Colloquia Archive: 2006

Friday, January 13th, 2006, 11:00am

Ozan Oktem, Sidec Technologies AB
Electron tomography. A short overview of methods and challenges.
Location: Physics 149

Already in 1968 one recognized that the transmission electron microscope could be used in a tomographic setting as a tool for structure determination of macromolecules. However, its usage in mainstream structural biology has been limited and the reason is mostly due to the incomplete data problems that leads to severe ill-posedness of the inverse problem. Despite these problems its importance is beginning to increase, especially in drug discovery. In order to understand the difficulties of electron tomography one needs to properly formulate the forward problem that models the measured intensity in the microscope. The electron-specimen interaction is modeled as a diffraction tomography problem and the picture is completed by adding a description of the optical system of the transmission electron microscope. For weakly scattering specimens one can further simplify the forward model by employing the first order Born approximation which enables us to explicitly express the forward operator in terms of the propagation operator from diffraction tomography acting on the specimen convolved with a point spread function, derived from the optics in the microscope. We next turn to the algorithmic and mathematical difficulties that one faces in dealing with the resulting inverse problem, especially the incomplete data problems that leads to severe ill-posedness. Even though we briefly mention single particle methods, our focus is will be on electron tomography of general weakly scattering specimens and we mention some of the progress that has been made in the field. Finally, if time permits, we provide some examples of reconstructions from electron tomography and demonstrate some of the biological interpretations that one can make.

Friday, January 27th, 2006, 3:00pm

Saikat Ray Majumder, Ph.D., Defense Colloquium , University of Wisconsin-Milwaukee
Location: Physics 135

The existence of gravitational waves is predicted by Einstein's theory of general relativity and yet their direct observation remains elusive. The Laser Interferometer Gravitational-wave Observatory (LIGO), an ambitious experimental effort to directly measure the effects of gravitational waves, is now operating at design sensitivity. I will discuss the basic properties of gravitational waves and give a brief overview of the operations and the science related to LIGO. Binary black hole (BBH) coalescences are expected to be one of the most important sources of gravitational radiation detectable by the terrestrial interferometric detectors. LIGO is sensitive to waves from the slow inspiral and the highly dynamic merger phases of the binary evolution. I will describe a methodology which has been used to search for inspiral and merger signals in LIGO data highlighting several issues which arise in the implementation on real data.

Friday, February 10, 2006, 3:00pm

Saikat Ray Majumder, Ph.D., Defense Colloquium , University of Wisconsin-Milwaukee
Short talks by UWM Physics faculty
Location: Physics 135

SERIES-06-1. Schedule for Friday, Feb 10 Room PHY 135 2:45-3:00: Coffee, tea, cookies. 3:00-3:20: JOHN FRIEDMAN: “Research in relativistic astrophysics”, 3:20-3:40: PAUL LYMAN: “Exploring surface structure with synchrotron x-ray scattering”, 3:40-4:00: SARAH PATCH: “Image Reconstruction and other Inverse Problems”. 4:00-4:15: further questions/discusions.

Friday, February 17, 2006, 3:00pm

Dr. Sarah Patch, University of Wisconsin-Milwaukee
Reconstructing Medical Images – “Cat” scans vs. MRI & how to handle squirmy patients
Location: Physics 135

We begin by exploring the differences between MR & CT data – and the differences in final reconstructed images. Next, we examine artifacts suffered by all MR scans, such as Gibbs ringing which results from sampling over only a finite region of k-space. k-space apodization reduces ringing artifacts. Next we consider spiral scanning, one of several non-Cartesian data acquisition schemes, and examine the process by which k-space data sampled on a non-Cartesian set of points are resampled onto a Cartesian lattice suitable for inversion via Fas Fourier Transform. Why this process works especially well for MRI data and how it can fail are discussed. Finally, we consider Propeller, a relatively new hybrid technique. Propeller fills Fourier space by sampling multiple rotated Cartesian data sets using fast spin echo (FSE), a standard – and slow – acquisition scheme. Acquisition is further slowed because by resampling the center of k- space many times over. Propeller's effective temporal resolution is improved by exploiting relationships amongst the redundant measurements to minimize motion artifacts.

Friday, February 24, 2006, 3:00pm

William Poyser, University of Wisconsin-Milwaukee
Weizsacker-Williams and Evaporation Methods Applied to
Location: Physics 135

Weizsacker-Williams and Evaporation Methods Applied to Calculate Single Nucleon Emission Double Differential Cross Sections for Relativistic Heavy Ion-Ion Interactions This talk will introduce the Weizsacker-Williams (WW) virtual photon method as it is applied to relativistic peripheral ion-ion interactions. The WW method is used to calculate approximate cross sections for Coulomb induced nuclear reactions. It can be used to extrapolate reactions based upon lower energy laboratory real photon reaction data and extremely energetic heavy ion cosmic ray interactions with any target of interest. The application will be for the secondary emission of a single neutron or proton from the projectile ion. This talk includes a brief review of the necessary nuclear physics of the giant dipole resonance (GDR) by photon excitation. The GDR is a collective vibrational mode common to all nuclei at relatively low excitation energy. Also reviewed is the way the GDR can de-excite through and evaporation mechanism releasing light particles. In heavy ions A > 100 this is primarily through neutron emission. And in light ions A < 40 primarily direct emission protons or neutrons. The goal is to couple the WW method with the statistical evaporation method of Weisskopf and an appropriate angular distribution to construct the WW emission double differential cross section (DDCS) for the projectile ion secondary emission of a neutron or proton. The WWDDCS will be shown in the projectile frame and Lorentz transformed to the laboratory frame. In the laboratory frame all emissions are confined to the forward cone along the straight line projectile trajectory. These emissions are boosted to high energy with very small polar angles in the laboratory.

Friday, March 3, 2006, 3:00pm

Professor Mark Schlossman, University of Illinois at Chicago
New Developments in Liquid Interfacial Nanoscience
Location: Physics 135

Liquid interfaces play an important role in many chemical and biological systems in addition to being interesting model systems to study the statistical physics of interfaces and membranes. As examples, water-oil interfaces are a model for the interaction of water with a hydrophobic molecular environment, important for protein folding and the formation of structures in complex fluids. Also, biological membranes exist at the interface between two aqueous regions and provide a dynamic platform for important cell processes. X-ray scattering measurements of liquid interfaces allow for the study of ordering and fluctuations on the nanometer length scale. We will discuss thermally driven fluctuations of liquid interfaces, ordering and phase transitions in a single layer of molecules located at the interface between two bulk liquids, and the use of liquid-liquid interfaces to determine the interactions of ions in liquids.

Friday, March 17, 2006, 3:00pm

Dr. Jim Hyde, Medical College of Wisconsin
Finite-Element Modeling of Fields in Loop-Gap Resonators
Location: Physics 135

Loop-gap resonators (LGR) were introduced into electron paramagnetic resonance (EPR) from the perspective of lumped circuits (i.e., recognizable R, L and C elements in the microwave circuit)[1]. Finite-element models of electromagnetic fields in LGRs do not require this approximation, resulting in a number of new insights. In the case of aqueous samples, some of these insights arise from a rigorous treatment of the dielectric properties of water. Two favorable geometries for aqueous samples have been defined: when the rf electric field is perpendicular to the aqueous surface, and when the sample lies in a node where the rf electric field is zero. For a cylindrical sample in a cylindrical loop of an LGR, the first condition is automatically satisfied because the rf electric field must be perpendicular to the conducting surface. This is one of the benefits of LGRs. There are additional benefits: 1) We have found that the loops can be surprisingly long – of the order of one to two wavelengths or more. In these long LGRs, the field is uniform over the sample, which permits larger amounts of aqueous sample to be used. 2) Very small LGRs can be built at, for example, W-band, with extremely narrow gaps and loops as small as 50 microns in diameter. And 3), LGRs can be designed in which the concentration-sensitivity is competitive with cavity resonators and the benefit of the design is high bandwidth, which is advantageous for pulse EPR.

Friday, March 31, 2006, 3:00pm

Professor Frans Pretorius, Princeton University
Simulation of Binary Black Hole Mergers
Location: Physics 135

The collision of two black holes is thought to be one of the most energetic events in the universe, emitting in gravitational waves as much as 5-10% of the rest mass energy of the black holes. An international effort is presently underway to detect gravitational waves from black hole collisions and other cataclysmic events in the universe. The early success of the detectors will rely on the matched filtering technique to extract what are, by the time the waves reach earth, very weak distortions in the local geometry of space and time. In the case of binary black hole mergers, obtaining the predicted waveforms for use in matched filters requires numerical solution of the merger process during the final stages of the collision. In this talk I will describe the computational challenges in simulating black holes within the framework of Einstein's theory of general relativity, and present results form recent successful simulations of black hole coalescence.

Tuesday, April 4, 2006, 3:00pm

Dr. Iosif Bena, Institute for Advanced Study, Princeton University
String Theory, QCD and Black Holes
Location: Physics 133

I will discuss how to use string theory to understand confining gauge theories, how to approach asymptotically free theories like QCD using integrability, and how to find N=4, N=1 and QCD tree-level and one-loop amplitudes using twistors and recursion. In the second part of the colloquium I intend to discuss some recent work on black holes, which indicates that black holes should be viewed as ensembles of smooth horizon-less geometries. I will also hint at some possible consequences of this pictures for LISA and for black holes at colliders.

Thursday, April 6, 2006, 3:00pm

Dr. Matthew Headrick, M.I.T.
The Shape of the Extra Dimensions
Location: Physics 135

String theory posits the existence of six extra dimensions of space, curled up into a microscopic manifold. In order to make predictions from the theory it is necessary to know the geometry of these extra dimensions. Unfortunately, the equations governing this geometry (among them the Einstein equation of General Relativity) are too complicated to solve analytically. In this talk I will describe a numerical method, exploiting the magic of supersymmetry, that was recently developed for this problem and has yielded the first explicit solutions. No prior knowledge of string theory or supersymmetry will be assumed.

Friday, April 7, 2006, 3:00pm

Dr. Jeff Weeks, Princeton University
Topological imprints on the microwave sky (Joint with Dept. Math)
Location: Physics 135

Spheres pervade the study of cosmic topology. At the most basic level, the sky is a 2-sphere. An elementary pictorial introduction to spherical harmonics lets one quantify the observed fluctuations on the microwave sky and – most importantly – compare them to theoretical expectations. The COBE and WMAP satellites found the broadest fluctuations to be far weaker than expected in an infinite Euclidean space, leading researchers to consider other candidates for the topology and geometry of the universe. Candidates based on a 3-sphere best fit the observed microwave sky. Where do these candidates come from? Their structure “lifts up” from the 2-sphere! How do we find their harmonics? Their harmonics lift up from the 2-sphere too! While it's premature to draw conclusions about the exact topology of space, an elementary argument shows that if the topological explanation for the weak broad-scale fluctuations is correct, the data favor a well-proportioned universe, that is, a universe whose three dimensions are of comparable size.

Wednesday, April 12, 2006, 3:00pm

Dr. Luis Anchordoqui, Physics Dept., Northeastern University
Exploring the Universe Beyond the Photon Window
Location: Physics 133

In this talk I will overview the present status of neutrino telescopes and delineate the prospects to identify cosmic ray accelerators that are high energy neutrino emitters. I will also discuss the potential of neutrino telescopes to probe new ideas in particle physics.Friday, April 14, 2006

Friday, April 14, 2006, 3:00pm

Dr. Virginijus Barza, University of Toronto, Canada
How muscles work: A glimpse into the muscle cells with non-linear microscopy
Location: Physics 135

Contraction of muscles brings static bio-world to life. Muscle contraction is a very complex event during which thousands of stepper nano-motors move in unison to produce macro-contraction. Synchronization of stepper motors occurs via ion fluxes and waves. The energy source that fuels contraction has to work in harmony with the nano-motors to keep up with the energy consumption. Large part of the machinery can be visualized and investigated with novel tools of non-linear microscopy. Investigations of muscle nano-contractions with optical harmonic generation microscopy will be presented and latest findings on the physical mechanisms of contractility will be overviewed.

Monday, April 17, 2006, 3:00pm

Dr. Howard Baer, Florida State University
Supersymmetric Dark Matter: Direct, Indirect and Collider Searches
Location: Physics 133

Supersymmetry is a highly motivated extension of the group of spacetime symmetries which forms one of the foundations of relativistic quantum field theory. The supersymmetrized version of the Standard Model provides a candidate particle– the lightest neutralino–which may account for cold dark matter (CDM) in the universe. I describe the various theoretical and experimental issues involved in the search for neutralino dark matter. A bevy of direct and indirect CDM search experiments have been or will soon be deployed. In addition, the CERN LHC, to begin operation in 2007, could turn out to be a CDM factory. Thus, colliding beam experiments have the ability to shed light on cold dark matter.

Friday, April 21, 2006, 3:00pm

Professor Marija Gajdardziska-Josifovska, University of Wisconsin-Milwaukee
Polar Oxide Surfaces, Interfaces and Nanostructures
Location: Physics 135

The question of the stability of polar interfaces is closely related to that of polar surfaces of ionic solids: the apparent presence of electric dipole moments in the unit cell perpendicular to the surface/interface leads to an electrostatic instability. These effects have been studied most extensively in compound semiconductors and more recently in the more ionic insulating oxides. The previously established view that polar oxide surfaces facet into neutral faces, while surface reconstructions stabilize the compound semiconductor polar surfaces, has been altered with discoveries of reconstruction stabilized polar oxide surfaces. I will briefly review the oxide surface faceting and reconstruction mechanisms to set the stage for our most recent work on hydrogen stabilization of unreconstructed polar surface, and in-situ environmental transmission electron microscopy studies on interactions of oxide surfaces with water. Our newest line of research is designed to explore if and how the oxide surface polarity can affect the epitaxial growth of polar oxide and nitride films with applications in spintronics and photonics. We combine atomic resolution electron microscopy with density functional theory to elucidate the atomic and electronic structure of these novel polar nanostructures and to develop fundamental understanding of polar interface stabilization.

Friday, May 5, 2006, 3:00pm

Dr. Anjum Ansari, University of Illinois at Chicago
Dynamics of Protein-DNA Interactions probed with
Location: Physics 135

Regulation of gene transcription involves formation of protein-DNA complexes in which specific proteins kink, bend or curve DNA. Sharply bent DNA is also critical for the packaging of DNA inside the cell. In many protein-DNA complexes, the protein also undergoes extensive conformational rearrangements to facilitate favorable interactions with DNA. These concerted changes in proteins and DNA are believed to be a key feature underlying the induced-fit mechanism proposed for the recognition of specific binding sites on the DNA by the proteins. An understanding of the forces that are responsible for the sharp bending of DNA and protein rearrangements to form specific complexes are thus of considerable biological significance. To elucidate the molecular mechanism, it is essential to study the dynamics of the conformational rearrangements that lead to the precise recognition. These dynamics occur on submillisecond time-scales, making them difficult to capture with conventional stopped-flow techniques. We use laser temperature-jump, combined with time-resolved fluorescence resonance energy transfer (FRET), to probe the dynamics of DNA bending/unbending in protein-DNA complexes, and to investigate the role of the flexibility and “bendability” of DNA in interactions with DNA-bending proteins.

Friday, May 12, 2006, 3:00pm

Michael J. Bedzyk, Department of Materials Science and Engineering, Northwestern University
X-Ray Standing Wave Imaging of Atoms At Interfaces
Location: Physics 135

Using conventional X-ray standing wave (XSW) analysis (based on single-crystal Bragg diffraction), the hkl Fourier component for a x-ray fluorescence-selected atomic species is measured. By summing together several such hkl Fourier components, it is possible to directly generate a 3D, direct-space, 0.5 resolution, image of the atomic distribution with respect to the bulk crystal primitive unit cell. We have recently demonstrated this for the cases of bulk impurity atoms [1], cations adsorbed at the aqueous / oxide interface [2], metallic atoms at semiconductor surfaces [3], and oxide supported catalysts. This new model-independent XSW imaging approach proves to be very insightful for complex cases in which atoms occupy unknown multiple crystallographic sites. In comparison to direct-methods based on conventional diffraction, the Fourier inversion process for generating an XSW image is much simpler, since the hkl phase (as well as amplitude) of each Fourier component is directly measured. Based on these model-independent XSW atomic images, we then develop models to refine the data analysis into 0.05 resolved atomic lattice positions that are used to measure effects such as strain. In separate XPS measurements, we correlate this structural information with the chemical state of the adsorbed species. We are now applying this method to ALD and MBE grown oxide/oxide and oxide/semiconductor heteroepitaxial structures and observing how the atoms at the interface redistribute after oxidation and reduction processes. We are also studying the atomic-scale and nano-scale structure of metal nanocrystals grown on oxide surfaces. [1] L. Cheng, P. Fenter, M. J. Bedzyk, N. C. Sturchio, Phys. Rev. Lett. 90, 255503-1 (2003). [2] Z. Zhang, P. Fenter, L. Cheng, N. C. Sturchio, M. J. Bedzyk, M. L. Machesky, D. J. Wesolowski, Surf. Sci. Lett., 554(2-3) L95 (2004). [3] A.A. Escuadro, D.M. Goodner, J.S. Okasinski, M.J. Bedzyk, Phys. Rev. B, 70 235416-1-7 (2004).

Tuesday, May 16, 2006, 3:00pm

Dr. Jeffrey Wesson, Kidney Disease Center of the Division of Medicine
Crystal Surface Interactions and Kidney Stones
Location: Physics 135

Kidney stones form as aggregates of crystals, most frequently calcium oxalate phases, with various organic materials, and they cause severely debilitating pain episodes intermittently in about 10% of people in the United States. Despite decades of research on the disease, the cause has yet to be defined, though it is widely believed that alterations in soluble macromolecules or cell surfaces lead to stone aggregate formation in affected individuals. Clearly, the process is controlled by interactions between the organic materials and various crystal surfaces, and we have been studying these interactions using a combination of bulk crystallization methods and atomic force microscopy. I will summarize some our key results, which have defined some of the critical structural features in the organic phase that regulate crystal formation and aggregation processes. In this summary, I also hope to illustrate the utility of using the materials science characterization to identify the cause of a significant disease process and the potential for a future cure.

Friday, May 26, 2006, 3:00pm

Michael Kosempa, UW-Milwaukee Physics Undergraduate Colloquium
Detecting Proteins on Yeast Cell Membranes by Study of Dielectric Properties
Location: Physics 135

Proteins are essential to the structure and function of all living cells. Knowing that dielectric properties are determined by morphological structure, we use impedance spectroscopy to characterize cell structure. Results from recent experiments on yeast cells will be presented. Acknowledgements: work performed with the group of Prof. V. Raicu.

Tuesday, May 30, 2006, 3:00pm

Brian Eichman, UW-Milwaukee Physics Undergraduate Colloquium
Zero Point Energy and the Casimir Effect
Location: Physics 135

Quantum Field Theory (QFT) assumes that each point of a field, such as the electric and magnetic fields, can be treated as a quantum system — usually as a quantum harmonic oscillator. Because of the non-zero energy of a quantum harmonic oscillator in its ground state, we can create an expression for the energy density of the vacuum fluctuation of EM fields. This expression shows us that their might be an extremely large amount of energy in the vacuum, and natural questions arise: How do we verify this result? Can we exploit this energy? A novel experiment to verify this result was designed by Hendirk Casimir. His idea was to restrict the number of possible modes of the EM field in between two conducting plates. This restriction would decrease the energy density in between the plates, but not in the region outside. Using very simple calculations, he created an expression for the force per unit area experienced by the plates, due to the vacuum energy. Later experiments have confirmed this result, and have also started the discussion about exploiting this energy.

Wednesday, June 7, 2006, 3:00pm

Raminder P. Kaur, UW-Milwaukee Physics Ph.D. Colloquium
Superconductivity and Broken Time Reversal / Inversion Symmetry
Location: Physics 135

Broken symmetries can lead to exciting new physical ground states: for example, conventional superconductivity is the result of broken gauge symmetry. In the ordinary Bardeen-Cooper-Schrieffer theory of superconductivity, Cooper pairs are formed from quasiparticle states with opposite spin and momenta near the Fermi surface. This requires degeneracy of the quasiparticle states under time reversal and inversion symmetries. In this talk, I will discuss the symmetry, and the physical consequences of the absence of time reversal and inversion symmetries on the superconducting ground state.

Friday, June 23, 2006, 3:00pm

Tarisa Lerro, UW-Milwaukee Physics Undergraduate Colloquium
The Inertia Tensor for a 3-D Rigid Body
Location: Physics 135

After a brief overview of tensor analysis, the inertia tensor will be derived by manipulating the expression for angular momentum. By examining the matrix of components of the inertia tensor (“inertia matrix” with respect to an arbitrary Cartesian coordinate system, the inertia tensor is shown to be symmetric. Every rigid body, therefore, has a set of principal coordinates — three orthogonal axes that coincide with the eigenvectors of the inertia tensor; off-diagonal terms in the inertia matrix, with respect to the principal coordinates, are zero. The presence of symmetry provides further conditions that render off-diagonal terms zero. Some surprising results will be demonstrated, both with mathematics and corresponding physical models.

Friday, September 8, 2006, 2:30pm

Professor Jayanth R.Banavar, Pennsylvania State University
Geometry and Physics of Proteins
Location: Physics 135

A framework is presented for understanding the common character of proteins. It is shown that the notion of a tube of non-zero thickness allows one to bridge the conventional compact polymer phase with a novel phase employed by Nature to house biomolecular structures. We build on the idea that a non-singular continuum description of a tube of arbitrary thickness entails discarding pairwise interactions and using appropriately chosen many body interactions. We suggest that the structures of folded proteins are selected based on geometrical considerations and are poised at the edge of compaction, thus accounting for their versatility and flexibility. We present an explanation for why helices and sheets are the building blocks of protein structures.

Friday, September 15, 2006, 3:00pm

F. Alberto Grunbaum, UC-Berkeley Math Department
The Phase Problem in Crystallography and the Use of Higher Order Invariants
Location: Physics 135

The phase problem in question arises in trying to determine the tree-dimensional structure of a unit cell in a crystal from X-ray diffraction data, a subject that starts with the Braggs (father and son). I will give a historical talk starting with the role of the mineral bixbyte in the consideration of the phase problem as a serious mathematical problem in crystallography. The role of L. Pauling and L. Patterson will be part of the story. The use of higher order invariants, in the fashion of Hauptman and Karle will be seen to provide a mathematically satisfactory solution. How far this is from a real life solution of the problem remains an interesting challenge.

Friday, September 22, 2006, 3:00pm

Abhay Ashtekar, Director, Institute for Gravitational Physics & Geometry, Penn State University
Quantum Nature of the Big Bang
Location: Physics 135

According to general relativity, space-time ends at singularities and classical physics just stops. In particular, the big bang is regarded as The Beginning. However, general relativity is incomplete because it ignores quantum effects. Through simple models, I will illustrate how the quantum nature of space-time geometry sheds entirely new light on the nature of the big bang. Quantum physics does not stop there. Quantum geometry in the deep Planck regime can serve as a bridge to another, vast classical space-time.

Friday, September 29, 2006, 3:00pm

Rohit Bhargava, Dept. of Bioengineering and Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign
Microstructures in a New Light: Chemical imaging in the mid-infrared spectral region
Location: Physics 135

Fourier transform infrared (FTIR) spectroscopic imaging is an emerging approach that combines the spatial selectivity of microscopy with the molecular specificity of vibrational spectroscopy. Following the civilian availability of array detector technology, we have modeled and implemented several ideas to provide rapid infrared imaging data. Applications have focused on three specific areas: automating human cancer diagnosis, studying macromolecular dynamics in composites and providing novel forensic capabilities. Traditionally, cancer diagnoses are based on optical examinations of stained tissue and involve a skilled recognition of morphological patterns of specific cell types (Histopathology). Consequently, histopathologic determinations are a time consuming, subjective process with innate intra- and inter-operator variability. Utilizing endogenous molecular contrast inherent in vibrational spectra, high throughput infrared imaging of designed tissue microarrays and pattern recognition of the recorded spatially-specific spectra yields automated classifications. The developed protocol is objective, statistically significant and, being compatible with current tissue processing procedures, holds potential for routine clinical diagnoses. We present the application of the concept to detection and grading of prostate cancer in biopsies. While FTIR spectroscopic imaging approaches have proven valuable in analyzing static samples, they are limited in the ability to observe dynamic events in real time. Emerging fast imaging data acquisition allows monitoring transient events, including polymer-solvent diffusion and transitions in polymer crystallization, occurring over a time scale of seconds. For repeatable molecular dynamics in heterogeneous composites, a time-resolved implementation provides complete spatial, spectral and temporal characterization with millisecond temporal resolution. Molecular and structural transitions are visualized using time-resolved imaging to monitor switching in electro-optical polymer-liquid crystal composites. Finally, we demonstrate the utility of FTIR spectroscopic imaging in forensic investigations, where the presence and identity of trace evidence contained within latent fingerprints is determined.

Friday, October 6, 2006, 3:00pm

Professor Patrick J. LaRiviere, University of Chicago, Dept. of Radiology
Development of Molecular Probes and Acoustic Attenuation Correction Schemes for Optoacoustic Tomography
Location: Physics 135

Optoacoustic tomography (OAT) is an emerging biomedical imaging modality that involves exposing a sample to pulses of electromagnetic radiation that cause small amounts of heating in the specimen. The heating engenders thermal expansion that, in turn, gives rise to acoustic waves. The resulting acoustic pressure signal is generally measured by transducers arrayed around the object and these data may be used to reconstruct images of the original electromagnetic absorption. In this talk, we will describe two projects we are pursuing in OAT. The first project, in collaboration with Mark Anastasio at the Illinois Institute of Technology, seeks to model and correct for the effects of acoustic attenuation during image reconstruction. Most treatments of the OAT inverse problem assume an idealized, uniform, non-dissipative acoustic medium. The problem of a dissipative medium, in which the acoustic waves are attenuated as they travel, has not been addressed, to our knowledge. The effect is potentially significant because OAT relies on broadband detection and ultrasonic attenuation is frequency-dependent, which can produce distortion of the optoacoustic signal and thus blurring and artifacts in reconstructed images. We have recently shown how to incorporate the effect of uniform attenuation into the optoacoustic wave equation and developed a method to correct for it during image reconstruction. The second project, in collaboration with James Norris of the University of Chicago Chemistry department, involves developing injectable molecular contrast agents for OAT that are sensitive to protease overexpression. Proteases are protein-cleaving proteins known to be overactive in a number of pathologies, including cancers and vascular disease. We are developing a molecule that absorbs strongly in the near infrared and that shifts its absorption peak when cleaved by a protease of interest. The molecule comprises two active sites, derivatives of natural photosynthetic bacteriochlorophylls that absorb in the near IR, conjugated to a lysine backbone by peptide spacers specific to the protease being imaged. When these bacteriochlorophylls dimerize and stack in the uncleaved molecule, their absorption peak shifts about 20-30 nm. When they are cleaved from the molecule the absorption peak shifts back to that of bacteriochlorophyll monomers. We have performed a preliminary synthesis of the molecule and confirmed by use of a spectrometer that the pairing of the bacteriochlorophylls leads to the expected absorption shift.

Friday, 13 October, 2006, 3:00pm

Luis Anchordoqui, Asst. Professor, University of Wisconsin-Milwaukee
Hunting Black Holes at the LHC
Location: Physics 135

Black hole production in elementary particle collisions is among the most promising probes of large extra spacetime dimensions. I will review the properties of such black holes and present estimates of their production rate at particle colliders incorporating the effects of inelasticity (i.e., energy radiated in gravitational waves by the multipole moments of the incoming shock waves). I will also discuss the prospects for discovering black holes at the LHC

Friday, October 20, 2006, 3:00pm

Felix T. Hong, Dept. of Physiology, Wayne State University
Absolute Physical Determinism and Its Conflict with the Notion of Free Will
Location: Physics 135

The conflict between physical determinism and free will was an old problem, perhaps dated back to the time of St. Augustine. The basic argument is simple and transparent. If we had free will, and if physics prescribes an absolutely deterministic position and momentum for each and every molecule, then we ought to be able to alter events that took place long before our birth. The advent of quantum mechanics along with the uncertainty principle provided a relief, and Heisenberg was once hailed as the hero who freed us from the bondage of physical determinism. Yet, Schrodinger put a stop to the claim by a counterclaim that indeterminism does not enter biology, in his famous 1945 book “What is Life?” He even explicitly said that free will is an illusion in a 1936 Nature article. On the other hand, the famous “Boltzmann-Zermelo” controversy seemed to have settled by a hand-waving argument, which managed to reconcile the paradox of macroscopic irreversibility and microscopic reversibility. Einstein, a strong believer of deterministic physics, even said, “Time is an illusion.” But in the course of teaching freshmen physiology, the speaker found it extremely odd for Nature to recruit “noise” – ion channel fluctuation – for the fundamental process of nerve excitation, perhaps the most crucial step in executing freedom of action. However, one readily recalled a remark made by Laplace, who had apparently been thoroughly impressed with the successful prediction of the 1759 return of Halley's Comet. He asserted that any belief that an event can be completely random and follow no deterministic natural laws is simply due to our ignorance of the cause. However, in a casual debate with a computer science student, the speaker accidentally found that Laplace's claim can neither be proven nor disproven, and, therefore, it was Laplace's epistemological choice rather than a scientific fact. Again, by virtue of serendipity, the speaker stumbled upon a simple one-page proof that absolutely deterministic physics is irreconcilably incompatible with statistical physics. The proof was based on simple probability argument. It is, therefore, almost impossible for the speaker to have inadvertently inserted mathematical or logic tricks for the purpose of [unconscious] self-deception. That is, if we are willing to accept macroscopic irreversibility as an irrefutable common human experience, then deterministic physics as well as microscopic irreversibility is just an approximation, a very good approximation nevertheless. The speaker suspected that Boltzmann himself might have stumbled upon this simple proof, thus precipitating his 1906 suicide. After all, Zermelo (as well as Poincar&eacute;) was right. But the verdict brought about a strange irony. Boltzmann became the first hero who had freed us from the tyranny of deterministic physics, even though he had vehemently denied this role, and perhaps had died for it out of sheer despair (according to Karl Popper).

Wednesday, October 25, 2006, 3:00pm

Professor So Nishikawa, Osaka University – Osaka, Japan
Single Bio-Molecule Motor Measurements Recent Developments
Location: Physics 135

All living organisms contain nano-machines: biomolecular motor proteins. We believe that exploring the unique operation of motor proteins will be the fastest path to the successful development of useful nanoscale devices. Biomolecular motor proteins are of nanometer size and are thus subject to Brownian motion. Such thermal effects become significant when the size of the particles becomes small. Thermal energy makes many processes stochastic and influences the protein's dynamics. Further, many motor proteins run on energy liberated from the hydrolysis of ATP (adenosine triphosphate). This input energy level is only 20 times that of thermal energy while artificial and macroscopic machines which have input energy levels many orders of magnitude higher. Indeed, machines created by mankind are designed to work without disturbance from thermal noise. Motor proteins, however, are able to perform their functions effectively without being disturbed by thermal noise. How do proteins accomplish this task? To address this question, we have directly observed the dynamic behavior of biomolecular motor proteins using single molecule detection (SMD) technology. Before SMD was available, protein f unction s were examined using ensemble measurements from large n umbers of molecules. The data were averaged over millions of molecules and stochastic processes and dynamic properties were hidden and obscured. The direct measurements of proteins' dynamic functions are only possible through SMD techniques.

Friday, October 27, 2006, 4:00pm

Anne Kenworthy, Dept. of Molecular Physiology and Biophysics, Vanderbilt University School of Medicine
The Search for Lipid Rafts: Chasing a Moving Target
Location: Physics 135

One of the most hotly debated areas in membrane biology is the structure and function of a class of membrane microdomains commonly referred to as lipid rafts. The lipid raft model invokes a critical role for cholesterol in generating liquid-ordered and liquid-disordered domains in membranes, which in turn are thought to organize proteins into functional complexes. The biological functions attributed to lipid rafts are many, including regulation of signal transduction, membrane trafficking, and pathogen entry and exit from cells. However, native lipid rafts have proven to be notoriously difficult to study, leading to the need for increasingly sophisticated approaches to probe their structure, composition, and dynamics in the context of living cells. I will discuss experiments from our laboratory which seek to “pin down” the nature of these domains, using a combination of experimental approaches sensitive to protein and lipid diffusion and inter-molecular distances in conjunction with mathematical modeling. Through these studies, we hope to gain a better understanding of the role lipid rafts play (or not) in regulating membrane architecture, protein and lipid dynamics, and cell membrane function.

Friday, November 3, 2006, 3:00pm

Professor Abbas Ourmazd, University of Wisconsin-Milwaukee
Crystallography Without Crystals: Determining the Structure of Biological Molecules
Location: Physics 135

The function of a biological molecule is determined by its atomic structure. Although NMR provides valuable insight into relative atomic positions, crystallography has been the technique of choice for determining the atomic structure of biomolecules. However, roughly 40% of all biomolecules do not crystallize, among them many membrane proteins, whose atomic structure is key to their function. Determining the structure of individual biomolecules is “tantalizingly close.” I will review some of the challenges. * In collaboration with Dilano Saldin and Valentin Shneerson

Friday, November 17, 2006, 3:00pm

Frank Vogt, Dept. of Chemistry, University of Tennessee
Advancing from Environmental Spectroscopic Sensing Towards 3-Dimensional Spectroscopic Imaging for Studies of Heterogeneous Samples
Location: Physics 135

Optical Spectroscopy is a common tool in analytical chemistry; nonetheless, new approaches are necessary in order to achieve lower limits of detection, to facilitate data evaluation and to probe 3-dimensional samples. The first topic focuses on atmospheric pollution monitoring where weak measurement signals introduce experimental challenges. A technique call UV derivative spectroscopy was developed to suppress non-information containing spectroscopic signatures and to enhance the analyte specific ones. This must be achieved during signal generation, i.e. before signal amplification and analog-to-digital conversion. In order to obtain high selectivity in mixtures this measurement technique was combined with chemometric calibration and data evaluation techniques. Many analytical techniques perform spot analyses and are thus restricted to homogeneous samples when it does not matter which part of the sample is probed. Heterogeneous samples, however, do require chemical sensing at high spatial resolution. For this purpose, spectroscopic imaging has been introduced which equips a spectrometer with a 2-dimensional detector array; two different experimental set-ups will be discussed. One of the challenges encountered in spectroscopic imaging — especially at high spatial and high spectral resolution — is the computational burden during data analysis. Due to large amounts of high-resolution data, computation times are often unacceptable. We have developed a data-compression method, which is based on high-dimensional wavelet transforms. In our examples, this technique can compress the amount of data to less than 1% and still achieves good results; computations were accelerated by up to one order of magnitude. Passive remote classification of different materials by mid-infrared spectroscopy will be used to demonstrate the algorithm's performance. Current research efforts focus on enhancing spectroscopic imaging techniques to facilitate studies of 3-dimensional samples. Augmenting a conventional imaging spectrometer will be discussed and first results will be presented. Anticipated applications include, but are not limited to, microscopic biomedical sensing and quality control in industry. in order to take full advantage of these sensing concepts, novel methodologies in data evaluation are required as well.

Friday, December 1, 2006, 3:00pm

Dan Hooper, Ph.D. and David Schramm Fellow, Theoretical Astrophysics, Fermi National Accelerator Laboratory
The Hunt for Dark Matter
Location: Physics 135

For seventy years, we have had evidence that much of the Universe's mass is non-luminous, but still today we have not identified what makes up this mysteriously dark substance. Many experimental programs that hope to change this are underway, however. Deep underground detectors, gamma-ray telescopes, neutrino and anti-matter detectors, as well as particle colliders, each are searching for clues of dark matter's identity. Possible dark matter candidates include supersymmetric particles or even ordinary particles traveling through extra dimensions of space. With the new technologies needed to observe these particles rapidly developing, the hunt to discover dark matter's identity has now truly begun.