Spring 2013

The biophysics seminars will be held on Tuesdays at 1:30 pm in P8445.2 unless otherwise stated.

Date Speaker Topic Abstract
Jan 8 Yaihab Wasnik
Self-organization in biological systems Biological systems are known to self organize. In this talk we illustrate a few physical principles involved in the self organization of proteins in biological systems. Specifically, we talk about curvature mediated protein localization during sporulation in Bacillus Subtilis. We present a model to explain the phenomenon of actin waves in Dictyostelium. We conclude by talking about the physical principles involved in the periodic positioning of receptors in Ecoli.
Jan 15 Antoine Baker
Linking the DNA strand asymmetry to the spatio-temporal replication program: from theory to the analysis of genomic and epigenetic data Two key cellular processes, namely transcription and replication, require the opening of the DNA double helix and act differently on the two DNA strands, generating different mutational patterns (mutational asymmetry) that may result, after long evolutionary time, in different nucleotide compositions on the two DNA strands (compositional asymmetry). Here, we propose to model the spatio-temporal program of DNA replication and its impact on the DNA sequence evolution. The mutational and compositional asymmetries observed in the human genome are shown to decompose into transcription- and replication-associated components. The replication-associated asymmetry is related to the replication fork polarity, which is also shown to be proportional to the derivative of the mean replication timing. The large-scale variation of the replication fork polarity delineate Mbp scale replication domains where the replication timing is shaped as a U. Such replication domains are also observed in the germline, where they are revealed by a N-shaped compositional asymmetry, which indicates the conservation of this replication program over several hundred million years. The replication domains borders are enriched in open chromatin markers, and correspond to regions permissive to transcription and replication initiation. The analysis of chromatin interaction data suggests that these replication domains correspond to self-interacting chromatin structural units, at the heart of a highly parallelized organization of the replication program in the human genome.
Jan 22 Rasoul Narimani
Morphological studies of ionic random graft copolymers based on scattering techniques We have studied the morphology of ionic random graft copolymers using small angle X-ray and neutron scattering (SAXS and SANS), and wide angle X-ray scattering (WAXS) techniques. I'll describe a self-consistent morphological model for both dry and hydrated samples, and show how factors such as the degree of crystallinity of the backbone and the ion content affect the phase separation of this polymer at the nano-scale level. Furthermore, I will explain how details of the morphology are correlated with water content and proton conductivity of the polymeric membranes.
Feb 12 Suckjoon Jun (UCSD Physics)
On the fundamentally soft nature of the bacterial chromosome Replicating bacterial chromosomes continuously demix from each other and segregate within a compact volume inside the cell called the nucleoid. Although many proteins involved in this process have been identified, the nature of the global forces that shape and segregate the chromosomes has remained unclear because of limited knowledge of the micromechanical properties of the chromosome. In the shorter first half of this talk, I will summarize the physics of polymer in confined space. In the second part, I will describe our recent experimental work that shows the bacterial chromosome in confined space remarkably behaves as a loaded entropic "spring". In particular, comparison with the viral DNA in a capsid reveals the fundamentally soft nature of the bacterial chromosome.
Feb 15 Pik-Yin Lai (National Central University, Chung-Li, Taiwan)
Nonlinear BioPhysics in Cardiac systems: control of oscillatory behavior I will briefly introduce the approach our group employed in the research of complex nonlinear biophysics. In particular I will discuss the physics involve in cardiac systems and discuss our recent theoretical and experimental work. The first is the frequency variation with time in cultured cardiac cells, whose oscillatory dynamics can be modeled by coupled excitable elements in the presence of noise giving rise to 'frequency enhancement'. The second is about the dramatic reduction of cardiac alternans by small perturbations in pacing scheme. Predictions and validity of this control method have been verified by both experiments performed with isolated heart preparations and numerical simulations. A nonlinear return map for this novel pacing scheme based on action potential duration restitution response is proposed to explain the working mechanism of the control.
Feb 19 Christy F. Landes (Rice University, Houston, TX)
In Search of Concurrence between Biological and Synthetic Single Molecule Structure/Function (sponsored by the Departments of Molecular Biology & Biochemistry (MBB) and Physics) One of the innate challenges in materials chemistry is the ability to engineer cheap, efficient, robust devices. In contrast, nature manufactures such materials from the cheapest of precursors. As we advance to scientific tools able to observe natures molecular level methods, we begin to understand that one reason nature can be so successful is that her strategy differs from ours. Whereas humans usually design materials with a single, well-defined function, nature often acts through redundant or degenerate channels that are singly not as efficient, but collectively, and in the face of damage or wear, outperform their synthetic cousins. Our central question is: Can we take cues from the structure-function interplay and use of cooperative pathways in natures biomolecular processes to inform design principles for tailored functional materials applications? The pursuit of answers to this question presents challenges for theory, measurement, and data interpretation. The talk will present insights into the overall question, as well as attempts to overcome some of the innate challenges encountered along the way.
Feb 26 Mark Zajac (UBC Mathematics)
Polymer Entropy Can Drive Cell Migration I will present a two-phase model for the solid cytoskeleton and fluid cytosol inside crawling nematode spermatozoa. Simulations demonstrate that entropy of the cytoskeletal polymer network can generate force that drives a cell forward. The drag force exerted by cytosolic fluid also plays a significant role. Simulations also show that cytoskeletal anisotropy is required to account for the dependance of cell speed on cell shape, as observed in experiments. I am using level set methods to provide an implicit representation of cell boundaries. Data analysis includes image processing as a minimization problem, leading to an Euler-Lagrange equation. Tracking cytoskeletal features makes use of correlations.
March 12 Bingyun Sun (SFU Chemistry),
Understanding stem cells from their surface: how technology can advance biology Cell surface membrane delineates cells from its environment. Proteins decorated at the cell surface connect the interior of a cell to its exterior. These functionally important proteins have remained to be the least understood protein class. I will talk about how we develop novel techniques to decode cell surface protein topology in understanding the uniqueness and commonality between individual cells and among different populations of cells, in a goal to understand the associated and influential decision making process for embryonic stem cells to choose their fates.
April 2 Steve Plotkin (UBC Physics)
Protein misfolding and degenerative disease: Connecting theory and experiment TBA