# Publications by Year: 2017

2017
D. Pardo and Torres-Verdín, C., “1.5D-based inversion of logging-while drilling resistivity measurements in 3D formations (Expanded Abstract),” European Association of Geoscientists and Engineers (EAGE) 79th Ann. Conference and Exhibition. Paris, France, June 12-15., 2017.
C. E. Schaefer, Ho, P., Gurr, C., Berns, E., and Werth, C. J., “Abiotic dechlorination of chlorinated ethenes in natural clayey soils: impacts of mineralogy and temperature,” Journal of Contaminant Hydrology, 2017. Publisher's VersionAbstract
Laboratory batch experiments were performed to assess the impacts of temperature and mineralogy on the abiotic dechlorination of tetrachloroethene (PCE) or trichloroethene (TCE) due to the presence of ferrous minerals in natural aquifer clayey soils under anaerobic conditions. A combination of x-ray diffraction (XRD), magnetic susceptibility, and ferrous mineral content were used to characterize each of the 3 natural soils tested in this study, and dechlorination at temperatures ranging from 20 to 55 °C were examined. Results showed that abiotic dechlorination occurred in all 3 soils examined, yielding reduced gas abiotic dechlorination products acetylene, butane, ethene, and/or propane. Bulk first-order dechlorination rate constants (kbulk), scaled to the soil:water ratio expected for in situ conditions, ranged from 2.0 × 10−5 day−1 at 20 °C, to 32 × 10−5 day−1 at 55 °C in the soil with the greatest ferrous mineral content. For the generation of acetylene and ethene from PCE, the reaction was well described by Arrhenius kinetics, with an activation energy of 91 kJ/mol. For the generation of coupling products butane and propane, the Arrhenius equation did not provide a satisfactory description of the data, likely owing to the complex reaction mechanisms associated with these products and/or diffusional mass transfer processes associated with the ferrous minerals likely responsible for these coupling reactions. Although the data set was too limited to determine a definitive correlation, the two soils with elevated ferrous mineral contents had elevated abiotic dechlorination rate constants, while the one soil with a low ferrous mineral content had a relatively low abiotic dechlorination rate constant. Overall, results suggest intrinsic abiotic dechlorination rates may be an important long-term natural attenuation component in site conceptual models for clays that have the appropriate iron mineralogy.
B. S. Wendel, He, C. F., Qu, M. J., Wu, D., Hernandez, S. M., Ma, K. Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., Ren, P. Y., Chen, K. K., and Jiang, N., “Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature Communications, vol. 8, 2017.Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (<12 months old) and toddlers (12-47 months old) with 4-8ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.
B. S. Wendel, He, C., Qu, M., Wu, D., Hernandez, S. M., Ma, K. - Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., and others,Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature communications, vol. 8, pp. 531, 2017.
X. Xu, Pan, Z., Jia, B., Wang, Y., and Chen, R. T., “All-optical switch with 1 ps response time enabled by graphene oxide infiltrated subwavelength grating waveguide,” Silicon Photonics XII, vol. 10108. San Francisco, California, United States, pp. 1010805, 2017. Publisher's VersionAbstract
In this paper, we propose an all-optical switch using graphene oxide (GO) infiltrated subwavelength grating (SWG) waveguide. Benefiting from the extremely large Kerr coefficient of GO (four orders of magnitude larger than conventional materials) and large mode volume overlap factor of the SWG (4~10 times larger than conventional strip waveguides), the switch is capable of achieving THz speed with less than 1 fJ energy consumption per bit, which is more than three orders of magnitude smaller than THz switches reported so far.
S. Ko, Kim, E. S., Park, S., Daigle, H., Milner, T. E., Huh, C., Bennetzen, M. V., and Geremia, G. A., “Amine functionalized magnetic nanoparticles for removal of oil droplets from produced water and accelerated magnetic separation,” Journal of Nanoparticle Research, vol. 19, no. 4, pp. 1-14, 2017. Publisher's VersionAbstract
Magnetic nanoparticles (MNPs) with surface coatings designed for water treatment, in particular for targeted removal of contaminants from produced water in oil fields, have drawn considerable attention due to their environmental merit. The goal of this study was to develop an efficient method of removing very stable, micron-scale oil droplets dispersed in oilfield produced water. We synthesized MNPs in the laboratory with a prescribed surface coating. The MNPs were superparamagnetic magnetite, and the hydrodynamic size of amine functionalized MNPs ranges from 21 to 255 nm with an average size of 66 nm. The initial oil content of 0.25 wt.% was reduced by as much as 99.9% in separated water. The electrostatic attraction between negatively charged oil-in-water emulsions and positively charged MNPs controls, the attachment of MNPs to the droplet surface, and the subsequent aggregation of the electrically neutral oil droplets with attached MNPs (MNPs-oils) play a critical role in accelerated and efficient magnetic separation. The total magnetic separation time was dramatically reduced to as short as 1 s after MNPs, and oil droplets were mixed, in contrast with the case of free, individual MNPs with which separation took about 36∼72 h, depending on the MNP concentrations. Model calculations of magnetic separation velocity, accounting for the MNP magnetization and viscous drag, show that the total magnetic separation time will be approximately 5 min or less, when the size of the MNPs-oils is greater than 360 nm, which can be used as an optimum operating condition.
C. Hegde, Daigle, H., Millwater, H., and Gray, K., “Analysis of rate of penetration (ROP) prediction in drilling using physics-based and data-driven models,” Journal of Petroleum Science and Engineering, vol. 159, pp. 295-306, 2017. Publisher's VersionAbstract
Modeling the rate of penetration of the drill bit is essential for optimizing drilling operations. This paper evaluates two different approaches to ROP prediction: physics-based and data-driven modeling approach. Three physics-based models or traditional models have been compared to data-driven models. Data-driven models are built using machine learning algorithms, using surface measured input features - weight-on-bit, RPM, and flow rate – to predict ROP. Both models are used to predict ROP; models are compared with each other based on accuracy and goodness of fit (R2). Based on the results from these simulations, it was concluded that data-driven models are more accurate and provide a better fit than traditional models. Data-driven models performed better with a mean error of 12% and improve the R2 of ROP prediction from 0.12 to 0.84. The authors have formulated a method to calculate the uncertainty (confidence interval) of ROP predictions, which can be useful in engineering based drilling decisions.
A. S. Massaro, Espinoza, N. D., Frydman, M., Barredo, S., and Cuervo, S., “Analyzing a suitable elastic geomechanical model for Vaca Muerta Formation,” Journal of South American Earth Sciences, vol. 79, pp. 472–488, 2017.
L. A. Hernandez-Uribe, Aman, M., and Espinoza, N. D., “Assessment of Mudrock Brittleness with Micro-scratch Testing,” Rock Mechanics and Rock Engineering, vol. 50, pp. 2849–2860, 2017.
X. Han, Jing, Z. F., Wu, W., Zou, B., Peng, Z. L., Ren, P. Y., Wikramanayake, A., Lu, Z. M., and Leblanc, R. M., “Biocompatible and blood-brain barrier permeable carbon dots for inhibition of A beta fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862-12866, 2017.Abstract
Amyloid-beta peptide (A beta) fibrillation is pathologically associated with Alzheimer's disease (AD), and this has resulted in the development of an A beta inhibitor which is essential for the treatment of AD. However, the design of potent agents which can target upstream secretases, inhibit A beta toxicity and aggregation, as well as cross the blood-brain barrier remains challenging. In, this research carbon dots for AD treatment were investigated in vitro using experimental and computational methods for the first time. The results presented here demonstrate a novel strategy for the discovery of novel antiamyloidogenic agents for AD treatments.
X. Han, Jing, Z., Wu, W., Zou, B., Peng, Z., Ren, P., Wikramanayake, A., Lu, Z., and Leblanc, R. M., “Biocompatible and blood–brain barrier permeable carbon dots for inhibition of A$\beta$ fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862–12866, 2017.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing Many-Body Interactions with Classical Dipole Induction Models,” Journal of Chemical Theory and Computation, vol. 13, pp. 2751–2761, 2017.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing many-body interactions with classical dipole induction models,” Journal of chemical theory and computation, vol. 13, pp. 2751–2761, 2017.
D. R. Bell, Cheng, S. Y., Salazar, H., and Ren, P., “Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations,” Scientific Reports, vol. 7, 2017.
D. R. Bell, Cheng, S. Y., Salazar, H., and Ren, P., “Capturing RNA folding free energy with coarse-grained molecular dynamics simulations,” Scientific Reports, vol. 7, pp. 45812, 2017.
W. Wu, Chai, Z., Gao, Y., Kong, D., He, F., Meng, X., and Wang, Y., “Carrier dynamics and optical nonlinearity of alloyed CdSeTe quantum dots in glass matrix,” Optical Materials Express, vol. 7, no. 5, pp. 1547-1556, 2017. Publisher's VersionAbstract
Size and pump-fluence dependent ultrafast carrier dynamics of CdSeTe QDs are investigated using femtosecond pump-probe techniques operating at two different repetition rates: 1 kHz (low-repetition rate), and 76 MHz (high-repetition rate). With a low-repetition rate laser and 3.1 eV excitation photon energy, multiple exciton generation (MEG) is observed and the optical responses of alloyed QDs clearly show three components: a fast decay ascribed to carrier recombination, an intermediate component associated with MEG decay, and a slow decay associated with radiative Auger recombination. With a high-repetition rate laser and excitation photon energy resonant with band-edge energy, obvious coherent phonon oscillations are observed in 4 nm CdSeTe QDs due to impulsive stimulated Raman scattering. Open-aperture Z-scan measurement is used to clarify the size and pump-fluence dependence of optical nonlinearity under femtosecond laser excitation. With increasing laser power, an evolution from saturable absorption to reverse saturable absorption in CdSeTe QDs is observed. The transition process is analyzed using a phenomenological model based on nonlinear absorption coefficient and saturation intensity. These results indicate that CdSeTe QDs in a glass matrix are a class of materials for potential application in all-optical switching devices.
A. M. Bergquist, Bertoch, M., Gildert, G., Strathmann, T. J., and Werth, C. J., “Catalytic denitrification in a trickle bed reactor: ion exchange waste brine treatment,” Journal-American Water Works Association, vol. 109, no. 5, pp. E129-E143, 2017. Publisher's VersionAbstract
Catalytic reduction of nitrate in ion exchange (IX) waste brine for reuse is a promising option for reducing IX costs and environmental impacts. A recycling trickle bed reactor (TBR) was designed and optimized using 0.5 percent byweight (wt%) palladium–0.05 wt% indium catalysts supported on US mesh size 12 × 14 or 12 × 30 activated carbon particles. Various liquid superficial velocities (Ur) and hydrogen gas superficial velocities (Ug-H2) were evaluated to assess performance in different flow regimes; catalyst activity increased with Ug-H2 at all Ur for both catalysts and was greatest for the 12 × 30 catalyst at thelowest Ur (8.9 m/h). The 12 × 30 catalyst demonstrated up to 100% higher catalytic activity and 280% higher mass transfer rate compared with the 12 × 14 catalyst. Optimal TBR performance was achieved with both catalysts in thetrickle flow regime. The results indicate that the TBR is a promising step forward, and continued improvements are possible to overcome remaining mass transfer limitations.
M. Bertoch, Bergquist, A. M., Gildert, G., Strathmann, T. J., and Werth, C. J., “Catalytic nitrate removal in a trickle bed reactor: direct drinking water treatment,” Journal-American Water Works Association, vol. 109, no. 5, pp. E144, 2017. Publisher's VersionAbstract
Palladium (Pd)-based catalysts hold promise as an alternative water treatment technology for nitrate (NO3–), but practical application requires a flow-through reactor that efficiently delivers hydrogen (H2) from gas to water. A trickle bed reactor (TBR) packed with a 0.1 percent by weight (wt%) Pd–0.01 wt% In/γ-Al2O3 (indium and porous aluminum oxide) catalyst was evaluated to address this challenge. Catalytic activity generally increased with H2 superficial velocity (0.65–29.6 m/h) and liquid (deionized water) superficial velocities from 14.8 to 26.6 m/h before decreasing at 38.5 m/h. This decrease corresponded to a change in flow regime and suggests that optimal TBR performance occurs at the transition from pulse to bubble flow. An optimal TBR activity of 19.5 ± 1.3 mg NO3–/min-g Pd was obtained; this is only ~18% of the batch reactor activity as a result of H2 mass transfer limitations, but three to 15 times greater than activities obtained with previous flow-through reactors. Catalyst deactivation occurred in the TBR after 41 days of operation, motivating the need for improved fouling mitigation strategies.
H. Jung, Espinoza, N. D., and others,Chemo-Poromechanical Properties of Tuscaloosa Sandstone: Implications on CO 2 Geological Storage,” in 51st US Rock Mechanics/Geomechanics Symposium, 2017.
R. Sitaram, Ros, T., Stoeckel, L., Haller, S., Scharnowski, F., Lewis-Peacock, J., Weiskopf, N., Blefari, M. L., Rana, M., Oblak, E., Birbaumer, N., and Sulzer, J., “Closed-loop brain training: the science of neurofeedback,” Nature Reviews Neuroscience, 2017.