Physical Sciences and Mathematics Commons^™

Heterogeneous Multi-Layered Network Model For Omics Data Integration And Analysis, Bohyun Lee, Shuo Zhang, Aleksandar Poleksic, Lei Xie

Faculty Publications

Advances in next-generation sequencing and high-throughput techniques have enabled the generation of vast amounts of diverse omics data. These big data provide an unprecedented opportunity in biology, but impose great challenges in data integration, data mining, and knowledge discovery due to the complexity, heterogeneity, dynamics, uncertainty, and high-dimensionality inherited in the omics data. Network has been widely used to represent relations between entities in biological system, such as protein-protein interaction, gene regulation, and brain connectivity (i.e. network construction) as well as to infer novel relations given a reconstructed network (aka link prediction). Particularly, heterogeneous multi-layered network (HMLN) has proven successful …

Evidence For A Bind-Then-Bend Mechanism For Architectural Dna Binding Protein Ynhp6a, Manas Kumar Sarangi, Viktoriya Zvoda, Molly Nelson Holte, Nicole A. Becker, Justin Peters, L. James Maher Iii, Anjum Ansari

Faculty Publications

The yeast Nhp6A protein (yNhp6A) is a member of the eukaryotic HMGB family of chromatin factors that enhance apparent DNA flexibility. yNhp6A binds DNA nonspecifically with nM affinity, sharply bending DNA by >60◦. It is not known whether the protein binds to unbent DNA and then deforms it, or if bent DNA conformations are ‘captured’ by protein binding. The former mechanism would be supported by discovery of conditions where unbent DNA is bound by yNhp6A. Here, we employed an array of conformational probes (FRET, fluorescence anisotropy, and circular dichroism) to reveal solution conditions in which an 18- base-pair DNA oligomer …

Structure And Magnetism Of Nifemngaxsn1-X (X=0, 0.25, 0.5, 0.75, 1.00) Heusler Compounds, Jace Waybright, Lee Halbritter, Bishnu Dahal, Hanyang Qian, Yung Huh, Pavel Lukashev, Parashu Kharel

Faculty Publications

The crystal structure and magnetic properties of NiFeMnGa_xSn_1-x (x = 0, 0.25, 0.50, 0.75 and 1.00) Heusler compounds have been investigated experimentally and theoretically. The computational results suggest that NiFeMnGa_0.75Sn_0.25 is nearly half-metallic with a spin polarization P of 87%. The bulk samples prepared using arc-melting and annealing exhibit a high degree of Y-type order. All the investigated samples show ferromagnetic spin order with the Curie temperatures ranging from 284 K for NiFeMnGa to 408 K for NiFeMnSn. The intermediate composition NiFeMnGa_0.75Sn_0.25, which is predicted to be nearly half metallic, …

Out-Of-Plane Electron Transport In Finite Layer Mos2, R Holzapfel, Jake Weber, Pavel Lukashev, Andrew Stollenwerk

Faculty Publications

Ballistic electron emission microscopy (BEEM) has been used to study the processes affecting electron transport along the [0001] direction of finite layer MoS2 flakes deposited onto the surface of Au/Si(001) Schottky diodes. Prominent features present in the differential spectra from the MoS2 flakes are consistent with the density of states of finite layer MoS2 calculated using density functional theory. The ability to observe the electronic structure of the MoS2 appears to be due to the relatively smooth density of states of Si in this energy range and a substantial amount of elastic or quasi-elastic scattering along the MoS2/Au/Si(001) path. Demonstration …

Magnetic And Magnetocaloric Properties Of Co2-Xfexvga Heusler Alloys, K. Schroeder, J. Waybright, P. Kharel, W. Zhang, S. Valloppilly, J. Herran, P. Lukashev, Y. Huh, R. Skomsk, D. J. Sellmyer

Faculty Publications

The magnetic and magnetocaloric properties of iron-substituted Co₂VGa alloys, Co_2-xFe_xVGa (x = 0, 0.1, 0.15, 0.2, 0.3), were investigated. The Fe-substituted samples, prepared by arc melting, melt spinning, and annealing, crystallized in the L2(1) Heusler structure, without any secondary phases. The Curie temperature and high-field magnetization at 50 K decreased from 345 K and 44 emu/g (1.90 mu(B)/f.u.) for Co₂VGa to 275 K and 39 emu/g (1.66 mu(B)/f.u.) for Co_1.7Fe_0.3VGa, respectively, but the maximum entropy change remained almost insensitive to Fe concentration for x 1.85Fe_0.15VGa. First-principle …

In Praise Of The Catenary, Fred Behroozi

Faculty Publications

When a chain hangs loosely from its end points, it takes the familiar form known as the catenary. Power lines, clothes lines, and chain links are familiar examples of the catenary in everyday life. Nevertheless, the subject is conspicuously absent from current introductory physics and calculus courses.1 Even in upper-level physics and math courses, the catenary equation is usually introduced as an example of hyperbolic functions or discussed as an application of the calculus of variations. We present a new derivation of the catenary equation that is suitable for introductory physics and mathematics courses.

Atomic Disorder Induced Modification Of Magnetization In Mncrval, Juliana Herran, Rishabh Dalal, Paul Gray, Parashu Kharel, Pavel Lukashev

Faculty Publications

We have investigated the physical mechanism behind magnetization reduction in a potential spingapless semiconducting compound MnCrVAl by analyzing various atomic disorder schemes. In particular, we show that depending on the degree of disorder, exchanging atomic positions between Mn/Cr and V/Al leads to reduced total magnetization due to either spin flip, or vanishing spin magnetic moments. The latter is attributed to the itinerant character of magnetism in Cr-, Mn-, and V-containing Heusler alloys, and to the frustration of antiferromagnetic exchange interactions, and is accompanied by a tetragonal distortion, but such distortion alone (i.e., in a fully ordered crystal, with no atomic …

Effect Of Fe Substitution On The Structural, Magnetic And Electron-Transport Properties Of Half-Metallic Co2tisi, Y. Yin, J. Waybright, P. Kharel, I. Tutic, J. Herran, P. Lukashev, S. Valloppilly, D. J. Sellmyer

Faculty Publications

The structural, magnetic and electron-transport properties of Co₂Ti_1-xFe_xSi (x = 0, 0.25, 0.5) ribbons prepared by arc-melting and melt-spinning were investigated. The rapidly quenched Co₂Ti_0.5Fe_0.5Si crystallized in the cubic L2₁ structure whereas Co₂Ti_0.75Fe_0.25Si and Co₂TiFe₀Si showed various degrees of B2-type disorder. At room temperature, all the samples are ferromagnetic, and the Curie temperature increased from 360 K for Co₂TiSi to about 800 K for Co₂Ti_0.5Fe_0.5Si. The measured magnetization also …

Effect Of Disorder On The Magnetic And Electronic Structure Of A Prospective Spin-Gapless Semiconductor Mncrval, P. Kharel, J. Herran, Pavel Lukashev, Y. Jin, J. Waybright, S. Gilbert, B, Staten, P. Gray, S. Valloppilly, Y. Huh, D. J. Sellmyer

Faculty Publications

Recent discovery of a new class of materials, spin-gapless semiconductors (SGS), has attracted considerable attention in the last few years, primarily due to potential applications in the emerging field of spin-based electronics (spintronics). Here, we investigate structural, electronic, and magnetic properties of one potential SGS compound, MnCrVAl, using various experimental and theoretical techniques. Our calculations show that this material exhibits ≈ 0.5 eV band gap for the majority-spin states, while for the minority-spin it is nearly gapless. The calculated magnetic moment for the completely ordered structure is 2.9 µ_B/f.u., which is different from our experimentally measured value of …

Large-Scaleoff-Target Identificationusing Fast And Accurate Dual Regularized Oneclass Collaborative Filtering And Its Application To Drug Repurposing, Hansaim Lim, Alexsandar Poleksic, Yuan Yao, Hanghang Tong, Di He, Luke Zhuang, Patrick Meng, Lei Xie

Faculty Publications

Target-based screening is one of the major approaches in drug discovery. Besides the intended target, unexpected drug off-target interactions often occur, and many of them have not been recognized and characterized. The off-target interactions can be responsible for either therapeutic or side effects. Thus, identifying the genome-wide off-targets of lead compounds or existing drugs will be critical for designing effective and safe drugs, and providing new opportunities for drug repurposing. Although many computational methods have been developed to predict drug-target interactions, they are either less accurate than the one that we are proposing here or computationally too intensive, thereby limiting …

Cycling State That Can Lead To Glassy Dynamics In Intracellular Transport, Monika Scholtz, Stanislav Burov, Kimberly L. Weirich, Björn J. Scholtz, S.M. Ali Tabei, Margaret L. Gardel, Aaron R. Dinner

Faculty Publications

Power-law dwell times have been observed for molecular motors in living cells, but the origins of these trapped states are not known. We introduce a minimal model of motors moving on a two-dimensional network of filaments, and simulations of its dynamics exhibit statistics comparable to those observed experimentally. Analysis of the model trajectories, as well as experimental particle tracking data, reveals a state in which motors cycle unproductively at junctions of three or more filaments. We formulate a master equation for these junction dynamics and show that the time required to escape from this vortexlike state can account for the …

Calculating Heat Of Formation Values Of Energetic Compounds: A Comparative Study, Michael S. Elioff, Jordon Hoy, John A. Bumpus

Faculty Publications

Heat of formation is one of several important parameters used to assess the performance of energetic compounds. We evaluated the ability of six different methods to accurately calculate gas-phase heat of formation (Δ _𝑓𝐻^𝑜 _298,g) values for a test set of 45 nitrogencontaining energetic compounds. Density functional theory coupled with the use of isodesmic or other balanced equations yielded calculated results in which 82% (37 of 45) of the Δ _𝑓𝐻^𝑜 _298,g values were within ±2.0 kcal/mol of the most recently recommended experimental/reference values available. This was compared to a procedure using density functional theory …

A Polynomial Time Algorithm For Computing The Area Under A Gdt Curve, Aleksandar Poleksic

Faculty Publications

Background

Progress in the field of protein three-dimensional structure prediction depends on the development of new and improved algorithms for measuring the quality of protein models. Perhaps the best descriptor of the quality of a protein model is the GDT function that maps each distance cutoff θ to the number of atoms in the protein model that can be fit under the distance θ from the corresponding atoms in the experimentally determined structure. It has long been known that the area under the graph of this function (GDT_A) can serve as a reliable, single numerical measure …

Observation Of Interlayer Phonon Modes In Van Der Waals Heterostructures, C. H. Lui, Zhipeng Ye, Chao Ji, Kuan-Chang Chiu, Cheng-Tse Chou, Trond I. Andersen, Casie Means-Shively, Heidi Anderson, Jenn-Ming Wu, Tim Kidd, Yi-Hsien Lee, Rui He

Faculty Publications

We have investigated the vibrational properties of van der Waals heterostructures of monolayer transition metal dichalcogenides (TMDs), specifically MoS₂/WSe₂ and MoSe₂/MoS₂ heterobilayers and twisted MoS₂ bilayers, by means of ultralow-frequency Raman spectroscopy. We discovered Raman features (at 30–40 cm−1) that arise from the layer-breathing mode (LBM) vibration between the two incommensurate TMD monolayers in these structures. The LBM Raman intensity correlates strongly with the suppression of photoluminescence that arises from interlayer charge transfer. The LBM is generated only in bilayer areas with direct layer-layer contact and an atomically clean interface. Its frequency also …

Manipulation Of Subsurface Carbon Nanoparticles In Bi2sr2cacu2o8+Δ Using A Scanning Tunneling Microscope, A. J. Stollenwerk, N. Hurley, B. Beck, K. Spurgeon, Tim Kidd, G. Gu

Faculty Publications

We present evidence that subsurface carbon nanoparticles in Bi₂Sr₂CaCu₂O_8+δ can be manipulated with nanometer precision using a scanning tunneling microscope. High-resolution images indicate that most of the carbon particles remain subsurface after transport observable as a local increase in height as the particle pushes up on the surface. Tunneling spectra in the vicinity of these protrusions exhibit semiconducting characteristics with a band gap of approximately 1.8 eV, indicating that the incorporation of carbon locally alters the electronic properties near the surface.

Iteration Modeled By Playlists: An Unexpected Occurrence Of The Triangular Numbers, Catherine M. Miller, Douglas J. Shaw

Faculty Publications

Our world is changing rapidly; one example is the growth of smart technologies that have become part of our lives. Smart playlists are the source for a mathematics problem that can be approached in a variety of ways. A playlist is a set of songs that can be played separately from the albums on digital music players. The device (mp 3 player, Ipod®, etc.) can create a smart playlist based on criteria inputted by the user.

A Meta Analysis Of Pancreatic Microarray Datasets Yields New Targets As Cancer Genes And Biomarkers, Nalin C. W. Goonesekere, Xiaosheng Wang, Lindsey Ludwig, Chittibabu Guda

Faculty Publications

The lack of specific symptoms at early tumor stages, together with a high biological aggressiveness of the tumor contribute to the high mortality rate for pancreatic cancer (PC), which has a five year survival rate of less than 5%. Improved screening for earlier diagnosis, through the detection of diagnostic and prognostic biomarkers provides the best hope of increasing the rate of curatively resectable carcinomas. Though many serum markers have been reported to be elevated in patients with PC, so far, most of these markers have not been implemented into clinical routine due to low sensitivity or specificity. In this study, …

W.R.I.T.E: Writing’S Role In Thoughtful Endeavors, Catherine M. Miller

Faculty Publications

“Mathematicians actually spend a great deal of time writing. If a mathematician wants to contribute to the greater body of mathematical knowledge, she must be able communicate her ideas in a way which is comprehensible to others.” Lee, 2014, pg. 1

Why should our students be different from the mathematicians Lee (2014) refers to in the quote above? Learning mathematics requires a confluence of spoken, written and mathematically abstract languages. After all, who thinks entirely in mathematical symbols? No one, except a few mathematical thinkers who are live in the abstract worlds they construct. Thinking about mathematics in the language …

On The Difference In Quality Between Current Heuristic And Optimal Solutions To The Protein Structure Alignment Problem, Mauricio Arriagada, Aleksandar Poleksic

Faculty Publications

The importance of pairwise protein structural comparison in biomedical research is fueling the search for algorithms capable of finding more accurate structural match of two input proteins in a timely manner. In recent years, we have witnessed rapid advances in the development of methods for approximate and optimal solutions to the protein structure matching problem. Albeit slow, these methods can be extremely useful in assessing the accuracy of more efficient, heuristic algorithms. We utilize a recently developed approximation algorithm for protein structure matching to demonstrate that a deep search of the protein superposition space leads to increased alignment accuracy with …

Simple, Complete, And Novel Quantitative Model Of Holography For Students Of Science And Science Education, Dale Olson

Faculty Publications

A Moiré graphical method for predicting the directions of all permitted image waves for thin and volume holograms is described. This method has been developed in connection with a holography centred optics course for students in science, technology and science education that has evolved over several decades. A somewhat unique view of the holographic process underlies this novel method of predicting the behaviour of diffraction gratings.

Mining Functional Subgraphs From Cancer Protein-Protein Interaction Networks, Ru Shen, Nalin Goonesekere, Chittibabu Guda

Faculty Publications

Background: Protein-protein interaction (PPI) networks carry vital information about proteins’ functions. Analysis of PPI networks associated with specific disease systems including cancer helps us in the understanding of the complex biology of diseases. Specifically, identification of similar and frequently occurring patterns (network motifs) across PPI networks will provide useful clues to better understand the biology of the diseases.

Results: In this study, we developed a novel pattern-mining algorithm that detects cancer associated functional subgraphs occurring in multiple cancer PPI networks. We constructed nine cancer PPI networks using differentially expressed genes from the Oncomine dataset. From these networks we …

Coulomb-Driven Cluster-Glass Behavior In Mn-Intercalated Ti1+Ys2, P. M. Shand, A. L. Meyer, M. Streicher, A. Wilson, T. Rash, Tim Kidd, L. H. Strauss

Faculty Publications

We have investigated the low-temperature spin-glasslike phase in the intercalated transition-metal dichalcogenide Mn_0.09Ti_1.1S₂. A departure from Curie–Weiss behavior in the paramagnetic regime indicated the formation of small ferromagnetically correlated clusters. The Vogel–Fulcher law provided an excellent description of relaxation times in the vicinity of the transition, showing that the glasslike phase occurs due to interaction between the clusters. Cole–Cole plots for data close to the transition were linear, which is consistent with a simple exponential distribution of cluster sizes. A Monte Carlo simulation of the dichalcogenide system, including excess self-intercalated Ti ions, gave an …

Quantum Many-Body Calculation Of Mixed-Parity Pairing In The Sr2ruo4 Superconductor Induced By Spin-Orbit Coupling, J. J. Deisz, Tim Kidd

Faculty Publications

The unusual superconducting state in Sr₂RuO₄ has long been viewed as being analogous to a superfluid state in liquid ³He. Nevertheless, calculations based on this odd-parity state are presently unable to completely reconcile the properties of Sr₂RuO₄. Using a self-consistent quantum many-body scheme that employs realistic parameters, we are able to model several signature properties of the normal and superconducting states of Sr₂RuO₄. We find that the dominant component of the model superconducting state is of even parity and closely related to superconducting state for the high-T_{c …}

Reconstructed Fermi Surface Of Underdoped Bi2sr2cacu2o8+Δ Cuprate Superconductors, H.-B. Yang, J. D. Rameau, Z.-H. Pan, G. D. Gu, P. D. Johnson, H. Claus, D. G. Hinks, Tim Kidd

Faculty Publications

The Fermi surface topologies of underdoped samples of the high-T_c superconductor Bi₂Sr₂CaCu₂O_8+δ have been measured with angle resolved photoemission. By examining thermally excited states above the Fermi level, we show that the observed Fermi surfaces in the pseudogap phase are actually components of fully enclosed hole pockets. The spectral weight of these pockets is vanishingly small at the magnetic zone boundary, creating the illusion of Fermi ‘‘arcs.’’ The area of the pockets as measured in this study is consistent with the doping level, and hence carrier density, of the samples measured. Furthermore, …

Properties Of Hydrogen Terminated Diamond As A Photocathode, J. D. Rameau, J. Smedley, E. M. Muller, T. E. Kidd, P. D. Johnson

Faculty Publications

Electron emission from the negative electron affinity (NEA) surface of hydrogen terminated, boron doped diamond in the [100] orientation is investigated using angle resolved photoemission spectroscopy (ARPES). ARPES measurements using 16 eV synchrotron and 6 eV laser light are compared and found to show a catastrophic failure of the sudden approximation. While the high energy photoemission is found to yield little information regarding the NEA, low energy laser ARPES reveals for the first time that the NEA results from a novel Franck-Condon mechanism coupling electrons in the conduction band to the vacuum. The result opens the door to the development …

Providing Preservice Teachers With Worthwhile Field-Based Experiences In Mathematics, Glenn Nelson

Faculty Publications

Providing preservice teachers with worthwhile field-based experiences is recognized as an important component in their development as good teachers. Because mathematics instruction in general has moved from a teacher-directed, procedurally-focused process to a more student-centered, conceptually-oriented approach, preservice mathematics education classes – especially methods courses - should reflect this shift as well. Field-based opportunities can be instances for preservice teachers to personally experience such a shift to real-world relevance.

Synthesis Of Freestanding Hfo2 Nanostructures, Tim Kidd, Aaron O'Shea, Kayla Boyle, Jeff Wallace, Laura Strauss

Faculty Publications

Two new methods for synthesizing nanostructured HfO₂ have been developed. The first method entails exposing HfTe₂ powders to air. This simple process resulted in the formation of nanometer scale crystallites of HfO₂. The second method involved a two-step heating process by which macroscopic, freestanding nanosheets of HfO₂ were formed as a byproduct during the synthesis of HfTe₂. These highly two-dimensional sheets had side lengths measuring up to several millimeters and were stable enough to be manipulated with tweezers and other instruments. The thickness of the sheets ranged from a few to a few …

Coercivity And Exchange Bias Of Mn0.25ti1.1s2 In The Cluster-Glass State, P. M. Shand, T. Rash, M. Streicher, T. E. Kidd, K. R. Boyle, Laura Strauss

Faculty Publications

Magnetic measurements have been carried out on the Mn-intercalated transition-metal dichalcogenide Mn_0.25Ti_1+yS₂. The material, which contained a concentration y≈0.1 of excess intercalated Ti, exhibited paramagnetic behavior at high temperatures with an effective moment per Mn ion of µ_eff=6.07 ± 0.23 µ_B, which shows that the system comprises localized Mn²⁺ moments. A Curie-Weiss temperature Θ_CW=-26 ± 1 K indicated that antiferromagnetic interactions were dominant. Deviation from Curie-Weiss behavior below 100 K signaled the formation of antiferromagnetically correlated clusters. Bifurcation of the zero-fieldcooled and field-cooled magnetizations below 20 K …

Meaningful Distributed Instruction— Conceptual Previews For Symbolic Procedures, Edward C. Rathmell

Faculty Publications

Understanding a symbolic procedure means far more than “getting the right answer.” A mathematical symbolic procedure or written skill involves step-bystep thinking that leads from a computational problem to a solution. Memorizing this step-by-step procedure may enable a student to answer the problem, even answer it correctly. Yes, that is important, but understanding means much more.

Health Literacy In The Mathematics Classroom: The Iowa Core Curriculum As An Opportunity To Deepen Students’ Understanding Of Mathematics, Elana Joram, Susan Dobie-Roberts, Nadene Davidson

Faculty Publications

By 2012, all high schools in Iowa will be required to incorporate the new Iowa Core Curriculum, followed by elementary and middle schools in 2014 (Iowa Department of Education, 2009). The Iowa Core Curriculum addresses the question: "How is Iowa's educational system preparing our youth for successful lives in the 21st-century global environment?" (Davidson, 2009). It consists of core content standards, and identifies essential concepts and skills for content areas. The Iowa Core Curriculum also includes the ―21st Century Skills‖ of ―health, financial, technology, and civic literacy, and employability skills. These skills are to be infused into existing subject matter …