SSE Lunch-time Faculty Research Seminars, Spring 2016

Location: LBC (Rechler 202 or Race 201)
Time: Tuesdays, starting at noon
Format: Two faculty making 20-minute presentations (+10 minutes for questions)
Food: Provided by SSE

January 19, 2016
LBC 201, Race

Bruce Gibb (CHEM): TBA

Lawrence Pratt (CBE): "What Landau did not know about the theory of liquids"
One outlook on the theory of liquids is the judgement of the Preface of early editions of STATISTICAL PHYSICS, L. D. Landau and E. M Lifshitz that "We have not included in this book the various theories of ordinary liquids and of strong solutions, which to us appear neither convincing nor useful." That outlook was widely absorbed and lives today in the common view that "there is no such thing as the theory of liquids." In response, Ben Widom has suggested "Now, a generation later, the situation has been wholly transformed ..." We place Widom's free energy formula, which Landau did not know of, at the center of that transformation. We discuss Widom’s formula and its recent extension as quasi-chemical theory (QCT) that makes it a practical modern approach to the statistical mechanical theory of real liquids. This discussion is arranged on examples including hydration of real ions in solutions of chemical interest, molecular theory of the matrix of life (liquid water), and the concentration dependence of the Flory-Huggins interaction parameter for aqueous solutions of capped polyethylene-oxide oligomers. Along the way, we note recent intrepid QCT studies of hydration of polypeptides at molecular scales.

January 26, 2016 (Start at noon sharp)
LBC 202, Rechler

Walter Lee Murfee (BME): "Watching Cells During Angiogenesis"
Microvascular growth and remodeling are linked to inflammation and multiple pathological conditions, including cancer. The design of molecular-based therapies requires understanding the related cell dynamics. In this presentation, I will introduce a new model platform for tacking cell fate and function in an intact network scenario that matches the complexity of a real tissue. The simplicity and novelty of such a model is that it enables observation of when and where cells go in a network. As one example, I will also share a current project focused on how such a model to generate new insights regarding the use of stem cells to regulate the growth of new blood vessels.

Jiang Wei (PHYS): "Effect of Quantum Confinement on Electron Correlation in Atomically Thin Nb3SiTe6"
The recent breakthroughs in two dimensional (2D) materials, represented by Dirac cone in graphene and large direct bandgaps with spin-valley coupling in transition metal dichalcogenides MX2 (M = Mo or W, X = S, Se) monolayers, highlight the potential that quantum confinement effect on electronic structures may lead to a wide spectrum of distinct properties in 2D atomic layered crystals. On the other hand, the coupling between electrons and phonons provides an alternative approach to tune the electronic properties by quantum confinement effects on phonons. This has been theoretically predicted but not well-supported by earlier experimental investigations. In this work, we reported the clear evidence of the suppression of electron-phonon (e-p) scattering by phonon dimensionality in atomically thin ternary chalcogenide Nb3SiTe6, whose thickness can be thinned down to one unit cell by mechanical exfoliation. Through quantum transport measurements on this new 2D system, we demonstrated that with decreasing thickness, this new 2D system displays surprising enhancement of electron phase coherence due to the weakening of electron-phonon (e-p) scattering. Our analyses imply that such unusual phenomenon originates from the reduction of acoustic phonon populations due to 2D quantum confinement effects on acoustic phonon spectra. We conclude that such long-predicted phonon dimensionality effects, though have never been observed by pervious quantum transport studies, universally exist and can be probed in layered materials.

February 2, 2016
LBC 202, Rechler Julie Albert (CBE): "Thin Film Self-Assembly of Nano- and Micro-structured Polymer Materials"
Nano- and micro-structured materials are important in templating and membrane applications, which require thin films with well-defined morphologies on application-specific length scales (e.g., peptide arrays ~ nm, cell arrays ~ μm). Polymer self-assembly offers a simple route to structure formation that eliminates the need for more complex and time-consuming methods. We access the nanoscale and the microscale with the use of block copolymers and polymer blends, respectively. For our nanostructured block copolymer materials, we are interested in how self-assembly in thin film geometries is affected by film thickness constraints, surface energetics at the substrate and free air interfaces, and the molecular architecture of the block copolymer. Our efforts on the microscale are focused on the thin film morphologies of biocompatible polymer blends. In these blends, one of the polymer components is semi-crystalline, which has led us to study the effect of confinement on crystallization kinetics and crystal morphology. Finally, we are studying how ternary block copolymer-homopoymer blends bridge nano- to micro- length scales in thin film geometries. We aim to apply the materials we develop to cell culture and purification membrane applications.

February 16, 2016
LBC 202, Rechler

Mac Hyman (MATH): "Quantifying the Uncertainty in Large-Scale Simulations"
In addition to providing the most accurate predictions for complex systems, scientists must quantify the uncertainty in these predictions and correlate how the prediction depends upon the assumptions made in the model. I will review some of the approaches used to determine how well a model represents the underlying physical phenomena and to quantify the confidence one can have in the model predictions. Although these questions are natural to ask, they can be hard to formulate and answer in a mathematically well-founded and useful way. I will describe how local sensitivity and global uncertainty analyses can be combined to address situations where the model parameters, initial conditions, and possibly even the mathematical model, are only known approximately.

Sunshine A. Van Bael (EEB): "Plant symbioses with fungi and bacteria"
Symbiotic associations can be disrupted by disturbance or by changing environmental conditions. Endophytes are fungal and bacterial symbionts of plants that can affect their performance. As in more widely known symbioses, acute or chronic stressor exposure might trigger disassociation of endophytes from host plants. Research in my lab addresses hypotheses related to symbioses and environmental disturbance in coastal & wetland plants of the southeastern US, as well as biofuel crop plants growing in the tropics. We use culturing of symbionts and high throughput sequencing to describe endophyte communities and we follow this with experimental work focusing on disturbance and endophyte function in plant communities. Ultimately our goals are to understand the long-term dynamics of plant-symbiont interactions in the face of environmental disturbances, including sea level rise, oil spills, and climate change. Moreover, we seek plant-symbiont combinations that confer stress resilience to plants and that hasten the restoration of degraded land.

March 1, 2016
LBC 202, Rechler

Quincy Brown (BME): TBA

Mark Sulkes (CHEM): "Chemistry of Biomass Pyrolysis: Molecular Beam Approach"
Plant biomass, a precursor to biofuels, constitutes a renewable source of organic carbon compounds. Biofuels generate significantly less greenhouse emissions than fossil fuels and can be greenhouse gas neutral if efficient production methods are developed. The most significant contributor is lignocellulosic (woody) biomass, but triglycerides (triacylglycerols or TGs, i.e. plant oils) may become more important, given the very large acreage yields possible with some algaes. In both instances chemical production methods proceed by pyrolysis processes; a very wide range of possible products and product yields is possible. They key to more viable fuel/organics production is pyrolysis product yields closer to useful fuels—requiring less subsequent refinement. From the view of fundamental chemistry, the way to improve the pyrolysis is to understand the early chemistry that may direct yields towards desirable final products. The classic research approach is to carry out laboratory scale pyrolysis under various conditions and identify/quantitate the extremely numerous (hundreds) of final products. The challenge is then to try to infer the key early chemistry. Cold molecular beams, combined with laser spectroscopies, have been used for years, typically to study selected exotic or novel reactive species, prepared in internally cold and nearly collision free conditions. While still little practiced for these purposes, molecular beam methods offer great utility for the study of very complex product chemistries. Here one has the ability to observe directly, in real time, early products and their evolution into subsequent products. Standard laser spectroscopies allow for mass spectrometric characterization of neutral species by mass; particular classes of products (e.g. aromatics) can be selective detected, to the exclusion of other product classes. We have begun applying these methods to TG pyrolysis. Results so far have confirmed and elaborated some hypotheses that were made more indirectly in the past. A number of additional experiments and technique developments will take place with TG pyrolysis before we begin experiments on lignocellulosic pyrolysis chemistry.

March 8, 2016
LBC 202, Rechler

Brent Venable (CS): "Constraints and preferences in artificial intelligence: examples of interdisciplinary applications"
Preferences and constraints are essential for a system to be called intelligent: they are a key component for a realistic and faithful modeling of the surrounding environment, they are unavoidable for enabling effective and sophisticated interaction, and they lie at the core of the definition and solving of optimization problems. Constraint-based modeling and solving of problems is one of the pillars of artificial intelligence. We will show how it can be applied in the context of cognitive modeling of attention in the auditory system. From a single-agent point of view compact preference models developed by the AI community, such as soft constraints and CP-nets have de facto enabled preferences to be embedded in intelligent systems. We will illustrate how they can be used to design smart artificial companions for supporting users with different types of impairments. As for humans, another fundamental capability for AI agents is collective decision making. To this end, we will describe how results from Economics' voting theory can be applied to societies of artificial agents in order to enable them to aggregate their preferences efficiently and fairly.

Carolyn Bayer (BME): "Functional and Molecular Ultrasound-Guided Photoacoustic Imaging"
My research develops novel medical imaging methods to study the dynamics of molecular expression and physiological function. Medical imaging systems are often optimized to produce images of anatomy. However, anatomical information alone is insufficient for optimal treatment of a disease condition. Imaging the physiological (functional) and biochemical (molecular) properties of the system could provide key information to halt disease progression and growth. We integrate ultrasound and contrast-enhanced photoacoustic imaging systems, develop algorithms for processing functional and molecular photoacoustic images, and evaluate photoacoustic and ultrasound contrast agents to generate new methods of visualizing molecular expression and physiological function. These imaging methods are being applied to the analysis of the functional and molecular environment during the development of birth defects.

March 15, 2016
LBC 202, Rechler

Noshir Pesika (CBE): "Load-Induced Hydrodynamic Lubrication of Porous Polymer Films"
We present an exploratory study of the tribological properties and mechanisms of porous polymer surfaces under applied loads in aqueous media. We show how it is possible to change the lubrication regime from boundary lubrication to hydrodynamic lubrication even at relatively low shearing velocities by the addition of vertical pores to a compliant polymer. It is hypothesized that the compressed, pressurized liquid in the pores produces a repulsive hydrodynamic force as it extrudes from the pores. The presence of the fluid between two shearing surfaces results in low coefficients of friction (μ≈0.31). The coefficient of friction is reduced further by using a boundary lubricant. The tribological properties are studied for a range of applied loads and shear velocities to demonstrate the potential applications of such materials in total joint replacement devices.

Scott Grayson (CHEM): "Tuning block copolymer architecture to control structure of self-assembled micelles"
Polymer micelles' compartmentalized nanostructure has been utilized for a range of applications from drug delivery to environmental remediation. By changing the composition of simple linear polymers with two different repeating units, the size and shape of the resulting micelles can be modified. However control of the polymer architecture (e.g. by incorporating branching) promises to yield even more refined control over the size and stability of self-assembled nanostructures. Our present efforts are exploring the application of multi-arm star polymers for transdermal drug delivery.

March 29, 2016
LBC 202, Rechler

Michael Moore (BME): "Engineering Structure & Function in Neural Tissue Cultures"
The focus of the Neural Microengineering Laboratory is to develop in vitro models of neural growth, physiology, and disease by manipulating the chemical and physical extracellular microenvironment. Toward this end, we employ a number of microengineering technologies such as microscale tissue engineering, novel nanomaterials, microfabrication, digital light projection microscopy, and optical modes of electrophysiological stimulation and recording. In particular, we are developing physiological models of demyelinating diseases (such as multiple sclerosis), toxic peripheral neuropathy, and Lyme disease.

Mark Fink (CHEM): "Mechanochemical Synthesis of Silicon Nanoparticles"
Silicon nanoparticles are interesting materials with potential applications in the areas of photovoltaics, Li-ion batteries, and biomedicine. In this talk, the efficient generation of silicon nanoparticles from elemental silicon through mechanical attrition is described. The high-energy ball milling of silicon wafers in the presence of reactive molecules, such as alkenes or alkynes, results in the extensive fracturing of the silicon surface and its subsequent reaction with the surrounding media. This results in the ultimate formation of colloidal surface-passivated silicon nanoparticles. The use of α,ω-dienes and α,ω-diynes in the reaction media result in functionalized surfaces terminated with either alkenes or alkynes, respectively. These surfaces can be further elaborated upon using either thiol-ene chemistry (for alkene terminated nanoparticles) or copper catalyzed azide-alkyne cycloadditions (for alkyne terminated nanoparticles) to afford functionalized nanoparticles with specifically tailored properties. The grafting of polymers, biomolecules, and porphyrins to silicon nanoparticles will be described.

April 5, 2016
LBC 202, Rechler

Daniel Shantz (CBE): "Designing Hybrid Materials for Chemical Transformations and Separations"
This talk will provide an overview of my laboratory's efforts designing hybrid materials for achieving chemical transformations and separations. After an overview of how the materials are made, the talk will describe our work using these tethered groups as solid base catalysts. The effect of ligand density, spacing, and chemistry will be assessed as it relates to the catalytic activity of these ligands for reactions including the Henry reaction and synthesis of methyl esters. I will then summarize the recent efforts of my lab in developing materials that achieve selective rejection or capture of oxygenate species from solution. The overarching theme is that by suitably designing an organic layer on a ceramic support it is possible to achieve selective capture or rejection. Future prospects in this area will be discussed.

Jeff Tasker (CMB): "In search of a membrane steroid receptor, a biochemical quest of a neurophysiologist"

April 12, 2016
LBC 202, Rechler

Shusheng Wang (CMB): "Where vascular biology meets ocular disease"
Vascular abnormalities underlie the pathogenesis of many ocular diseases. Ocular vasculature has been successfully used as an efficient and accessible target for ocular drug discoveries. One of the research focuses in the lab is to understand the role of noncoding RNAs, including microRNAs and long non-coding RNAs, in vascular biology and vascular retinopathies. In this presentation, I will introduce the mouse models and an ex vivo human system we recently developed to study the mechanism of angiogenesis. The function and mechanism of a few vasculature-enriched noncoding RNAs in ocular angiogenesis will be discussed.

James Donahue (CHEM): "Reversible Property Changes in Coordination Compounds"
Redox chemistry is a simple but powerful mechanism for reversible switching of the properties of coordination compounds. In this presentation, two very different systems with reversible property changes are discussed. Part one of this talk discusses homoleptic bis(dithiolene) complexes of iron and cobalt. The fully oxidized complexes are dimeric, while the fully reduced forms separate into monomers. These iron and cobalt bis(dithiolene) complexes bind exogenous ligands such as phosphines and imines to form square pyramidal adducts. By analogy to reversible dimerization as function of redox state, these ligands also bind reversibly as the metal complexes are reduced. Such reversible ligand binding could find applications in the separation of heteroatom-containing molecules from hydrocarbon streams or in chemical sensing. The dithiolene ligand used throughout this work is 1,2-di(p-anisyl)-ene-1,2-dithiolate. In part 2, the tetracarbonyl compounds [W(mdt)(CO)₄] and [W(Me₂pipdt)(CO)₄] are presented, which both have dithiolene-type ligands (mdt = 1,2-dimethyl-ene-1,2-dithiolate; Me₂pipdt = 1,4-dimethylpiperazine-2,3-dithione) but different geometries -- rigonal prismatic (TP) and octahedral, respectively. Structural data suggest an ene-1,2-dithiolate ligand description, hence W^II ion, for [W(mdt)(CO)₄] and a dithioketone ligand, hence W⁰ oxidation state, for [W(Me₂pipdt)(CO)₄]. Reduction of [W(mdt)(CO)₄] induces a geometry change to octahedral because the singly oxidized molecular orbital (SOMO) is at lower energy in this geometry. EPR data for [W(mdt)(CO)4]^1- and [W(Me₂pipdt)(CO)4]^1- are both diagnostic of dithiolene ligand-based sulfur radical, indicating that 1 e^- reduction of [W(mdt)(CO)₄] involves 2 e^- reduction of tungsten and offsetting one-electron oxidation of dithiolene ligand.

April 19, 2016
LBC 202, Rechler

Michelle Lacey (MATH): "Identification of Disease Biomarkers via Integrated Analysis of Longitudinal Clinical and Genomic Data"
The challenge of identifying meaningful diagnostic or prognostic genotypic biomarkers for many diseases is complicated by the range of phenotypes that are observed in the patient population. Such phenotypic variation is often captured through clinical records, but these are not commonly employed in the analysis of genomic data. In previous work (Luo et al (2014), Frontiers in Genetics), we developed a Bayesian hierarchical B-spline approach to fit disease trajectory models for primates exposed to low doses of Mycobacterium tuberculosis (Mtb) based on their clinical profiles. Disease severity estimates derived from these fitted curves were employed to identify genes significantly associated with disease progression, increasing the value of information extracted from the expression profiles and contributing to the identification of predictive biomarkers for TB susceptibility. We now present a second application of our approach to the analysis of gene expression profiles associated with induced colitis in both wild type (WT) and genetically modified mice lacing the TNFR1 receptor. Disease trajectory models were estimated on the basis of body weight and hematochezia, and all animals were biopsied following euthanasia. Through an integrated analysis of clinical trajectories, pathology data, and gene expression profiles, we show significant associations between the severity and duration of symptomatic illness and tumor development. Our results demonstrate that the incorporation of individual disease trajectory estimates enhances existing approaches for biomarker identification and offers the potential to provide insights into personalized treatment strategies for complex diseases.

Igor Rubtsov (CHEM): "Modulation of electron and energy transfer rates in molecules with mid-IR radiation"
Two research projects will be described; one is related to finding ways of modulating electron transfer rates in donor-bridge-acceptor (DBA) compounds and another targeting fast energy propagation via oligomer backbone. Electron transfer is one of the fundamental reactions involved in essential steps of numerous natural and technological processes and it is very attractive to find ways of manipulating ET rates by external stimuli. We have demonstrated that electron transfer rate donor-bridge-acceptor compounds can be changed by vibrational excitation of the vibrational modes at the bridge. In materials, energy can propagate by means of two limiting regimes: diffusive and ballistic - the same regimes of energy transport in molecules (oligomers) were found and charachterized. Ballistic energy transport can be fast and efficient and often occurs with a constant speed. Using two-dimensional infrared spectroscopy methods, we found ballistic energy transport via individual polyethylene chains with a remarkably high speed of 1440 m/s and that the transport speed can be changed depending on the way the transport is initiated. Applications to SAM junctions are discussed.

April 26, 2016
LBC 202, Rechler

Brian Summa (CS): "Visualization, Interaction, and Analysis"
In this talk I will give a high level overview of my past and ongoing work in visualization, computer graphics, and data analysis. Topics will include my work in large image creation from a mosaic and progressive image processing. In addition, I will discuss my interdisciplinary work in large data visualization, image segmentation, high-dimensional data visualization, and topological data analysis.

Carola Wenk (CS): "Algorithms for discrete geometric shapes in applications"
Discrete geometric shapes arise in many applications. We study the case of polygonal curves in the form of GPS trajectory data, and use this kind of data to construct road maps. We will also see how to meaningfully compare two different road maps. In a different line of work, we investigate the use of a mathematical tool from algebraic topology, persistent homology, to describe cyclic patterns in histopathology images of prostate specimen. This will allow us to develop quantitative descriptors of prostate cancer biopsies.