Physical Sciences and Mathematics Commons^™

Deformations Associated With Rigid Algebras, M Gerstenhaber, Anthony Giaquinto

Mathematics and Statistics: Faculty Publications and Other Works

The deformations of an infinite dimensional algebra may be controlled not just by its own cohomology but by that of an associated diagram of algebras, since an infinite dimensional algebra may be absolutely rigid in the classical deformation theory for single algebras while depending essentially on some parameters. Two examples studied here, the function field of a sphere with four marked points and the first Weyl algebra, show, however, that the existence of these parameters may be made evident by the cohomology of a diagram (presheaf) of algebras constructed from the original. The Cohomology Comparison Theorem asserts, on the other …

What's In An Algorithm?, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

How can we rethink the definition of algorithm, and through that, produce another age of enlightenment in modern scientific programming and software development in general? Removing these limitations in our own thoughts is the key for expanding the possibilities in alternative paradigms and exploiting parallel and next-generation hardware.

Response To David Quigley, John D. Cunningham

Physics: Faculty Publications and Other Works

No abstract provided.

On The Origin Of Mode- And Bond-Selectivity In Vibrationally Mediated Reactions On Surfaces, Daniel Killelea, Arthur L. Utz

Chemistry: Faculty Publications and Other Works

The experimental observations of vibrational mode- and bond-selective chemistry at the gas–surface interface indicate that energy redistribution within the reaction complex is not statistical on the timescale of reaction. Such behavior is a key prerequisite for efforts to use selective vibrational excitation to control chemistry at the technologically important gas–surface interface. This paper outlines a framework for understanding the origin of non-statistical reactivity on surfaces. The model focuses on the kinetic competition between intramolecular vibrational energy redistribution (IVR) within the reaction complex, which in the long-time limit leads to statistical behavior, and quenching, scattering, or desorption processes that restrict the …

Spectroscopic Evidence Of Work Function Alterations Due To Photoswitchable Monolayers On Gold Surfaces, Matthew Alan Bartucci, Jan Florian, Jacob W. Ciszek

Chemistry: Faculty Publications and Other Works

Taking advantage of surfaces’ response to interfacial dipoles, a class of photochromophores (dihydroindolizine) is demonstrated to alter the work function of the underlying substrate (∼170 meV). This same molecule also provides spectroscopic signatures for correlating the change in molecular structure to the induced change in the surfaces’ electronic properties. Polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS) allows analysis of the characteristic dihydroindolizine C═C (1559 cm^–1) and pyridinium (1643 cm^–1) stretch as a function of photoexcitation. Structural assignments of this photochromophore are corroborated to density function theory calculations. Conformational changes in the monolayers appear in parallel with …

Statistical Analysis Of Aerosol Species, Trace Gases, And Meteorology In Chicago, Katrina Binaku, Timothy O'Brien, Martina Schmeling, Tinamarie Fosco

Chemistry: Faculty Publications and Other Works

Both canonical correlation analysis (CCA) and principal component analysis (PCA) were applied to atmospheric aerosol & trace gas concentrations and meteorological data collected in Chicago during the summer months of 2002, 2003, and 2004. Concentrations of ammonium, calcium, nitrate, sulfate, and oxalate particulate matter, as well as, meteorological parameters temperature, wind speed, wind direction, and humidity were subjected to CCA & PCA. Ozone and nitrogen oxide mixing ratios were also included in the data set. The purpose of statistical analysis was to determine the extent of existing linear relationship(s), or lack thereof, between meteorological parameters and pollutant concentrations in addition …

Guest Editors Introduction: Cloud Computing, Manish Parashar, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The guest editors discuss this special issue on cloud computing, exploring how cloud platforms and abstractions can be effectively used to support real-world science and engineering applications.

Evaluation Of The Impacts Computer Science Presentations, Steven Mcgee, Ronald I. Greenberg, Dale F. Reed, Jennifer Duck

Computer Science: Faculty Publications and Other Works

Recent computer science enrollments have shown positive trends. However, these trends are not evenly distributed by gender and race. Efforts to recruit underrepresented students should focus on providing information that demystifies the field of computer science. This paper reports on such an effort to inform underrepresented high school students about the field and its diversity. The results suggest that increasing awareness in an enjoyable format can increase student interest in pursuing computer science. These results can provide guidance about ways to encourage students to take high school computer science classes as motivation and preparation for college-level computer science.

Teaching And Assessing Programming Fundamentals For Non Majors With Visual Programming, William L. Honig

Computer Science: Faculty Publications and Other Works

Visual programming tools and mobile device applications are a natural tool to engage university students; but, are they effective in teaching quantitative thinking skills to non computer science majors? Answering this question can be based on careful assessment of the learning outcomes.

This paper reports the results from teaching over 100 students mobile app development with App Inventor in a university core course. Results were measured using an assessment process motivated by Bloom's Taxonomy that included student self assessment, ratings by instructors, and comparisons of the two results. The categories in the assessment were mapped to specific levels of skills …

Unraveling The Activation Mechanism Of The Potato Tuber Adp-Glucose Pyrophosphorylase, Carlos M. Figueroa, Misty L. Kuhn, Christine A. Falaschetti, Ligin Solamen, Kenneth W. Olsen, Miguel Ballicora, Alberto A. Iglesias

Chemistry: Faculty Publications and Other Works

ADP-glucose pyrophosphorylase regulates the synthesis of glycogen in bacteria and of starch in plants. The enzyme from plants is mainly activated by 3-phosphoglycerate and is a heterotetramer comprising two small and two large subunits. Here, we found that two highly conserved residues are critical for triggering the activation of the potato tuber ADP-glucose pyrophosphorylase, as shown by site-directed mutagenesis. Mutations in the small subunit, which bears the catalytic function in this potato tuber form, had a more dramatic effect on disrupting the allosteric activation than those introduced in the large subunit, which is mainly modulatory. Our results strongly agree with …

Spring­11: Pdc In Cs1/2 And A Mobile/Cloud Intermediate Mobile/Cloud Intermediate Software Design Course, Joseph P. Kaylor, Konstantin Läufer, Chandra N. Sekharan, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Recent changes in the environment of Loyola University Chicago’s Department of Computer Science include a better differentiation of our four undergraduate majors, growing interest in computing among science majors, and an increased demand for graduates with mobile and cloud skills. In our continued effort to incorporate parallel and distributed computing topics into the undergraduate curriculum, we are focusing on these three existing courses:

CS1: In response to a request from the physics department, we started to offer a CS1 section aimed at majors in physics and other hard sciences this spring semester. This section includes some material on numerical methods …

Building Capable, Energy-Efficient, Flexible Visualization And Sensing Clusters From Commodity Tablets, Thomas Delgado Dias, Xian Yan, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

We explore the application of clusters of commodity tablet devices to problems spanning a “trilogy” of concerns: visualization, sensing, and computation. We conjecture that such clusters provide a low-cost, energy-efficient, flexible, and ultimately effective platform to tackle a wide range of problems within this trilogy. This is a work in progress, and we now elaborate our position and give a preliminary status report.

A wide range of Android tablet devices are available in terms of price and capabilities. “You get what you pay for” w.r.t. display resolution, sensors, and chipset---corresponding to the trilogy. $200 gets one a 1280x800-pixel touch display, …

Network Technologies Used To Aggregate Environmental Data, Paul Stasiuk, Konstantin Läufer, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

The goal of the Loyola Weather Service (lws) project is to design and build a system of functioning environmental monitoring widgets that can intelligently and autonomously control the environment around them based on set thresholds and triggers. The widgets will also have the ability to aggregate their data and easily display this data in various ways: through a user interface in the room that the widget is placed, via a web application, and programmatically via a RESTful web service.

Productivity In The Cognitive Overload Era, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

Could technologies that emphasize the concept of "we" rather than "me" help modern society overcome its information overload?

A Polyglot Approach To Bioinformatics Data Integration: Phylogenetic Analysis Of Hiv-1, Steven Reisman, Catherine Putonti, George K. Thiruvathukal, Konstantin Läufer

Computer Science: Faculty Publications and Other Works

RNA-interference has potential therapeutic use against HIV-1 by targeting highly-functional mRNA sequences that contribute to the virulence of the virus. Empirical work has shown that within cell lines, all of the HIV-1 genes are affected by RNAi-induced gene silencing. While promising, inherent in this treatment is the fact that RNAi sequences must be highly specific. HIV, however, mutates rapidly, leading to the evolution of viral escape mutants. In fact, such strains are under strong selection to include mutations within the targeted region, evading the RNAi therapy and thus increasing the virus’ fitness in the host. Taking a phylogenetic approach, we …

Large-Scale Structural Rearrangement Of A Serine Hydrolase From Francisella Tularensis Facilitates Catalysis, Ekaterina V. Filippova, Leigh A. Watson, Misty L. Kuhn, Brett Geissler, Daniel Becker

Chemistry: Faculty Publications and Other Works

Tularemia is a deadly, febrile disease caused by infection by the gram-negative bacterium, Francisella tularensis. Members of the ubiquitous serine hydrolase protein family are among current targets to treat diverse bacterial infections. Herein we present a structural and functional study of a novel bacterial carboxylesterase (FTT258) from F. tularensis, a homologue of human acyl protein thioesterase (hAPT1). The structure of FTT258 has been determined in multiple forms, and unexpectedly large conformational changes of a peripheral flexible loop occur in the presence of a mechanistic cyclobutanone ligand. The concomitant changes in this hydrophobic loop and the newly exposed hydrophobic substrate binding …

Gendered Jobs And The New Gender Gap, George K. Thiruvathukal, Jon Ross

Computer Science: Faculty Publications and Other Works

This presentation discusses how to address 21st Century employment challenges by dismantling gender-specific barriers to entry. We take an interdisciplinary approach by focusing on areas such as education, public policy, culture, and media (among others).

Unintended Consequences Of Imprecise Notation – An Example From Mechanics, Asim Gangopadhyaya, Gordon Ramsey

Physics: Faculty Publications and Other Works

We present a conundrum that results from the imprecise use of notation for partial derivatives. Taking an example from mechanics, we show that lack of proper care in re presenting partial derivatives in Lagrangian and Hamiltonian formulations paradoxically leads to two different values for the time derivative of the canonical momentum. This problem also exists in other areas of physics,such as thermodynamics.

Functionalization Of Organic Semiconductor Crystals Via The Diels–Alder Reaction, Brittni A. Qualizza, Srividya Prasad, M. Paul Chiarelli, Jacob W. Ciszek

Chemistry: Faculty Publications and Other Works

A surface adlayer is generated on organic single crystals (tetracene and rubrene) using the site specific Diels–Alder reaction and a series of vapor phase dienophiles. X-ray photoelectron spectroscopy (XPS) confirms adsorption on the surfaces of tetracene and rubrene and mass spectrometry demonstrates the reaction’s applicability to a range of dienophiles.

Apparent Alkyl Transfer And Phenazine Formation Via An Aryne Intermediate, Daniel Becker, Andria M. Panagopoulos, Doug Steinman, Alexandra Goncharenko, Kyle Geary, Carlene Schleisman, Elizabeth Spaargaren, Matthias Zeller

Chemistry: Faculty Publications and Other Works

Treatment of chlorotriaryl derivatives 3a and 3d or fluorotriaryl derivatives 3b and 3e with potassium diisopropylamide afforded alkyl-shifted phenazine derivatives 5a/5b, rather than the expected 9-membered triazaorthocyclophane 2a. The phenazine derivatives were isolated in 78–98% yield depending on the halogen and alkyl group present. In the absence of the halogen (chloro or fluoro), the apparent alkyl shift proceeds more slowly and cannot proceed via the intermediacy of the aryne intermediate. Mechanistic possibilities include intramolecular nucleophilic attack on an aryne intermediate leading to a zwitterionic intermediate and alkyl transfer via a 5-endo-tet process, or via a Smiles rearrangement.

Rearrangement Of Cyclotriveratrylene (Ctv) Diketone: 9,10-Diarylanthracenes With Oled Applications, Samuel R. Sarsah, Marlon R. Lutz Jr., Matthias Zeller, David S. Crumrine, Daniel Becker

Chemistry: Faculty Publications and Other Works

Electroluminescent 9,10-diaryl anthracenes have been shown to be promising host and hole-transporting materials in organic electroluminescence due to their high thermal stability, electrochemical reversibility, and wide band gap useful for organic light-emitting diodes (OLEDs), especially blue OLEDs. Oxidation of cyclotriveratrylene (CTV) to the corresponding diketone and subsequent bromination resulted in an unexpected rearrangement to a highly functionalized 9-aryl-10-bromoanthracene derivative, which was employed in Suzuki couplings to synthesize a series of 9,10-diaryl compounds that are structural analogues of anthracene derivatives used in the preparation of OLEDs but are more highly functionalized, including electron-donating methoxy groups in addition to substitution by a …

Computational Science, Demystified...The Future, Revealed...And Cise, 2013, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

What are some of the exciting avenues that computational science is exploring, and how can we best give a voice to such emerging ideas?

The Ancestral Activation Promiscuity Of Adp-Glucose Pyrophosphorylases From Oxygenic Photosynthetic Organisms, Misty L. Kuhn, Carlos M. Figueroa, Alberto A. Iglesias, Miguel Ballicora

Chemistry: Faculty Publications and Other Works

Background

ADP-glucose pyrophosphorylase (ADP-Glc PPase) catalyzes the first committed step in the synthesis of glycogen in bacteria and starch in algae and plants. In oxygenic photosynthetic organisms, ADP-Glc PPase is mainly activated by 3-phosphoglycerate (3-PGA) and to a lesser extent by other metabolites. In this work, we analyzed the activation promiscuity of ADP-Glc PPase subunits from the cyanobacterium Anabaena PCC 7120, the green alga Ostreococcus tauri, and potato (Solanum tuberosum) tuber by comparing a specificity constant for 3-PGA, fructose-1,6-bisphosphate (FBP), fructose-6-phosphate, and glucose-6-phosphate.

Results

The 3-PGA specificity constant for the enzymes from Anabaena (homotetramer), O. tauri, …

Lysine Biosynthesis In Bacteria: A Metallodesuccinylase As A Potential Antimicrobial Target, Danuta M. Gillner, Daniel P. Becker Ph.D., Richard C. Holz

Chemistry: Faculty Publications and Other Works

In this review, we summarize the recent literature on dapE-encoded N-succinyl-l,l-diaminopimelic acid desuccinylase (DapE) enzymes, with an emphasis on structure–function studies that provide insight into the catalytic mechanism. Crystallographic data have also provided insight into residues that might be involved in substrate and hence inhibitor recognition and binding. These data have led to the design and synthesis of several new DapE inhibitors, which are described along with what is known about how inhibitors interact with the active site of DapE enzymes, including the efficacy of a moderately strong DapE inhibitor.

Investigating The Electrostatic Role Of A Critical Arginine For The Catalysis Of E. Coli Adp-Glucose Pyrophosphorylase, Angela Mahaffey, Saleh Aiyash, Miguel Ballicora, Ligin Solamen

Chemistry: Faculty Publications and Other Works

ADP-glucose pyrophosphorylase (ADP-Glc PPase) is the regulatory enzyme of the pathway for starch synthesis in plants and glycogen in mammals and enteric bacteria. It exists as a 200 kDa homotetramer (α4) in enteric bacteria, and as a heterotetramer (α2β2) in plants. In both in vivo and in vitro the substrates (Glucose 1-Phosphate; Glc-1P and Adenosine 5'-Triphosphate; ATP) are converted into a glucose donor ADP-Glucose and a pyrophosphate (PPi) via the ADP-Glc PPase enzyme. It has been noted that some residues are conserved in homotetrameric bacterial ADP-Glc PPases, but are not in some plant forms. One of them is …

Modeling Dengue Virus Infection Patients For Each Severity Of Dengue Disease In Thailand, Montip Tiensuwan, Timothy O'Brien

Mathematics and Statistics: Faculty Publications and Other Works

Dengue is an infectious mosquito-borne viral disease. Dengue or dengue-like epidemics ranks highly among new and newly emerging infectious diseases in public health significance and may affect persons of all ages in dengue endemic area. Dengue virus infections may lead to dengue fever (DF), dengue haemorrhagic fever (DHF) and may lead to hypovolaemic shock (dengue shock syndrome, DSS) then we separate dengue data by severity of dengue disease, i.e., DF, DHF and DSS. The objective of this study is to find factors which affect the dengue virus infection patients for each severity of dengue disease in Thailand by using multiple …

Differentiation Of Surface Contaminants And Implanted Material On Genesis Solar Wind Samples Using Total Reflection X-Ray Fluorescence Spectometry And Grazing Incidence X-Ray Fluorescence, Martina Schmeling, Peter J. Eng, J.E. Stubbs, Y. Choi, Igor V. Veryovkin

Chemistry: Faculty Publications and Other Works

During the Genesis mission solar wind was implanted in collector materials for analysis by various instrumental methods. Unfortunately the space craft crash landed upon return to Earth shattering the collectors into small fragments and exposing them to desert soil and spacecraft debris. Thus only small fragments are available for analysis with each having different degrees of contamination present at and embedded within the surface. Cleaning procedures were developed and applied to remove the contamination. To aid in this process bench top total reflection X-ray fluorescence spectrometry (TXRF) was used to characterize a sample surface before and after various cleaning steps. …

Functionalization Of Organic Semiconductor Crystals Via The Diels-Alder Reaction, Brittni A. Qualizza, Srividya Prasad, M. Paul Chiarelli, Jacob W. Ciszek

Chemistry: Faculty Publications and Other Works

A surface adlayer is generated on organic single crystals (tetracene and rubrene) using the site specific Diels–Alder reaction and a series of vapor phase dienophiles. X-ray photoelectron spectroscopy (XPS) confirms adsorption on the surfaces of tetracene and rubrene and mass spectrometry demonstrates the reaction’s applicability to a range of dienophiles.

Identification Of A Histidine Metal Ligand In The Arge-Encoded N-Acetyl-L-Ornithine Deacetylase From Escherichia Coli, Wade C. Mcgregor, Danuta M. Gillner, Sabina I. Swierczek, Dali Liu, Richard C. Holz

Chemistry: Faculty Publications and Other Works

The H355A, H355K, H80A, and H80K mutant enzymes of the argE-encoded N-acetyl-L-ornithine deacetylase (ArgE) from Escherichia coli were prepared, however, only the H355A enzyme was found to be soluble. Kinetic analysis of the Co(II)-loaded H355A exhibited activity levels that were 380-fold less than Co(II)-loaded WT ArgE. Electronic absorption spectra of Co(II)-loaded H355A-ArgE indicate that the bound Co(II) ion resides in a distorted, five-coordinate environment and Isothermal Titration Calorimetry (ITC) data for Zn(II) binding to the H355A enzyme provided a dissociation constant (K_d) of 39 μM. A three-dimensional homology model of ArgE was generated using the …

Who Needs Tablets? We Do, George K. Thiruvathukal

Computer Science: Faculty Publications and Other Works

What role do tablets play increasingly in our daily lives? Is it possible that they could revolutionize the future of publishing and education?