George R. Brown School of Engineering and Computing

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1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes
(Wiley, 2017) He, Ya; Mathieu, Jacques; da Silva, Marcio L.B.; Li, Mengyan; Alvarez, Pedro J.J.
Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4-dioxane (dioxane) as a sole carbon and energy source. Their specific dioxane degradation rates at 30°C, pH = 7 (i.e. 5.7 to 7.1 g-dioxane per g-protein per day) were comparable to those of two dioxane-metabolizing archetypes: Pseudonocardia dioxanivoransCB1190 and Mycobacterium dioxanotrophicusPH-06. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. Acetylene inhibition tests suggest that dioxane degradation was mediated by monooxygenases. However, qPCR analyses targeting the tetrahydrofuran/dioxane monooxygenase gene (thmA/dxmA) (which is, to date, the only sequenced dioxane monooxygenase gene) were negative, indicating that other (as yet unknown) catabolic gene(s) were responsible. DNA sequence analyses also showed threefold to sevenfold enrichment of group 5 and group 6 soluble di-iron monooxygenase (SDIMO) genes relative to the original soil samples. Whereas biodegradation of trace levels of dioxane is a common challenge at contaminated sites, both consortia degraded dioxane at low initial concentrations (300 μg l−1) below detectable levels (5 μg l−1) in bioaugmented microcosms prepared with impacted groundwater. Overall, this work shows that dioxane-degrading bacteria (and the associated natural attenuation potential) exist even in some uncontaminated soils, and may be enriched to broaden bioaugmentation options for sites experiencing insufficient dioxane catabolic capacity.
1-bit Phase Shifters for Large-Antenna Full-Duplex mmWave Communications
(IEEE, 2020) da Silva, José Mairton Barros Jr.; Sabharwal, Ashutosh; Fodor, Gábor; Fischione, Carlo
Millimeter-wave using large-antenna arrays is a key technological component for the future cellular systems, where it is expected that hybrid beamforming along with quantized phase shifters will be used due to their implementation and cost efficiency. In this paper, we investigate the efficacy of full-duplex mmWave communication with hybrid beamforming using low-resolution phase shifters. We assume that the self-interference can be sufficiently cancelled by a combination of propagation domain and digital self-interference techniques, without any analog self-interference cancellation. We formulate the problem of joint self-interference suppression and downlink beamforming as a mixed-integer nonconvex joint optimization problem. We propose LowRes, a near-to-optimal solution using penalty dual decomposition. Numerical results indicate that LowRes using low-resolution phase shifters perform within 3% of the optimal solution that uses infinite phase shifter resolution. Moreover, even a single quantization bit outperforms half-duplex transmissions, respectively by 29% and 10% for both low and high residual self-interference scenarios, and for a wide range of practical antenna to radio-chain ratios. Thus, we conclude that 1-bit phase shifters suffice for full-duplex millimeter-wave communications, without requiring any additional new analog hardware.
25th Anniversary Article: Ordered Polymer Structures for the Engineering of Photons and Phonons
(Wiley, 2014) Lee, Jae-Hwang; Koh, Cheong Yang; Singer, Jonathan P.; Jeon, Seog-Jin; Maldovan, Martin; Stein, Ori; Thomas, Edwin L.
The engineering of optical and acoustic material functionalities via construction of ordered local and global architectures on various length scales commensurate with and well below the characteristic length scales of photons and phonons in the material is an indispensable and powerful means to develop novel materials. In the current mature status of photonics, polymers hold a pivotal role in various application areas such as light-emission, sensing, energy, and displays, with exclusive advantages despite their relatively low dielectric constants. Moreover, in the nascent field of phononics, polymers are expected to be a superior material platform due to the ability for readily fabricated complex polymer structures possessing a wide range of mechanical behaviors, complete phononic bandgaps, and resonant architectures. In this review, polymer-centric photonic and phononic crystals and metamaterials are highlighted, and basic concepts, fabrication techniques, selected functional polymers, applications, and emerging ideas are introduced.
2D and 2.5D Kirchhoff Inversion Using Upwind Finite Difference Amplitudes
(1996-07) Araya, Kidane; Symes, William W.
Finite difference solution of the transport equation provides an efficient and accurate method for computation of 2.5D geometric acoustics amplitudes. These amplitudes can be used in simulation, migration and inversion formulas. Remodeled data based on high frequency asymptotic inversion using these amplitudes shows excellent agreement with both synthetic and field input data.
2D material integrated macroporous electrodes for Li-ion batteries
(Royal Society of Chemistry, 2017) Gullapalli, Hemtej; Kalaga, Kaushik; Vinod, Soumya; Rodrigues, Marco-Tulio F.; George, Antony; Ajayan, Pulickel M.
Three-dimensionally structured architectures are known to improve the performance of electrodes used in Li ion battery systems. In addition, integration of select 2D materials into 3D structures, for enhancing both electrical conductivity and electrochemical activity, will prove advantageous. Here a scalable one-step chemical vapor deposition technique is demonstrated for the controlled etching and simultaneous graphene growth on stainless steel substrates resulting in a 3D micro-mesh architecture that is ideal for high rate/high capacity electrodes; the graphene coated 3D stainless steel current collector is used with an MoS2 electrode material for demonstrating high stability and rate capacity in Li-ion batteries.
The 2nu-SVM: A Cost-Sensitive Extension of the nu-SVM
(2005-12-01) Davenport, Mark A.; Digital Signal Processing (http://dsp.rice.edu/)
Standard classification algorithms aim to minimize the probability of making an incorrect classification. In many important applications, however, some kinds of errors are more important than others. In this report we review cost-sensitive extensions of standard support vector machines (SVMs). In particular, we describe cost-sensitive extensions of the C-SVM and the nu-SVM, which we denote the 2C-SVM and 2nu-SVM respectively. The C-SVM and the nu-SVM are known to be closely related, and we prove that the 2C-SVM and 2nu-SVM share a similar relationship. This demonstrates that the 2C-SVM and 2nu-SVM explore the same space of possible classifiers, and gives us a clear understanding of the parameter space for both versions.
3-D Local Radon Power Spectra for Seismic Attribute Extraction
(1998-01-15) Steeghs, Philippe; Fokkema, Jacob T; Diephuis, Gerhard; Digital Signal Processing (http://dsp.rice.edu/)
In this paper we discuss a method for volume attribute extraction that is based on a new type of local Radon power spectrum. The new algorithm results in robust and geologically meaningful volume attributes, such as volume dip and azimuth. Seismic volume attribute analysis greatly facilitates the interpretation of large 3-D seismic data volumes. However, horizon attribute maps are generally more easy to interpret than volume attribute images, which are usually time slices or cross-sections. We show that, for dip estimation, the volume attribute image is very similar to the horizon dip map.
3-D segmentation and volume estimation of radiologic images by a novel, feature driven, region growing technique
(1992) Agris, Jacob Martin; de Figueiredo, Rui J. P.
Magnetic Resonance (MR) imaging is a 3-D, multi-slice, radiological technique that acquires multiple intensities corresponding to each voxel. The transverse relaxation time, T$\sb1$, and the axial relaxation time, T$\sb2$, are two commonly obtained intensities that tend to be orthogonal. Automated segmentation of 3-D regions is very difficult because some borders may be delineated only in T$\sb1$ images, while others are delineated only in T$\sb2$ images. Classical segmentation techniques based on either global histogram segmentation or local edge detection often fail due to the non-unique and random nature of MR intensities. A 3-D, neighborhood based, segmentation method was developed based on both spatial and intensity criteria. The spatial criterion requires that only voxels connected by an edge or face to a voxel known to be in the region be considered for inclusion. Therefore, the region "grows" outward from an initial voxel. An intensity criterion that tries to balance local and global properties must also be satisfied. It determines the vector distance between the intensity of the voxel in question and a characteristic intensity for the neighboring voxels known to be in the region. Voxel intensities within a 95% confidence interval of the characteristic intensity are considered part of the region. The kernel size used to determine the characteristic intensity determines the balance between global and local properties. The segmentation terminates when no additional voxels satisfy both spatial and error criteria. Some regions, such as the brain compartments, are highly convoluted, resulting in a large number of border voxels containing a mixture of adjoining tissues. A sub-voxel estimate of the fractional composition is necessary for accurate quantification. A least-squares estimator was derived for the fractional composition of each voxel. Additionally, a maximum likelihood estimator was derived to globally estimate the fraction for all mixture voxels. This estimator is a minimum variance estimator in contrast to the least-squares estimator. The estimation methods in conjunction with the 3-D, neighborhood based, segmentation method resulted in an automated, highly accurate, quantification technique shown to be successful even for the brain compartments. Widespread applicability of these methods was further demonstrated by segmentation of kidneys in CT images.
3-Dimensional spatially organized PEG-based hydrogels for an aortic valve co-culture model
(Elsevier, 2015) Puperi, Daniel S.; Balaoing, Liezl R.; O'Connell, Ronan W.; West, Jennifer L.; Grande-Allen, K. Jane
Physiologically relevant inﾠvitro models are needed to study disease progression and to develop and screen potential therapeutic interventions for disease. Heart valve disease, in particular, has no early intervention or non-invasive treatment because there is a lack of understanding the cellular mechanisms which lead to disease. Here, we establish a novel, customizable synthetic hydrogel platform that can be used to study cell-cell interactions and the factors which contribute to valve disease. Spatially localized cell adhesive ligands bound in the scaffold promote cell growth and organization of valve interstitial cells and valve endothelial cells in 3D co-culture. Both cell types maintained phenotypes, homeostatic functions, and produced zonally localized extracellular matrix. This model extends the capabilities of inﾠvitro research by providing a platform to perform direct contact co-culture with cells in their physiologically relevant spatial arrangement.
3D bioprinting: improving in vitro models of metastasis with heterogeneous tumor microenvironments
(The Company of Biologists, 2017) Albritton, Jacob L.; Miller, Jordan S.
Even with many advances in treatment over the past decades, cancer still remains a leading cause of death worldwide. Despite the recognized relationship between metastasis and increased mortality rate, surprisingly little is known about the exact mechanism of metastatic progression. Currently available in vitro models cannot replicate the three-dimensionality and heterogeneity of the tumor microenvironment sufficiently to recapitulate many of the known characteristics of tumors in vivo. Our understanding of metastatic progression would thus be boosted by the development of in vitro models that could more completely capture the salient features of cancer biology. Bioengineering groups have been working for over two decades to create in vitro microenvironments for application in regenerative medicine and tissue engineering. Over this time, advances in 3D printing technology and biomaterials research have jointly led to the creation of 3D bioprinting, which has improved our ability to develop in vitro models with complexity approaching that of the in vivo tumor microenvironment. In this Review, we give an overview of 3D bioprinting methods developed for tissue engineering, which can be directly applied to constructing in vitro models of heterogeneous tumor microenvironments. We discuss considerations and limitations associated with 3D printing and highlight how these advances could be harnessed to better model metastasis and potentially guide the development of anti-cancer strategies.
3D Covalent Organic Frameworks with Interpenetrated pcb Topology Based on 8-Connected Cubic Nodes
(American Chemical Society, 2022) Shan, Zhen; Wu, Miaomiao; Zhu, Dongyang; Wu, Xiaowei; Zhang, Kan; Verduzco, Rafael; Zhang, Gen
The connectivity of building units for 3D covalent organic frameworks (COFs) has long been primarily 4 and 6, which have severely curtailed the structural diversity of 3D COFs. Here we demonstrate the successful design and synthesis of a porphyrin based, 8-connected building block with cubic configuration, which could be further reticulated into an unprecedented interpenetrated pcb topology by imine condensation with linear amine monomers. This study presents the first case of high-connectivity building units bearing 8-connected cubic nodes, thus greatly enriching the topological possibilities of 3D COFs.
3D Geometry Coding using Mixture Models and the Estimation Quantization Algorithm
(2002-09-01) Lavu, Sridhar; Lavu, Sridhar; Digital Signal Processing (http://dsp.rice.edu/)
3D surfaces are used in applications such as animations, 3D object modeling and visualization. The geometries of such surfaces are often approximated using polygonal meshes. This thesis aims to compress 3D geometry meshes by using an algorithm based on normal meshes and the Estimation-Quantization (EQ) algorithm. Normal meshes are multilevel representations where finer level vertices lie in a direction normal to the local surface and therefore compress the vertex data to one scalar value per vertex. A mixture distribution model is used for the wavelet coefficients. The EQ algorithm uses the local neighborhood information and Rate-Distortion optimization to encode the wavelet coefficients. We achieve performance gains of 0.5-1dB compared to the zerotree coder for normal meshes.
3D Macroporous Solids from Chemically Cross-linked Carbon Nanotubes
(Wiley, 2014) Ozden, Sehmus; Narayanan, Tharangattu N.; Tiwary, Chandra S.; Dong, Pei; Hart, Amelia H.C.; Vajtai, Robert; Ajayan, Pulickel M.
Suzuki reaction for covalently interconnected 3D carbon nanotube (CNT) architectures is reported. The synthesis of 3D macroscopic solids made of CNTs covalently connected via Suzuki cross-coupling, a well-known carbon-carbon covalent bond forming reaction in organic chemistry, is scalable. The resulting solid has a highly porous, interconnected structure of chemically cross-linked CNTs. Its use for the removal of oil from contaminated water is demonstrated.
3D microfabrication of single-wall carbon nanotube/polymer composites by two-photon polymerization lithography
(Elsevier, 2013) Ushiba, Shota; Shoji, Satoru; Masui, Kyoko; Kuray, Preeya; Kono, Junichiro; Kawata, Satoshi
We present a method to develop single-wall carbon nanotube (SWCNT)/polymer composites into arbitrary three-dimensional micro/nano structures. Our approach, based on two-photon polymerization lithography, allows one to fabricate three-dimensional SWCNT/polymer composites with a minimum spatial resolution of a few hundreds nm. A near-infrared femtosecond pulsed laser beam was focused onto a SWCNT-dispersed photo resin, and the laser light solidified a nanometric volume of the resin. The focus spot was three-dimensionally scanned, resulting in the fabrication of arbitrary shapes of SWCNT/polymer composites. SWCNTs were uniformly distributed throughout the whole structures, even in a few hundreds nm thick nanowires. Furthermore, we also found an intriguing phenomenon that SWCNTs were self-aligned in polymer nanostructures, promising improvements in mechanical and electrical properties. Our method has great potential to open up a wide range of applications such as micro- and nanoelectromechanical systems, micro/nano actuators, sensors, and photonics devices based on CNTs.
3D printed fiber optic faceplates by custom controlled fused deposition modeling
(Optical Society of America, 2018) Wang, Ye; Gawedzinski, John; Pawlowski, Michal E.; Tkaczyk, Tomasz S.
A 3D printing technique for manufacturing air-clad coherent fiber optic faceplates is presented. The custom G-code programming is implemented on a fused deposition modeling (FDM) desktop printer to additively draw optical fibers using high-transparency thermoplastic filaments. The 3D printed faceplate consists of 20000 fibers and achieves spatial resolution 1.78 LP/mm. Transmission loss and crosstalk are characterized and compared among the faceplates printed from four kinds of transparent filaments as well as different faceplate thicknesses. The printing temperature is verified by testing the transmission of the faceplates printed under different temperatures. Compared with the conventional stack-and-draw fabrication, the FDM 3D printing technique simplifies the fabrication procedure. The ability to draw fibers with arbitrary organization, structure and overall shape provides additional degree of freedom to opto-mechanical design. Our results indicate a promising capability of 3D printing as the manufacturing technology for fiber optical devices.
3D tissue-engineered model of Ewing's sarcoma
(Elsevier, 2014) Lamhamedi-Cherradi, Salah-Eddine; Santoro, Marco; Ramammoorthy, Vandhana; Menegaz, Brian A.; Bartholomeusz, Geoffrey; Iles, Lakesla R.; Amin, Hesham M.; Livingston, J. Andrew; Mikos, Antonios G.; Ludwig, Joseph A.
Despite longstanding reliance upon monolayer culture for studying cancer cells, and numerous advantages from both a practical and experimental standpoint, a growing body of evidence suggests that more complex three-dimensional (3D) models are necessary to properly mimic many of the critical hallmarks associated with the oncogenesis, maintenance and spread of Ewing's sarcoma (ES), the second most common pediatric bone tumor. And as clinicians increasingly turn to biologically-targeted therapies that exert their effects not only on the tumor cells themselves, but also on the surrounding extracellular matrix, it is especially important that preclinical models evolve in parallel to reliably measure antineoplastic effects and possible mechanisms of de novo and acquired drug resistance. Herein, we highlight a number of innovative methods used to fabricate biomimetic ES tumors, encompassing both the surrounding cellular milieu and the extracellular matrix (ECM), and suggest potential applications to advance our understanding of ES biology, preclinical drug testing, and personalized medicine.
3D touchless multiorder reflection structural color sensing display
(American Association for the Advancement of Science, 2020) Kang, Han Sol; Han, Sang Won; Park, Chanho; Lee, Seung Won; Eoh, Hongkyu; Baek, Jonghyeok; Shin, Dong-Gap; Park, Tae Hyun; Huh, June; Lee, Hyungsuk; Kim, Dae-Eun; Ryu, Du Yeol; Thomas, Edwin L.; Koh, Won-Gun; Park, Cheolmin
The development of a lightweight, low-power, user-interactive three-dimensional (3D) touchless display in which a human stimulus can be detected and simultaneously visualized in noncontact mode is of great interest. Here, we present a user-interactive 3D touchless sensing display based on multiorder reflection structural colors (SCs) of a thin, solid-state block copolymer (BCP) photonic crystal (PC). Full-visible-range SCs are developed in a BCP PC consisting of alternating lamellae, one of which contains a chemically cross-linked, interpenetrated hydrogel network. The absorption of a nonvolatile ionic liquid into the domains of the interpenetrated network allows for further manipulation of SC by using multiple-order photonic reflections, giving rise to unprecedented visible SCs arising from reflective color mixing. Furthermore, by using a hygroscopic ionic liquid ink, a printable 3D touchless interactive display is created where 3D position of a human finger is efficiently visualized in different SCs as a function of finger-to-display distance.
3D Ultrastructure of the Cochlear Outer Hair Cell Lateral Wall Revealed By Electron Tomography
(Frontiers, 2019) Triffo, William Jeffrey; Palsdottir, Hildur; Song, Junha; Morgan, David Gene; McDonald, Kent L.; Auer, Manfred; Raphael, Robert M.
Outer Hair Cells (OHCs) in the mammalian cochlea display a unique type of voltage-induced mechanical movement termed electromotility, which amplifies auditory signals and contributes to the sensitivity and frequency selectivity of mammalian hearing. Electromotility occurs in the OHC lateral wall, but it is not fully understood how the supramolecular architecture of the lateral wall enables this unique form of cellular motility. Employing electron tomography of high-pressure frozen and freeze-substituted OHCs, we visualized the 3D structure and organization of the membrane and cytoskeletal components of the OHC lateral wall. The subsurface cisterna (SSC) is a highly prominent feature, and we report that the SSC membranes and lumen possess hexagonally ordered arrays of particles. We also find the SSC is tightly connected to adjacent actin filaments by short filamentous protein connections. Pillar proteins that join the plasma membrane to the cytoskeleton appear as variable structures considerably thinner than actin filaments and significantly more flexible than actin-SSC links. The structurally rich organization and rigidity of the SSC coupled with apparently weaker mechanical connections between the plasma membrane (PM) and cytoskeleton reveal that the membrane-cytoskeletal architecture of the OHC lateral wall is more complex than previously appreciated. These observations are important for our understanding of OHC mechanics and need to be considered in computational models of OHC electromotility that incorporate subcellular features.
802.11b Operating in a Mobile Channel: Performance and Challenges
(2003-09-20) Steger, Christopher; Radosavljevic, Predrag; Frantz, Patrick; Center for Multimedia Communications (http://cmc.rice.edu/)
In the past, the worlds of wireless voice and data transmission have been largely disjoint. Voice traffic has been carried over circuit-switched cellular links, and data has been largely restricted to packet-switched wireless LANs. Now, as consumers demand higher bandwidth connections without sacrificing mobility and traffic transitions from primarily voice to data, service providers must produce what is essentially a ubiquitous wireless LAN. To this end, we have studied the effects of a mobile channel on current generation 802.11 A, B, and G wireless LAN cards to see how readily they can be applied to more challenging environments. Not surprisingly, current WLAN technology suffers from significantly degraded performance when subjected to the rigors of a mobile channel. We created emulated bi-directional peer-to-peer links in which we were able to manipulate individual channel parameters. By isolating individual propagation effects and testing several different implementations of the standards, we have discovered which channel parameters have the most significant impact on performance. For instance, the large delay spreads typical of an outdoor channel seem to produce the most deleterious effect on throughput in 802.11b. We use our observations to evaluate the viability of direct-sequence spread-spectrum systems (similar to 802.11b) versus that of OFDM systems (like 802.11a and 802.11g). Then we offer suggestions for how future systems should be adapted in order to manage these effects, and we project the ultimate limitations and possibilities for subsequent 802.11-like systems.
A 2-D simulation study on CO2ﾠsoluble surfactant for foam enhanced oil recovery
(Elsevier, 2019) Zeng, Yongchao; Farajzadeh, Rouhi; Biswal, Sibani L.; Hirasaki, George J.
This paper probes the transport of CO2ﾠsoluble surfactant for foaming in porous media. We numerically investigate the effect of surfactant partitioning between the aqueous phase and the gaseous phase on foam transport for subsurface applications when the surfactant is injected in the CO2ﾠphase. A 2-D reservoir simulation is developed to quantify the effect of surfactant partition coefficient on the displacement conformance and CO2ﾠsweep efficiency. A texture-implicit local-equilibrium foam model is embedded to describe how the partitioning of surfactant between water and CO2ﾠaffects the CO2ﾠfoam mobility control when surfactant is injected in the CO2ﾠphase. We conclude that when surfactant has approximately equal affinity to both the CO2ﾠand the water, the transport of surfactant is in line with the gas propagation and therefore the sweep efficiency is maximized. Too high affinity to water (small partition coefficient) results in surfactant retardation whereas too high affinity to CO2ﾠ(large partition coefficient) leads to weak foam and insufficient mobility reduction. This work sheds light upon the design of water-alternating-gas-plus-surfactant-in-gas (WAGﾠ+ﾠS) process to improve the conventional foam process with surfactant-alternating-gas (SAG) injection mode during which significant amount of surfactant could possibly drain down by gravity before CO2ﾠslugs catch up to generate foam in situ the reservoir.

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