Complex Matter and Biophysics Seminar: Spring 2008
From WolfWikis
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Spring 2008 Schedule
Thursdays 11:45 to 1pm, 202 Riddick (grad office conference room), unless otherwise noted.
Please bring a lunch if you'd like, and join us for tea/coffee/cookies and discussion following the seminar.
Jan 17
Frederic Lechenault (NC State Physics)
Critical scaling and heterogeneous superdiffusion across the Jamming transition
ABSTRACT: The dynamical properties of a dense horizontally vibrated bidisperse granular monolayer are experimentally investigated. We provide decisive experimental evidence that the appearance of macroscopic rigidity is a critical phenomenon, with increasingly collective and heterogeneous dynamics. Correlation time and length soar on both sides of the transition, as the volume fraction varies over a remarkably tiny range. We characterize the dynamics of individual grains, which becomes super-diffusive at the jamming transition, signalling long-ranged temporal correlations. Correspondingly, the system exhibits long-ranged four-point dynamical correlations in space that obey critical scaling at the transition density.
Host: Karen Daniels
TUESDAY Jan 22
Faculty Candidate
Molecular memory circuits on a nanoscale scaffold
12:00pm, Cox 400 (note alternate time/location)
ABSTRACT: Significant challenges exist in assembling the building blocks of a nanoscale device. Self-assembly is one of the few practical strategies for making ensembles of nanostructures and will therefore be an essential part of nanotechnology. In order to generate complex structures through self-assembly, it is essential to develop methods by which different components in solution can come together in an ordered fashion. Using viruses as nanoscale scaffolds for devices offers the promise of exquisite control over positioning nanoscale components on a protein scaffold that also allows further self assembly of the nanoscale devices. Using Cowpea Mosaic Virus, modified to express cysteine residues on the capsid exterior, gold nanoparticles were attached to the viral scaffold in a pattern to produce specific interparticle distances. The nanoparticles were then interconnected using thiol-terminated conjugated organic molecules that can act as "molecular wires", resulting in a three-dimensional spherical conductive network which is only 30 nm in diameter. By using molecules that exhibit bistable voltage controlled switching, molecular memory circuits were assembled and characterized.
Jan 24
Faculty Candidate
Single-molecule and local studies of mechanical (un)folding of proteins, enzymatic catalysis, and water structure at solid surfaces.
12:00pm, Cox 400 (note alternate time/location)
ABSTRACT: With the ability to watch one molecule at a time single-molecule techniques are unique in observing the processes, which otherwise are hidden in macroscopic observables or averaged out by ensemble measurements. In the force-clamp AFM spectroscopy piconewtons of force can be applied along a precisely defined direction, and to a single molecule. First, I will show how to identify several distinct regimes associated with (un)folding of single protein molecules, and what kind of physical information can be extracted from there. Mechanical forces exerted on single protein molecules are inherently present in biological systems. Our muscles, cell transport, and cell motility (i.e., ability to move spontaneously) rely heavily on these forces. Next, using single molecule force-clamp spectroscopy and an engineered disulfide-bonded protein, I will show how to obtain the details about dynamics and conformational changes of the substrate-enzyme during an enzymatic disulfide bonds reduction by thioredoxin - a ubiquitously expressed disulfide reductase critical for maintaining redox balance in cells. Finally, in a series of local AFM measurements we studied water molecules confined in sub-nanometer gaps. Water in sub-nanometer gaps defines physical properties of cell membranes, and permeation of ion channels inside each cell membrane. On both hydrophilic and hydrophobic surfaces, we observed the oscillatory solvation forces arising from the density fluctuations within confined water layers, and we obtained an approximate viscosity of each water layer.
MONDAY Jan 28
Faculty Candidate
Exploring protein organization and dynamics in model membranes and cells
12:00pm, 206 Mann (note alternate time/location)
ABSTRACT: Cell membranes are characteristically heterogeneous, both structurally and dynamically. The spatial arrangement and dynamic movement of proteins in cell membranes are essential for coordinating many cellular functions, contributing to the specificity and sensitivity of a cell's response to its environment. I will discuss two routes toward understanding these heterogeneities, using either model membranes or mammalian cells. In the controlled environment of model membranes, we studied the influence of membrane-tethered proteins and lipid compositions on membrane organization. We found that protein and lipid organization in this simple model system were coupled. While heterogeneities in model membranes can be large enough to measure using diffraction-limited optical microscopy, heterogeneities in cell membranes generally exist on smaller scales. We addressed this by combining the super-resolution technique of photoactivated localization microscopy (PALM) with live cell single particle tracking (SPT). Photo-switchable, genetically expressed probes are used to create spatially resolved maps of single-molecule motions. We explored the capabilities of this method by imaging the membrane proteins Gag and VSVG, obtaining up to thousands of trajectories per cell, several orders of magnitude more than enabled by traditional SPT. This new method allows us to correlate structural and dynamic heterogeneities at the molecular scale.
Feb 21
Brandon Choi (Weninger Group)
Spontaneous conformational fluctuation of SNARE proteins observed with single molecule fluorescence resonance energy transfer (smFRET)
ABSTRACT: Conformational changes of protein are often linked to biological functions. For example, an assembly of a highly structured complex of SNARE proteins is essential for most cases of intra-cellular membrane fusion. Biochemical and high-resolution structural studies of SNAREs suggest that a large open-closed conformational transition in the syntaxin family of SNARE proteins regulates its ability to enter SNARE complex. We have used intra-molecular, single molecule fluorescence resonance energy transfer (smFRET) to observe spontaneous open/close conformational switching in syntaxin type proteins. Site directed mutagenesis was used to introduce fluorescent dyes into each of the two major domains involved in the open-close transitions. Proteins are immobilized by encapsulation within surface tethered lipid vesicles to allow observation of individual proteins for extended periods. With this assay we have analyzed the kinetics of the open-closed transitions for several mutants and homologues of syntaxin. Characterization of the open-closed transitions in syntaxin that are thought to contribute to regulation of SNARE complex assembly will provide insight into SNARE mediated membrane fusion.
Mar 13
Aric Meyer (Ade Group)
Organic Electronics: Survey of the Field
ABSTRACT: Electronic devices based on conducting polymers and other organic materials are now entering the market, yet greater utilization of these materials is limited by our lack of understanding of and control over them. This talk will begin with an introduction to the basic science, promise, and challenges of organic electronics. It will continue with a more detailed overview of the state of polymer photovoltaics, and will conclude with a brief description of related work being performed in the Ade research group.
Mar 27
Todd Chadwick (NSCU Physics: Hallen Lab)
Some Findings in the Utility of the Resonance Raman Effect
ABSTRACT: Presentation of some preliminary observations in ultraviolet resonance Raman spectroscopy will be outlined. Current research in resonance Raman spectroscopy is largely focused on visible and infrared spectrum, however some great potentials are available with probing in the shorter wavelengths. There will be a brief coverage of what the resonance Raman effect is and what makes the resonance enhancement a useful tool. Observations of these enhancements in benzene and toluene will be discussed as well as potential applications of this new technique to different fields.
Apr 3
Christopher Fecko (UNC Chemistry)
Imaging protein dynamics at transcriptionally active genes
ABSTRACT: Although extensive biochemical and genetic studies have identified proteins that are essential for the transcription of genes, the required movements and interactions of these proteins remain poorly understood. We are investigating the dynamics of RNA polymerase and histone proteins during active transcription with multiphoton imaging of polytene nuclei in live cells. Upon heat shock, we observe the recruitment of RNA polymerase II and simultaneous reduction in histone H2B density at activated hsp70 gene loci in real time. I will present experimental results that support protein recycling as a mechanism for efficient transcription, and will describe efforts that are underway to probe chromatin dynamics during transcription.
Host: Robert Riehn
Apr 17
Laura Clarke (NCSU Physics)
Observing rotational dynamics within self-assembled monolayers via sensitive dielectric spectroscopy
ABSTRACT: In this talk, I'll discuss the motivation to study dipolar phase transitions in two-dimensions and our work in observing molecular motion in self-assembled monolayers towards this end. I plan the talk as an introduction to these topics, with plenty of time for discussion. I'll also discuss our primary technique, surface-sensitive dielectric spectroscopy, and our recent results on rotational motion within alkylsilanes.
April 24
Ryohei Yasuda (Duke Neurobiology)
Imaging signal transduction in single synapses
ABSTRACT:
The activity dependent regulation of synaptic strength and the formation and retraction of synapses is believed to underlie learning and memory. Calcium influx into dendritic spines, tiny (~0.1 femtoliter) postsynaptic compartments, activates signaling networks composed of tens of molecules to regulate synaptic strength. However, a quantitative understanding of how calcium levels are translated into the spatial and temporal patterns of biochemical reactions which modify synaptic strength remains elusive. Identifying and following the spatiotemporal activation of the molecules necessary for synaptic plasticity will further our understanding of this complex process.
To achieve this goal, we have developed a technique to image biochemical signaling in individual spines. Signaling activity can be visualized using fluorescent resonance energy transfer (FRET)-based sensors that probe protein-protein interactions. FRET occurs when two fluorophores are in close proximity (~5 nm), such that the excited donor fluorophore transfers energy to the acceptor fluorophore. As a quantitative readout of FRET, we use fluorescence lifetime, the time elapsed between fluorophore excitation and photon emission. The fluorescence lifetime of the donor decreases as FRET efficiency increases, and is independent of the fluorophore concentration or the wavelength-dependent light scattering. To measure the fluorescence lifetime with high spatial resolution and sensitivity in light scattering brain tissue, we combined fluorescence lifetime measurements with two-photon microscopy (2-photon fluorescence lifetime imaging microscopy or 2-photon FLIM). We further combined 2-photon glutamate uncaging with 2-photon FLIM to measure signaling activity in response to specific patterns of [Ca2+] influx at the level of a single spine.
Using these techniques, we studied the spatiotemporal patterns of the GTPase Ras and Ca2+ calmodulin kinase II (CaMKII) following stimulation of individual spines. Under a condition where NMDA-type glutamate receptors are strongly stimulated, we observed the enlargement of the stimulated spines and increases in the number of glutamate receptors at the synapse. This functional and structural plasticity is specific to the stimulated spine, and lasts more than 1 hour. The same stimulation produced Ras activation in the stimulated spine, which spread into dendrites and nearby spines. In contrast, CaMKII activity was restricted to the stimulated spines. Pharmacological studies suggest that the CaMKII and Ras signaling pathways act together to produce synaptic plasticity. Thus, while Ras activity is diffuse, the combination of spine specific CaMKII signaling and non-specific Ras signaling causes the spine-specificity of synaptic plasticity.
Host: Robert Riehn