Engineering Commons^™

Fingering Instabilities On Reaction Fronts In The Co Oxidation Reaction On Pt(100), D. Bilbao, Jochen A. Lauterbach

Faculty Publications

Fingering instabilities arising from local perturbations to planar reaction fronts in the CO oxidation reaction on Pt(100) are presented. CO oxidation represents a heterogeneous nonlinear system with the necessary kinetic and diffusive transport properties to support the development of fingered wave fronts. External forcing was utilized to create CO wave fronts on an otherwise monostable, O-covered surface, which, upon destabilization, gave rise to fingers of adsorbed CO extending into the O adlayer ahead of the reaction front. Finger spreading and tip-splitting were observed as the finger pattern evolved towards an intrinsic wavelength, independent of the length of the reaction front, …

Gene Order Phylogeny Of The Genus Prochlorococcus, Haiwei Luo, Jian Shi, William Arndt, Jijun Tang, Robert Friedman

Faculty Publications

Background
Using gene order as a phylogenetic character has the potential to resolve previously unresolved species relationships. This character was used to resolve the evolutionary history within the genus Prochlorococcus, a group of marine cyanobacteria.

Methodology/Principal Findings
Orthologous gene sets and their genomic positions were identified from 12 species of Prochlorococcus and 1 outgroup species of Synechococcus. From this data, inversion and breakpoint distance-based phylogenetic trees were computed by GRAPPA and FastME. Statistical support of the resulting topology was obtained by application of a 50% jackknife resampling technique. The result was consistent and congruent with nucleotide sequence-based and gene-content based …

Predicting Young’S Modulus Of Nanowires From First-Principles Calculations On Their Surface And Bulk Materials, Guofeng Wang, Xiaodong Li

Faculty Publications

Using the concept of surface stress, we developed a model that is able to predict Young’s modulus of nanowires as a function of nanowire diameters from the calculated properties of their surface and bulk materials. We took both equilibrium strain effect and surface stress effect into consideration to account for the geometric size influence on the elastic properties of nanowires. In this work, we combined first-principles density functional theory calculations of material properties with linear elasticity theory of clamped-end three-point bending. Furthermore, we applied this computational approach to Ag, Au, and ZnOnanowires. For both Ag and Aunanowires, our theoretical predictions …

A Special-Purpose Architecture For Solving The Breakpoint Median Problem, Jason D. Bakos, Panormitis E. Elenis

Faculty Publications

In this paper, we describe the design for a co-processor for whole-genome phylogenetic reconstruction. Our current design performs a parallelized breakpoint median computation, which is an expensive component of the overall application. When implemented on a field-programmable gate array (FPGA), our hardware breakpoint median achieves a maximum speedup of 1005times over software. When the coprocessor is used to accelerate the entire reconstruction procedure, we achieve a maximum application speedup of 417times. The results in this paper suggest that FPGA-based acceleration is a promising approach for computationally expensive phylogenetic problems, in spite of the fact that the involved algorithms are based …

Improving Reversal Median Computation Using Commuting Reversals And Cycle Information, William Arndt, Jijun Tang

Faculty Publications

In the past decade, genome rearrangements have attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. Methods for reconstructing phylogeny from genome rearrangements include distance-based methods, MCMC methods, and direct optimization methods. The latter, pioneered by Sankoff and extended with the software suites GRAPPA and MGR, is the most accurate approach, but is very limited due to the difficulty of its scoring procedure—it must solve multiple instances of the reversal median problem to compute the score of a given tree. The reversal median problem is known to be NP-hard and all …

Multi-Break Rearrangements And Breakpoint Re-Uses: From Circular To Linear Genomes, Max A. Alekseyev

Faculty Publications

Multi-break rearrangements break a genome into multiple fragments and further glue them together in a new order. While 2-break rearrangements represent standard reversals, fusions, fissions, and translocations, 3-break rearrangements represent a natural generalization of transpositions. Alekseyev and Pevzner (2007a, 2008a) studied multi-break rearrangements in circular genomes and further applied them to the analysis of chromosomal evolution in mammalian genomes. In this paper, we extend these results to the more difficult case of linear genomes. In particular, we give lower bounds for the rearrangement distance between linear genomes and for the breakpoint re-use rate as functions of the number and proportion …

Evaluating Shape Correspondence For Statistical Shape Analysis: A Benchmark Study, Brent C. Munsell, Pahal Dalal, Song Wang

Faculty Publications

This paper introduces a new benchmark study to evaluate the performance of landmark-based shape correspondence used for statistical shape analysis. Different from previous shape-correspondence evaluation methods, the proposed benchmark first generates a large set of synthetic shape instances by randomly sampling a given statistical shape model that defines a ground-truth shape space. We then run a test shape-correspondence algorithm on these synthetic shape instances to identify a set of corresponded landmarks. According to the identified corresponded landmarks, we construct a new statistical shape model, which defines a new shape space. We finally compare this new shape space against the ground-truth …

Phylogenetic Reconstruction From Transpositions, Feng Yue, Meng Zhang, Jijun Tang

Faculty Publications

Background
Because of the advent of high-throughput sequencing and the consequent reduction in the cost of sequencing, many organisms have been completely sequenced and most of their genes identified. It thus has become possible to represent whole genomes as ordered lists of gene identifiers and to study the rearrangement of these entities through computational means. As a result, genome rearrangement data has attracted increasing attentions from both biologists and computer scientists as a new type of data for phylogenetic analysis. The main events of genome rearrangements include inversions, transpositions and transversions. To date, GRAPPA and MGR are the most accurate …

The 5 Ghz Airport Surface Area Channel: Part Ii, Measurement And Modeling Results For Small Airports, Indranil Sen, David W. Matolak

Faculty Publications

This paper describes results from a channel measurement campaign performed at several small airports in the U.S. in the 5-GHz band. This paper is a companion to another paper, which describes channel models for large airports. We classify the small airport surface channel into three propagation regions based upon different delay dispersion conditions. The channel characteristics of these regions in the delay and frequency domains are discussed with examples. We provide empirical stochastic channel models (of different bandwidths) to accurately represent the channel on the airport surface area for all propagation regions. The models are provided in the form of …

Predicting The Hydrogen Pressure To Achieve Ultralow Friction And Diamondlike Carbon Surfaces From First Principles, Haibo Guo, Yue Qi, Xiaodong Li

Faculty Publications

Hydrogen atmosphere can significantly change the tribological behavior at diamond and diamondlike carbon (DLC) surfaces and the friction-reducing effect depends on the partial pressure of hydrogen. We combined density functional theory modeling and thermodynamic quantities to predict the equilibrium partial pressures of hydrogen at temperature T, P_H2 (T), for a fully atomic hydrogen passivated diamondsurface. Above the equilibrium P_H2 (T), ultralow friction can be achieved at diamond and DLC surfaces. The calculation agrees well with friction tests at various testing conditions. We also show that P_H2 (T) …

Vehicle-Vehicle Channel Models For The 5 Ghz Band, Indranil Sen, David W. Matolak

Faculty Publications

In this paper, we describe the results of a channel measurement and modeling campaign for the vehicle-to-vehicle (V2V) channel in the 5-GHz band. We describe measurements and results for delay spread, amplitude statistics, and correlations for multiple V2V environments. We also discuss considerations used in developing statistical channel models for these environments and provide some sample results. Several statistical channel models are presented, and using simulation results, we elucidate tradeoffs between model implementation complexity and fidelity. The channel models presented should be useful for system designers in future V2V communication systems.

Channel Modeling For Vehicle-To-Vehicle Communications, David W. Matolak

Faculty Publications

Physical layer channel modeling is critical for design and performance evaluation at multiple layers of the communications protocol stack. In this article we describe and provide results for modeling vehicle-to-vehicle (V2V) wireless channels. V2V settings produce some unique conditions, and due to these conditions, V2V channels often exhibit greater dynamics than many conventional channels and, in addition, can also exhibit more severe fading. Thus, new channel models are needed to characterize this setting in order to evaluate contending transmission schemes and aid in V2V communication system design. A brief review of key statistical channel parameters is provided. Then both analytical …

The Role Of Filler-Matrix Interaction On Viscoelastic Response Of Biomimetic Nanocomposite Hydrogels, Alireza S. Sarvestani, Xuezhong He, Esmaiel Jabbari

Faculty Publications

The effect of a glutamic acid (negatively charged) peptide (Glu6), which mimics the terminal region of the osteonectin glycoprotein of bone on the shear modulus of a synthetic hydorgel/apatite nanocomposite, was investigated. One end of the synthesized peptide was functionalized with an acrylate group (Ac-Glu6) to covalently attach the peptide to the hydrogel phase of the composite matrix. The addition of Ac-Glu6 to hydroxyapatite (HA) nanoparticles (50 nm in size) resulted in significant reinforcement of the shear modulus of the nanocomposite (% increase in elastic shear modulus). The reinforcement effect of the Glu6 peptide, a sequence in the terminal region …

Novel Wideband Directional Dipole Antenna On A Mushroom Like Ebg Structure, Mohammed Z. Azad, Mohammod Ali

Faculty Publications

A new method to design thin wideband directional dipole antennas on electromagnetic bandgap (EBG) structure is introduced. At the heart of this method is the idea to understand and properly utilize the complex interactions between the dipole impedance and the EBG reflection phase characteristics. Using the proposed technique a thin wideband printed dipole is designed, fabricated and tested. The antenna can satisfy applications, such as Digital Communication System (DCS, 1.71-1.88 GHz), Global System for Mobile Communication (GSM, 1.85-1.99 GHz), Personal Communication System (PCS, 1.85-2.05 GHz), Universal Mobile Telecommunication System (UMTS, 1.92-2.17 GHz) and Wireless Local area Network (WLAN, 2.4-2.485 GHz) …

Spectrally Shaped Generalized Mc-Ds-Cdma With Dual Band Combining For Increased Diversity, Wenhui Xiong, David W. Matolak

Faculty Publications

A new multicarrier spread spectrum modulation scheme is proposed in this paper. This scheme uses sinusoidal chip waveforms to shape the spectrum of each subcarrier of a multicarrier direct sequence spread spectrum (DS-SS) signal. As a result, each subcarrier has two distinct spectral lobes, one a lower sideband (LSB) and the other an upper sideband (USB). By properly selecting the parameters of the sinusoidal chip waveforms, the two sideband signals can be made to undergo independent fading in a dispersive fading channel. These two independently-faded sideband signals, when combined at the receiver, provide diversity gain to the system. Our analysis …

Gene Rearrangement Analysis And Ancestral Order Inference From Chloroplast Genomes With Inverted Repeat, Feng Yue, Liying Cui, Claude W. Depamphilis, Bernard M.E. Moret, Jijun Tang

Faculty Publications

Background
Genome evolution is shaped not only by nucleotide substitutions, but also by structural changes including gene and genome duplications, insertions, deletions and gene order rearrangements. The most popular methods for reconstructing phylogeny from genome rearrangements include GRAPPA and MGR. However these methods are limited to cases where equal gene content or few deletions can be assumed. Since conserved duplicated regions are present in many chloroplast genomes, the inference of inverted repeats is needed in chloroplast phylogeny analysis and ancestral genome reconstruction.

Results
We extend GRAPPA and develop a new method GRAPPA-IR to handle chloroplast genomes. A test of GRAPPA-IR …

Wideband Smaller Unit-Cell Planar Ebg Structures And Their Application, M. Faisal Abedin, Mohammed Z. Azad, Mohammod Ali

Faculty Publications

A new low-cost smaller unit-cell planar electromagnetic bandgap (ERG) structure operating at the lower GHz frequencies (below 6 GHz) is proposed. ERG structures based on this new geometry are designed on a number of commonly available substrates. Characteristics of such structures, such as bandgap and reflection phase profile are analyzed. a simple empirical model is proposed to predict the surface wave stopband frequency of the proposed ERG structure. Finally, a low-profile dipole antenna is designed and tested for operation on the ERG structure.

Globally Optimal Grouping For Symmetric Closed Boundaries By Combining Boundary And Region Information, Joachim S. Stahl, Song Wang

Faculty Publications

Many natural and man-made structures have a boundary that shows a certain level of bilateral symmetry, a property that plays an important role in both human and computer vision. In this paper, we present a new grouping method for detecting closed boundaries with symmetry. We first construct a new type of grouping token in the form of symmetric trapezoids by pairing line segments detected from the image. A closed boundary can then be achieved by connecting some trapezoids with a sequence of gap-filling quadrilaterals. For such a closed boundary, we define a unified grouping cost function in a ratio form: …

Web-Scale Workflow: Integrating Distributed Services, M. Brian Blake, Michael N. Huhns

Faculty Publications

Modular applications, components, and services are all ways of describing the product of an organization's efforts to embody its capabilities in autonomous software modules. In fact, the integration of services using well-established workflow paradigms could amplify an organization's capabilities with the creation of a full-blown, inter-organizational system of systems. This is the essence of Web-scale workflows. Considering the recent popularity and acceptance of service-oriented technologies, the application of such distributed systems is only limited by imagination, but it's also important to understand existing research challenges and their implications to various Web-scale workflow domains.

Hydrogen Peroxide Formation Rates In A Pemfc Anode And Cathode: Effect Of Humidity And Temperature, Vijay A. Sethuraman, John W. Weidner, Andrew T. Haug, Sathya Motupally, Lesia V. Protsailo

Faculty Publications

Hydrogen peroxide (H₂O₂) formation rates in a proton exchange membrane fuel cell (PEMFC) anode and cathode were estimated as a function of humidity and temperature by studying the oxygen reduction reaction (ORR) on a rotating ring disk electrode. Fuel cell conditions were replicated by depositing a film of Pt/Vulcan XC-72 catalyst onto the disk and by varying the temperature, dissolved O₂ concentration, and the acidity levels in hydrochloric acid (HClO₄). The HClO₄ acidity was correlated to ionomer water activity and hence fuel cell humidity. The H₂O₂ formation rates showed …

Analytical Expression For The Impedance Response For A Lithium-Ion Cell, Godfrey Sikha, Ralph E. White

Faculty Publications

An analytical expression to predict the impedance response of a dual insertion electrode cell (insertion electrodes separated by an ionically conducting membrane) is presented. The expression accounts for the reaction kinetics and double-layer adsorption processes at the electrode-electrolyte interface, transport of electroactive species in the electrolyte phase, and insertion of species in the solid phase of the insertion electrodes. The accuracy of the analytical expression is validated by comparing the impedance response predicted by the expression to the corresponding numerical solution. The analytical expression is used to predict the impedance response of a lithium-ion cell consisting of a porous LiCoO …

Parameter Estimation And Life Modeling Of Lithium-Ion Cells, Shriram Santhanagopalan, Qi Zhang, Karthikeyan Kumaresan, Ralph E. White

Faculty Publications

Lithium-ion pouch cells were cycled at five different temperatures (5, 15, 25, 35, and 45°C ), and rate capability studies were performed after every hundred cycles. The data were used with a simple physics-based model to estimate parameters that capture the capacity fade in the cell, with cycling. The weight of active material within each electrode was estimated as a function of time, using rate capability data at the C/33 rate. The C-rate for these cells is 1.656 A. The capacity fade due to the loss of active material and that due to the loss of cyclable lithium …

Enhanced Dielectric Properties In Single Crystal-Like Bifeo3 Thin Films Grown By Flux-Mediated Epitaxy, S.-H. Lim, M. Murakami, J. H. Yang, S.-Y. Young, Jason R. Hattrick-Simpers, M. Wuttig, L. G. Salamanca-Riba, I. Takeuchi

Faculty Publications

We have fabricated single crystal-like BiFeO₃ (BFO) thin films by flux-mediated epitaxy using pulsed laser deposition(PLD). The Bi–Cu–O flux composition and its thickness were optimized using composition spread, thickness gradient, and temperature gradient libraries. The optimized BFO thin films grown with this technique showed larger grain size of ∼2μm and higher dielectric constant in the range of 260–340 than those for standard PLD grown films. In addition, the leakage current density of the films was reduced by two orders of magnitude compared to that of standard PLD grown films.

Elastic Wave Field Computation In Multilayered Nonplanar Solid Structures: A Mesh-Free Semianalytical Approach, Sourav Banerjee, Tribikram Kundu

Faculty Publications

Multilayered solid structures made of isotropic, transversely isotropic, or general anisotropic materials are frequently used in aerospace, mechanical, and civil structures. Ultrasonic fields developed in such structures by finite size transducers simulating actual experiments in laboratories or in the field have not been rigorously studied. Several attempts to compute the ultrasonic field inside solid media have been made based on approximate paraxial methods like the classical ray tracing and multi-Gaussian beam models. These approximate methods have several limitations. A new semianalytical method is adopted in this article to model elastic wave field in multilayered solid structures with planar or nonplanar …

Combinatorial Investigation Of Magnetostriction In Fe-Fa And Fe-Ga-Al, Jason R. Hattrick-Simpers, Dwight Hunter, Corneliu M. Craciunescu, Kyu Sung Jang, Makoto Murakami, James Cullen, Manfred Wuttig, Ichiro Takeuchi, Samuel E. Lofland, Leonid Bendersky, Noble Woo, Robert Bruce Vandover, Toshiya Takahashi, Yasubumi Furuya

Faculty Publications

A high-throughput high-sensitivity optical technique for measuringmagnetostriction of thin-film composition-spread samples has been developed. It determines the magnetostriction by measuring the induced deflection of micromachined cantilever unimorph samples. Magnetostrictionmeasurements have been performed on as-deposited Fe–Ga and Fe–Ga–Al thin-film composition spreads. The thin-film Fe–Ga spreads display a similar compositional variation of magnetostriction as bulk. A previously undiscovered peak in magnetostriction at low Ga content was also observed and attributed to a maximum in the magnetocrystalline anisotropy. Magnetostrictive mapping of the Fe–Ga–Al ternary system reveals the possibility of substituting up to 8at.%Al in Fe₇₀Ga₃₀ without significant degradation of magnetostriction.

High-Throughput Screening Of Shape Memory Alloy Thin-Film Spreads Using Nanoindentation, Arpit Dwivedi, Thomas J. Wyrobek, Oden L. Warren, Jason R. Hattrick-Simpers, Olubenga O. Famodu, Ichiro Takeuchi

Faculty Publications

We have demonstrated the utility of nanoindentation as a rapid characterization tool for mapping shape memoryalloy compositions in combinatorial thin-film libraries. Nanoindentation was performed on Ni–Mn–Al ternary composition spreads. The indentation hardness and the reduced elastic modulus were mapped across a large fraction of the ternary phase diagram. The large shape memoryalloy composition region, located around the Heusler composition (Ni₂MnAl), was found to display significant departure in these mechanical properties from the rest of the composition spread. In particular, the modulus and the hardness values are lower for the martensite region than those of the rest of the …

Acceptor Levels In Gase:In Crystals Investigated By Deep-Level Transient Spectroscopy And Photoluminescence, Y. Cui, R. Dupere, A. Burger, D. Johnstone, K. C. Mandal, S. A. Payne

Faculty Publications

No abstract provided.

Durability Of Perfluorosulfonic Acid And Hydrocarbon Membranes: Effect Of Humidity And Temperature, Vijay A. Sethuraman, John W. Weidner, Andrew T. Haug, Lesia V. Protsailo

Faculty Publications

The effect of humidity on the chemical stability of two types of membranes [i.e., perfluorosulfonic acid type (PFSA, Nafion 112) and biphenyl sulfone hydrocarbon type, (BPSH-35)] was studied by subjecting the membrane electrode assemblies (MEAs) to open-circuit voltage (OCV) decay and potential cycling tests at elevated temperatures and low inlet-gas relative humidities. The BPSH-35 membranes showed poor chemical stability in ex situ Fenton tests compared to that of Nafion membranes. However, under fuel cell conditions, BPSH-35 MEAs outperformed Nafion 112 MEAs in both the OCV decay and potential cycling tests. For both membranes, (i) at a given temperature, …

The Role Of Filler-Matrix Interaction On Viscoelastic Response Of Biomimetic Nanocomposite Hydrogels, Alireza S. Sarvestani, Xuezhong He, Esmaiel Jabbari

Faculty Publications

The effect of a glutamic acid (negatively charged) peptide (Glu6), which mimics the terminal region of the osteonectin glycoprotein of bone on the shear modulus of a synthetic hydorgel/apatite nanocomposite, was investigated. One end of the synthesized peptide was functionalized with an acrylate group (Ac-Glu6) to covalently attach the peptide to the hydrogel phase of the composite matrix. The addition of Ac-Glu6 to hydroxyapatite (HA) nanoparticles (50 nm in size) resulted in significant reinforcement of the shear modulus of the nanocomposite (~100% increase in elastic shear modulus). The reinforcement effect of the Glu6 peptide, a sequence in the terminal region …

Thermal Model For A Li-Ion Cell, Karthikeyan Kumaresan, Godfrey Sikha, Ralph E. White

Faculty Publications

A thermal model for a lithium-ion cell is presented and used to predict discharge performance at different operating temperatures. The results from the simulations are compared to experimental data obtained from lithium-ion pouch cells. The model includes a set of parameters (and their concentration and temperature dependencies) that has been obtained for a lithium-ion cell composed of a mesocarbon microbead anode, LiCoO₂ cathode in 1 M LiPF₆ salt, in a mixture of ethylene carbonate, propylene carbonate, ethyl-methyl carbonate, and diethyl carbonate electrolyte. The parameter set was obtained by comparing the model predictions to the experimental discharge profiles obtained …