JECS Faculty Research

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GPU-Based Computation of Discrete Periodic Centroidal Voronoi Tessellation in Hyperbolic Space
(2012-02) Shuai, Liang; Guo, Xiaohu
Periodic centroidal Voronoi tessellation (CVT) in hyperbolic space provides a nice theoretical framework for computing the constrained CVT on high-genus (genus > 1) surfaces. This paper addresses two computational issues related to such hyperbolic CVT framework: (1) efficient reduction of unnecessary site copies in neighbor domains on the universal covering space, based on two special rules; (2) GPU-based parallel algorithms to compute a discrete version of the hyperbolic CVT. Our experiments show that with the dramatically reduced number of unnecessary site copies in neighbor domains and the GPU-based parallel algorithms, we significantly speed up the computation of CVT for high-genus surfaces. The proposed discrete hyperbolic CVT guarantees to converge and produces high-quality results.
On the coarseness of bicolored point sets
(Elsevier B. V., 2012-04-24) Bereg, Sergey; Díaz-Báñez, J. M.; Lara, D.; Pérez-Lantero, P.; Seara, C.; Urrutia, J.; Bereg, Sergey
Let R be a set of red points and B a set of blue points on the plane. In this paper we introduce a new concept, which we call coarseness, for measuring how blended the elements of S=R⊃B are. For X∪S, let Δ(X)=
Investigation of interfacial oxidation control using sacrificial metallic Al and La passivation layers on InGaAs
(2012-05-25) Brennan, Barry; Milojevic, Marko; Contreras-Guerrero, Roccio; Kim, Hyun-Chul; Lopez-Lopez, Maximo; Kim, Jiyoung; Wallace, Robert M.; 70133685 (Kim, J)
The ability of metallic Al and La interlayers to control the oxidation of InGaAs substrates is examined by monochromatic x-ray photoelectron spectroscopy (XPS) and compared to the interfacial chemistry of atomic layer deposition (ALD) of Al2O3 directly on InGaAs surfaces. Al and La layers were deposited by electron-beam and effusion cell evaporators, respectively, on In0.53Ga0.47As samples with and without native oxides present. It was found that both metals are extremely efficient at scavenging oxygen from III-V native oxides, which are removed below XPS detection limits prior to ALD growth. However, metallic Ga//In/As species are simultaneously observed to form at the semiconductor-metal interface. Upon introduction of the samples to the ALD chamber, these metal bonds are seen to oxidize, leading to Ga/In-O bond growth that cannot be controlled by subsequent trimethyl-aluminum (TMA) exposures. Deposition on an oxide-free InGaAs surface results in both La and Al atoms displacing group III atoms near the surface of the semiconductor. The displaced substrate atoms tend to partially oxidize and leave both metallic and III-V oxide species trapped below the interlayers where they cannot be "cleaned-up" by TMA. For both Al and La layers the level of Ga-O bonding detected at the interface appears larger then that seen following ALD directly on a clean surface.
A protocol for the secure linking of registries for HPV surveillance
(2012-07-02) El Emam, Khaled; Samet, Saeed; Hu, Jun; Peyton, Liam; Earle, Craig; Jayaraman, Gayatri C.; Wong, Tom; Kantarcioglu, Murat; Dankar, Fida; Essex, Aleksander
Introduction: In order to monitor the effectiveness of HPV vaccination in Canada the linkage of multiple data registries may be required. These registries may not always be managed by the same organization and, furthermore, privacy legislation or practices may restrict any data linkages of records that can actually be done among registries. The objective of this study was to develop a secure protocol for linking data from different registries and to allow on-going monitoring of HPV vaccine effectiveness. Methods: A secure linking protocol, using commutative hash functions and secure multi-party computation techniques was developed. This protocol allows for the exact matching of records among registries and the computation of statistics on the linked data while meeting five practical requirements to ensure patient confidentiality and privacy. The statistics considered were: odds ratio and its confidence interval, chi-square test, and relative risk and its confidence interval. Additional statistics on contingency tables, such as other measures of association, can be added using the same principles presented. The computation time performance of this protocol was evaluated. Results: The protocol has acceptable computation time and scales linearly with the size of the data set and the size of the contingency table. The worse case computation time for up to 100, 000 patients returned by each query and a 16 cell contingency table is less than 4 hours for basic statistics, and the best case is under 3 hours. Discussion: A computationally practical protocol for the secure linking of data from multiple registries has been demonstrated in the context of HPV vaccine initiative impact assessment. The basic protocol can be generalized to the surveillance of other conditions, diseases, or vaccination programs. © 2012 El Emam et al.
In Situ Chemical Oxidation of Ultrasmall MoOx Nanoparticles in Suspensions
(2012-07-23) Lee, Yun-Ju; Barrera, Diego; Luo, Kaiyuan; Hsu, Julia W. P.; 0000 0003 8600 0978 (Hsu, JWP); 243648305 (Hsu, JWP)
Nanoparticle suspensions represent a promising route toward low cost, large area solution deposition of functional thin films for applications in energy conversion, flexible electronics, and sensors. However, parameters such size, stoichiometry, and electronic properties must be controlled to achieve best results for the target application. In this report, we demonstrate that such control can be achieved via in situ chemical oxidation of M o O 𝑥 nanoparticles in suspensions. Starting from a microwave-synthesized suspension of ultrasmall ( 𝑑 ∼ 2 nm) M o O 𝑥 nanoparticles in n-butanol, we added H2O2 at room temperature to chemically oxidize the nanoparticles. We systematically varied H2O2 concentration and reaction time and found that they significantly affected oxidation state and work function of MoO𝑥 nanoparticle films. In particular, we achieved a continuous tuning of MoO𝑥 work function from 4.4 to 5.0 eV, corresponding to oxidation of as-synthesized MoO𝑥 nanoparticle (20% Mo6+) to essentially pure MoO3. This was achieved without significantly modifying nanoparticle size or stability. Such precise control of MoO𝑥 stoichiometry and work function is critical for the optimization of MoO𝑥 nanoparticles for applications in organic optoelectronics. Moreover, the simplicity of the chemical oxidation procedure should be applicable for the development of other transition oxide nanomaterials with tunable composition and properties.
Wet chemical surface functionalization of oxide-free silicon
(Elsevier Limited, 2012-09-13) Thissen, Peter; Seitz, Oliver; Chabal, Yves J.; 0000 0000 4239 3958 (Chabal, YJ); 89624105 (Chabal, YJ)
Silicon is by far the most important semiconductor material in the microelectronic industry mostly due to the high quality of the Si/SiO2 interface. Consequently, applications requiring chemical functionalization of Si substrates have focused on molecular grafting of SiO2 surfaces. Unfortunately, there are practical problems affecting homogeneity and stability of many organic layers grafted on silicon oxide (SiO2), such as silanes and phosphonates, related to polymerization and hydrolysis of Si-O-Si and Si-O-P bonds. These issues have stimulated efforts in grafting functional molecules on oxide-free Si surfaces, mostly with wet chemical processes. This review focuses therefore directly on wet-chemical surface functionalization of oxide-free Si surfaces, starting from H-terminated Si surfaces. The main preparation methods of oxide-free H-terminated Si and their stability are first summarized. Functionalization is then classified into indirect substitution of H-termination by functional organic molecules, such as hydrosilylation, and direct substitution by other atoms (e.g. halogens) or small functional groups (e.g. OH, NH2) that can be used for further reaction. An emphasis is placed on a recently discovered method to produce a nanopattern of functional groups on otherwise oxide-free, H-terminated and atomically flat Si(111) surfaces. Such model surfaces are particularly interesting because they make it possible to derive fundamental knowledge of surface chemical reactions.
Comparison endpoint study of process plasma and secondary electron beam exciter optical emission spectroscopy
(American Vacuum Society, 2012-10-03) Thamban, P. L. Steven; Padron-Wells, Gabriel; Hosch, Jimmy W.; Yun, Stuart; Goeckner, Matthew J.; 0000 0001 2766 4681 (Thamban, PLS); 0000 0000 5396 3610 (Goeckner, MJ); 2008008261‏ (Goeckner, MJ)
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Optimizing Diode Thickness for Thin-Film Solid State Thermal Neutron Detectors
(American Institute of Physics, 2012-10-04) Murphy, John W.; Mejia, Israel; Quevedo-López, Manuel A.; Gnade, Bruce E.; 0000 0003 8371 1336 (Gnade, BE); 00049719‏ (Gnade, BE); Erik Jonsson School of Engineering and Computer Science
In this work, we investigate the optimal thickness of a semiconductor diode for thin-film solid state thermal neutron detectors. We evaluate several diode materials, Si, CdTe, GaAs, C (diamond), and ZnO, and two neutron converter materials, 10B and 6LiF. Investigating a coplanar diode/converter geometry, we determine the minimum semiconductor thickness needed to achieve maximum neutron detection efficiency. By keeping the semiconductor thickness to a minimum, gamma rejection is kept as high as possible. In this way, we optimize detector performance for different thin-film semiconductor materials.
In situ atomic layer deposition half cycle study of Al2O 3 growth on AlGaN
(American Institute of Physics, 2012-11-10) Brennan, Barry; Qin, Xiaoye; Dong, Hong; Kim, Jiyoung; Wallace, Robert M.; 70133685 (Kim, J)
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Synthetic Mammalian Transgene Negative Autoregulation
(2013-06-04) Shimoga, Vinay; White, Jacob T.; Li, Yi; Sontag, Eduardo; Bleris, Leonidas; 0000 0001 2535 9739 (Bleris, L); 2012076942‏ (Bleris, L)
Biological networks contain overrepresented small-scale topologies, typically called motifs. A frequently appearing motif is the transcriptional negative-feedback loop, where a gene product represses its own transcription. Here, using synthetic circuits stably integrated in human kidney cells, we study the effect of negative-feedback regulation on cell-wide (extrinsic) and gene-specific (intrinsic) sources of uncertainty. We develop a theoretical approach to extract the two noise components from experiments and show that negative feedback results in significant total noise reduction by reducing extrinsic noise while marginally increasing intrinsic noise. We compare the results to simple negative regulation, where a constitutively transcribed transcription factor represses a reporter protein. We observe that the control architecture also reduces the extrinsic noise but results in substantially higher intrinsic fluctuations. We conclude that negative feedback is the most efficient way to mitigate the effects of extrinsic fluctuations by a sole regulatory wiring.;
Transcripts for Combined Synthetic MicroRNA and Gene Delivery
(2013-06-26) Kashyap, Neha; Pham, Bich; Xie, Zhen; Bleris, Leonidas; 0000 0001 2535 9739 (Bleris, L)
MicroRNAs (miRNAs) are a class of short noncoding RNAs which are endogenously expressed in many organisms and regulate gene expression by binding to messenger RNA (mRNA). MicroRNAs are either produced from their independent transcription units in intergenic regions or lie in intragenic regions. Intragenic miRNAs and their host mRNAs are produced from the same transcript by the microprocessor and the spliceosome protein complex respectively. The details and exact timing of the processing events have implications for downstream RNA interference (RNAi) efficiency and mRNA stability. Here we engineer and study in mammalian cells a range of synthetic intragenic miRNAs co-expressed with their host genes. Furthermore, we study transcripts which carry the target of the miRNA, thereby emulating a common regulation mechanism. We perform fluorescence microscopy and flow cytometry to characterize the engineered transcripts and investigate the properties of the underlying biological processes. Our results shed additional light on miRNA and pre-mRNA processing but importantly provide insight into engineering transcripts customized for combined delivery and use in synthetic gene circuits.;
Energy Transfer from Colloidal Nanocrystals into Si Substrates Studied via Photoluminescence Photon Counts and Decay Kinetics
(2013-08-16) Nguyen, H. M.; Seitz, Oliver; Gartstein, Yuri N.; Chabal, Yves J.; Malko, Anton V.; 0000 0001 2678 9765 (Malko, AV); Nguyen, H. M.; Seitz, Oliver; Gartstein, Yuri N.; Chabal, Yves J.; Malko, Anton V.
We use time-resolved photoluminescence (PL) kinetics and PL intensity measurements to study the decay of photoexcitations in colloidal CdSe/ZnS nanocrystals grafted on SiO₂ - Si substrates with a wide range of the SiO₂ spacer layer thicknesses. The salient features of experimental observations are found to be in good agreement with theoretical expectations within the framework of modification of spontaneous decay of electric-dipole excitons by their environment. Analysis of the experimental data reveals that energy transfer (ET) from nanocrystals into Si is a major enabler of substantial variations in decay rates, where we quantitatively distinguish contributions from nonradiative and radiative ET channels. We demonstrate that time-resolved PL kinetics provides a more direct assessment of ET, while PL intensity measurements are also affected by the specifics of the generation and emission processes.
In Situ Study of the Role of Substrate Temperature during Atomic Layer Deposition of HfO2 on InP
(2013-10-16) Dong, Hong; Santosh, KC; Qin, Xiaoye; Brennan, Barry; McDonnell, Steven; Zhernokletov, Dmitry; Hinkle, Christopher L.; Kim, Jiyoung; Cho, Kyeongjie; Wallace, Robert M.; 70133685 (Kim, J)
The dependence of the "self cleaning" effect of the substrate oxides on substrate temperature during atomic layer deposition (ALD) of HfO₂ on various chemically treated and native oxide InP (100) substrates is investigated using in situ X-ray photoelectron spectroscopy. The removal of In-oxide is found to be more efficient at higher ALD temperatures. The P oxidation states on native oxide and acid etched samples are seen to change, with the total P-oxide concentration remaining constant, after 10 cycles of ALD HfO₂ at different temperatures. An (NH₄)₂ S treatment is seen to effectively remove native oxides and passivate the InP surfaces independent of substrate temperature studied (200°C, 250°C and 300°C) before and after the ALD process. Density functional theory modeling provides insight into the mechanism of the changes in the P-oxide chemical states.
Structural Variation of Donor-Acceptor Copolymers Containing Benzodithiophene with Bithienyl Substituents to Achieve High Open Circuit Voltage in Bulk Heterojunction Solar Cells
(Royal Soc Chemistry, 2013-11-06) Kularatne, Ruvini S.; Taenzler, Ferdinand J.; Magurudeniya, Harsha D.; Du, Jia; Murphy, John W.; Sheina, E. E.; Gnade, Bruce E.; Biewer, Michael C.; Stefan, Mihaela C.; 0000 0003 8371 1336 (Gnade, BE); 00049719‏ (Gnade, BE); 55039821 (Stefan, MC); Gnade, Bruce E.; Biewer, Michael C.; Stefan, Mihaela C.
Three new donor-acceptor copolymers P1, P2, and P3 were synthesized with benzodithiophene with bithienyl substituents as the donor and 5,6-difluorobenzo[c][1,2,5]thiadiazole, 4,7-di(thiophen-2-yl)benzo[c][1,2,5] thiadiazole, and 5,6-difluoro-4,7-di(thiophen-2-yl)benzo[c][1,2,5]thiadiazole as the acceptors, respectively. The insertion of thiophene spacer between the donor and the acceptor broadened the absorption of the polymers P2 and P3 and resulted in a red shift of ~30 nm as compared to that of the polymer P1. However, the inclusion of fluorine atoms on the polymer had detrimental effects on the photovoltaic properties of the polymers. The synthesized donor-acceptor polymers were tested in bulk heterojunction (BHJ) solar cells with [6,6]-phenyl C71 butyric acid methyl ester (PC71BM) acceptor. Polymer P2 gave a PCE of 3.52% with PC71BM in which the active layer was prepared in chloroform with 3% v/v 1,8-diiodooctane (DIO) additive. The effect of fluorine substitution and thiophene group insertion on the UV/Vis absorbance, photovoltaic performances, morphology, and charge carrier mobilities for the polymers are discussed.
Selectivity of Metal Oxide Atomic Layer Deposition on Hydrogen Terminated and Oxidized Si(001)-(2x1) Surface
(A V S Amer Inst Physics, 2014-02-10) Longo, Roberto C.; McDonnell, Stephen; Dick, D.; Wallace, Robert M.; Chabal, Yves J.; Owen, James H. G.; Ballard, Josh B.; Randall, John N.; Cho, Kyeongjae; 0000 0000 4239 3958 (Chabal, YJ); 89624105 (Chabal, YJ)
In this work, the authors used density-functional theory methods and x-ray photoelectron spectroscopy to study the chemical composition and growth rate of HfO₂, Al₂O₃, and TiO₂ thin films grown by in-situ atomic layer deposition on both oxidized and hydrogen-terminated Si(001) surfaces. The growth rate of all films is found to be lower on hydrogen-terminated Si with respect to the oxidized Si surface. However, the degree of selectivity is found to be dependent of the deposition material. TiO₂ is found to be highly selective with depositions on the hydrogen terminated silicon having growth rates up to 180 times lower than those on oxidized Si, while similar depositions of HfO₂ and Al₂O₃ resulted in growth rates more than half that on oxidized silicon. By means of density-functional theory methods, the authors elucidate the origin of the different growth rates obtained for the three different precursors, from both energetic and kinetic points of view.
Chemical Bonding and Defect States of LPCVD Grown Silicon-Rich Si₃N₄ for Quantum Dot Applications
(A V S: Science & Technology of Materials, Interfaces, and Processing, 2014-03) Mohammed, Shakil; Nimmo, Michael T.; Malko, Anton V.; Hinkle, Christopher L.; 0000 0001 2678 9765 (Malko, AV); Mohammed, Shakil; Nimmo, Michael T.; Malko, Anton V.; Hinkle, Christopher L.
Si-rich Si₃N₄ (SRN) thin films were investigated to understand the various defect states present within the SRN that can lead to reduced performance in quantum dot based devices made of these materials. The SRN films, deposited by low pressure chemical vapor deposition followed by furnace anneals over a range of temperatures, were determined to be comprised of two distinct phase separated SRN regions with different compositions (precipitates within a host matrix). Photoluminescence (PL) spectra showed multiple peaks convoluted together within the visible and near-visible range. Depending on deposition and annealing conditions, the films displayed changes in PL peak intensities which were correlated with chemical bonding utilizing x-ray photoelectron spectroscopy, Fourier transform infrared spectroscopy, spectroscopic ellipsometry, and capacitance-voltage measurements. It is found that the PL originates from defect-state to defect-state and band edge to defect-state electronic transitions.
Benzodithiophene Homopolymers Synthesized by Grignard Metathesis (GRIM) and Stille Coupling Polymerizations
(Royal Soc Chemistry, 2014-04-16) Magurudeniya, Harsha D.; Kularatne, Ruvini S.; Rainbolt, Elizabeth A.; Bhatt, Mahesh P.; Murphy, John W.; Sheina, Elena E.; Gnade, Bruce E.; Biewer, Michael C.; Stefan, Mihaela C.; 0000 0003 8371 1336 (Gnade, BE); 00049719‏ (Gnade, BE); 55039821 (Stefan, MC); Gnade, Bruce E.; Biewer, Michael C.; Stefan, Mihaela C.
Poly{4,8-bis(95-dodecylthiophene-2-yl) benzo[1,2-b: 4,5-b'] dithiophene} has been synthesized by both Grignard metathesis (P1) and Stille coupling polymerizations (P2). Polymers P1 and P2 were characterized and their optoelectronic properties, charge carrier mobilities, and photovoltaic properties were compared. The field-effect mobilities of the polymers were measured on both untreated and heptadecafluoro-1,1,2,2-tetrahydro-decyl-1-trimethoxysilane (FS) treated organic field effect transistor (OFET) devices. The polymers were also evaluated in bulk heterojunction (BHJ) solar cells with [6,6]-phenyl-C-71-butyric acid methyl ester (PC71BM) as the acceptor.
Effects of Nanostructure Geometry on Nanoimprinted Polymer Photovoltaics
(RSC Pub, 2014-04-23) Yang, Yi; Mielczarek, Kamil; Aryal, Mukti; Zakhidov, Anvar A.; Hu, Wenchuang (Walter); 0000 0003 5287 0481 (Zakhidov, AA); 2005061514 (Hu, W); Zakhidov, Anvar A.; Hu, Wenchuang (Walter)
We demonstrate the effects of nanostructure geometry on the nanoimprint induced poly(3-hexylthiophene-2,5-diyl) (P3HT) chain alignment and the performance of nanoimprinted photovoltaic devices. Out-of-plane and in-plane grazing incident X-ray diffraction techniques are employed to characterize the nanoimprint induced chain alignment in P3HT nanogratings with different widths, spacings and heights. We observe the dependence of the crystallite orientation on nanostructure geometry such that a larger width of P3HT nanogratings leads to more edge-on chain alignment while the increase in height gives more vertical alignment. Consequently, P3HT/6,6]-phenyl-C61-butyric-acid-methyl-ester (PCBM) solar cells with the highest density and aspect ratio P3HT nanostructures show the highest power conversion efficiency among others, which is attributed to the efficient charge separation, transport and light absorption.
Assembly and Validation of Versatile Transcription Activator-Like Effector Libraries
(Nature Publishing Group, 2014-05-06) Li, Yi; Ehrhardt, Kristina; Zhang, Michael Q.; Bleris, Leonidas; 0000 0001 2535 9739 (Bleris, L); 0000 0001 1707 1372 (Zhang, MQ); 2012076942‏ (Bleris, L); 99086074‏ ‎(Zhang, MQ); Zhang, Michael Q.
The ability to perturb individual genes in genome-wide experiments has been instrumental in unraveling cellular and disease properties. Here we introduce, describe the assembly, and demonstrate the use of comprehensive and versatile transcription activator-like effector (TALE) libraries. As a proof of principle, we built an 11-mer library that covers all possible combinations of the nucleotides that determine the TALE-DNA binding specificity. We demonstrate the versatility of the methodology by constructing a constraint library, customized to bind to a known p53 motif. To verify the functionality in assays, we applied the 11-mer library in yeast-one-hybrid screens to discover TALEs that activate human SCN9A and miR-34b respectively. Additionally, we performed a genome-wide screen using the complete 11-mer library to confirm known genes that confer cycloheximide resistance in yeast. Considering the highly modular nature of TALEs and the versatility and ease of constructing these libraries we envision broad implications for high-throughput genomic assays. ;
Accumulation Capacitance Frequency Dispersion of Ⅲ-Ⅴ Metal-Insulator-Semiconductor Devices due to Disorder Induced Gap States
(American Institute of Physics Inc., 2014-07-07) Galatage, R. V.; Zhernokletov, Dmitry M.; Dong, Hong; Brennan, Barry; Hinkle, Christopher L.; Wallace, Robert M.; Vogel, E. M.
The origin of the anomalous frequency dispersion in accumulation capacitance of metal-insulator-semiconductor devices on InGaAs and InP substrates is investigated using modeling, electrical characterization, and chemical characterization. A comparison of the border trap model and the disorder induced gap state model for frequency dispersion is performed. The fitting of both models to experimental data indicate that the defects responsible for the measured dispersion are within approximately 0.8nm of the surface of the crystalline semiconductor. The correlation between the spectroscopically detected bonding states at the dielectric/III-V interface, the interfacial defect density determined using capacitance-voltage, and modeled capacitance-voltage response strongly suggests that these defects are associated with the disruption of the III-V atomic bonding and not border traps associated with bonding defects within the high-k dielectric.

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