongs to the Kardar-Parisi-Zhang (KPZ) universality class. The critical exponents of the various avalanche distributions should follow KPZ values. The numerical values are indeed close, but differ sufficiently to warrant a detailed study of whether avalanche correlated Monte Carlo sampling changes the scaling exponents of KPZ interfaces.

MONDAY, 23 September at 3:30 p.m. in room AQ 5027.

Speaker: Daniel Kandel, Weizmann Institute
Title: Phospholipid Membranes with Embedded Inclusions

The motivation for this work comes from recent experimental biological studies. They show that cells of living organisms control the local shape of their membranes, and their biological function, by varying the local concentration of various macromolecules embedded in the membrane. I will show theoretically how embedded molecules can lead to shape instabilities in membrane vesicles, by inducing a local spontaneous curvature which depends on their concentration. The coupling between this concentration, the local curvature of the membrane and global geometrical constraints brings about shape instabilities, such as pearling in hollow membrane tubes, coiling in full tubes and tubulation in pancake-like vesicles. This work is inspired by experimental studies of artificial membrane vesicles with anchored polymer molecules.

Wednesday, 6 November at 10:30 a.m. in P8445B.

"Mechanical evolution of the cell"
David Boal, Simon Fraser University

Within a decade, NASA expects to bring Martian rocks to Earth for analysis, adding another dimension to the search for extraterrestrial life. Already, the suggestion that submicron features on a Martian meteorite might be remnants of early life forms has posed a series of questions about extraterrestrial cells:
Is there a lower limit to the size of a viable cell?
What architectural scaffolding is required to produce cells of various shapes?
How must the physical attributes of a cell - for example, the thickness of its boundary - scale with its size?
As it applies to terrestrial cells, many of the underlying principles of Nature's building code have been determined in the past two decades. This code helps us to understand the limits to cell architecture and to assess the likelihood that a particular cell design could arise under various conditions in the history of a planet.

Wednesday, 20 November at 10:30 a.m. in P8445B.

Yuekan Jiao
Physics, Simon Fraser University

Dynamic Interactions of p53 with DNA observed by Atomic Force Microscopy

The specific binding of a protein to DNA in solution can be achieved by three-dimensional diffusion of both molecules. However the protein may bind to specific targets on DNA at an apparently higher rate than expected from collisional interactions alone. Atomic force microscopy (AFM) can resolve biological samples in solution with nanometer resolution, which has been a powerful tool in the studies of biological structure and activity. While AFM has been very sucessful in observing biological structure, more challenging is the in situ viewing of biological activity. In this talk I will focus on the AFM application in real time observation of p53 and DNA interactions. I will discuss the microscopic technique and sample preparation methods, and will show the various interactions found from which a second pathway of p53 to reach the specific sites on DNA was concluded.

TUESDAY, 26 November at 10:30 a.m. in P8445B.

Hue Sun Chan
Biochemistry, University of Toronto

Generic Protein Properties as Powerful Experimental Constraints
on Modeling: The Cases of Thermodynamic and Kinetic Cooperativity

I will discuss how generic thermodynamic and kinetic properties of small single-domain proteins may be used to evaluate protein chain models. Many residue-based interaction schemes are found to be insufficient for the experimental criteria for two-state cooperativity, which include the requirement that the van't Hoff to calorimetric enthalpy ratio being approximately unity. Protein folding/unfolding kinetics provides even more discriminating constraints. Although some models --- including popular Go constructs --- exhibit proteinlike thermodynamic cooperativity, they fail to reproduce the type of simple two-state kinetics observed experimentally for small single-domain proteins. These findings suggest strongly that interactions in real proteins may be much more specific than commonly posited. Hence more complex nonadditive multiple-body interactions may be needed for a basic account of real protein energetics.

Chan, Proteins 40:543 (2000);
Kaya & Chan, Proteins 40:637 (2000); Phys Rev Lett 85:4823 (2000);
J Mol Biol 315:899 (2002);
Shimizu & Chan, Proteins 48:15 (2002)


The last talk in the soft matter / biophysics series for the fall term will
be on TUESDAY, 10 December at 10:30 in P8445B.Evan Evans
Physics and Pathology
University of British Columbia
"Membrane Rupture: 2-D cavitation"

Puzzled over since the time of Kelvin in the 19th century, opening a
molecular-size cavity in a fluid by reducing pressure seems virtually
impossible since the ratio of cavity surface energy to the applied
mechanical work diverges at small size. However, Kramers’ marvelous insight
into thermally activated kinetics in liquids (1940) stimulated Zeldovich
(1943) to develop the classical nucleation theory for cavitation in 3-D
liquids -- later extended by Deryagin and Gutop to failure of 2-D fluid
films – which provided comforting rationalization of the dilemma. Still, the
kinetic theory has had little success in predicting practical behavior like
bubbling in liquids under reduced pressure or near high speed propellers of
submarines. But here, I show that rupturing fluid membranes over time
frames from less than a millisecond to many minutes reveals a causal
sequence of kinetic events – nucleation of a nanoscale defect followed by
opening of a mesoscopic hole (cavitation) – which is well matched by the
classical theory.