Complex Matter and Biophysics Seminar: Spring 2009

From WolfWikis

Tuesdays 4:00 to 5:00pm, 315 Riddick unless otherwise noted.

Tea/coffee/cookies will be served starting at 3:30pm in 415 Riddick.

Feb 3: Benjamin Watts

Paul Scherrer Institut

Nanoscale Quantitative Composition and Efficiency Maps of Polymer Photovoltaic Devices

Solar cells based on thin blend films of conjugated polymers and/or fullerene derivatives are a promising alternative to the currently available silicon-based solar cells. However, these systems tend to display complex segregation of the organic components during film formation and the fundamental details of the relationship between the morphology of conjugated polymer blend films and their performance in photovoltaic devices is still not clear. In this talk, I'll present our experimental efforts to map out the morphology and photovoltaic performance of solar cell devices based on segregated PFB:F8BT blend films, utilising both conventional scanning transmission soft X-ray spectromicroscopy (STXM) and our novel extension to STXM, Soft X-ray Beam Induced Current (SoXBIC).

Host: Harald Ade

Feb 10: Sharon Lubkin

NCSU, Department of Mathematics

The Mechanics of Branching Ducts

Tissues grow, change shape, and differentiate, function normally or abnormally, get diseased or injured, repair themselves, and sometimes atrophy. This complex suite of behaviors is governed by a complex suite of controls. Nonetheless, we can identify some general principles at work in the dynamics of tissues. Our goal is to understand how a tissue’s mechanics and biology regulate each other.

Our models use a biologically-based continuum framework to track the mechanics, biology, and mechanobiology of the component cells, fluids, signaling molecules, and extracellular matrix materials. The presentation will describe our modeling approach, reveal some of the general principles we have identified, and discuss some of the questions our findings have raised about branching morphogenesis.

Host: Karen Daniels

Feb 24: Amy Oldenburg

UNC-Chapel Hill, Department of Physics and Astronomy

Magnetic and Plasmon-Resonant Nanoparticle Contrast Agents in Optical Coherence Tomography and Multi-Modality Imaging

Abstract: Optical coherence tomography (OCT) is a powerful method for visualizing tissue microstructure a few millimeters in depth. Because conventional fluorescent markers do not provide coherence imaging signals, I will present the development of nanoparticle contrast agents for OCT. Plasmon-resonant gold nanorods provide spectroscopic absorption contrast, and magnetic iron oxide nanoparticles can be actively modulated for contrast in OCT while also providing MRI contrast.

Host: Keith Weninger

Mar 10: Thomas Ward

NCSU, Department of Mechanical and Aerospace Engineering

Flow Focusing: Drop Size and Scaling in Pressure versus Flow-Rate-Driven Fluid Pumping

The production of micrometer sized droplets using microfluidic technology and a flow-focusing geometry is studied experimentally. Two distinct methods of flow control are compared: (1) control of the flow rates of the two phases and (2) control of the inlet pressures of the two phases (Ward et al., Electrophoresis, 2005). In each type of experiment the drop size L, velocity U and production frequency f are measured and compared as either functions of the flow-rate ratio or the inlet pressure ratio. The minimum drop size in each experiment is on the order of the flow focusing contraction width a. The variation in drop size as the flow control parameters are varied is significantly different between the flow-rate and inlet pressure controlled experiments. The quantitative differences suggest a fundamental difference in drop break up between the two types of experiments. Also, some new results on experiments involving a first order chemical reaction that produces a surfactant will be introduced.

Host: Karen Daniels

Mar 24: Patrick Charbonneau

Duke Univ., Department of Chemistry

Geometrical Frustration: the Case of 4d Hard Spheres

Most glasses form under conditions where the thermodynamically stable state of the system is crystalline. Good glass formers should therefore be poor crystallizers. Geometrical frustration is one of the factors that prevent the formation of ordered phases and therefore help glass formation. Simple liquids are often considered frustrated because the five-fold symmetry of icosahedral clusters cannot tile a regular lattice. This contrasts with what happens in a fluid of two-dimensional disks, where hexagonal order is both locally and globally preferred and where crystallization is particularly easy. Yet the nature of 3d frustration is ambiguous. To resolve the ambiguity and learn more about the structure of simple liquids, we explore the properties four-dimensional hard spheres. Bring your imagination.

Host: Karen Daniels

Apr 7: Volodymyr Babin

Roland/Sagui Group, NCSU Physics

Molecular Dynamics and Free Energies

I am going to briefly overview the molecular dynamics approach and then to talk about the activities pursued in our group. In particular, I am going to focus on the non-equilibrium methods targeting the computation of the free energy surface of a reaction coordinate that have become popular over the past few years. The methods in this category use the history of the sampling process to bias the simulation thus forcing it to explore as of yet unexplored values of the reaction coordinate. In context of molecular dynamics the idea was first introduced by the local elevation method by Huber, Torda and van Gunsteren (the Wang-Landau algorithm employs similar ideas in context of Monte Carlo simulations). More recent approaches include the adaptive-force bias method, and the non-equilibrium metadynamics. Our group has developed yet another variation on the same theme (adaptively biased molecular dynamics) that benefits from a smoother biasing potential and replica exchange mechanism. I am going to present the method along with some examples.

Apr 14 : Diana Streng

Riehn Lab, NCSU Physics

The Nanofluidic Analysis of Chromatin

DNA is the carrier of all genetic information within a cell. Within eukaryotic cells DNA is efficiently packed into chromatin through the formation of a complex of DNA and histone proteins. This complex is called chromatin. Because of the formation of chromatin, DNA is extraordinarily condensed in eukaryotic cells. This condensation leads to a very limited resolution of optical techniques that investigate the structure and function of DNA by attaching fluorescent markers. It would thus be of considerable utility to develop a method for stretching chromatin to a predictable extension, so that a direct relationship between base pair number and spatial location is obtained. Such methods exist for bare DNA, but not chromatin. I investigate methods for stretching chromatin using surface and nanofluidic stretching. My results indicate that nanofluidic stretching of chromatin may become useful for future studies that aim to directly image epigenetic modifications on chromatin molecules.

Apr 28: John J. Sakon

Weninger Lab, NCSU Physics

Studying Conformation and Dynamics of Individual Proteins in Live Cells using Single Molecule FRET

This talk reports progress towards the use of single molecule fluorescence resonance energy transfer (smFRET) in the cytoplasmic environment of live cells to study individual proteins. Recombinantly expressed, externally dye-labeled SNARE proteins were microinjected into cultured cells, tracked and imaged to observe real-time conformational dynamics. We discuss the many obstacles that lower signal:noise in vivo (cellular and coverslip autofuorescence, dye photobleaching) and our methods for overcoming them. Initial findings and the applications for this technique will also be discussed.