Publications by Type: Journal Article

2016
D. R. Bell, Qi, R., Jing, Z., Xiang, J. Y., Mejias, C., Schnieders, M. J., Ponder, J. W., and Ren, P., “Calculating binding free energies of host–guest systems using the AMOEBA polarizable force field,” Physical Chemistry Chemical Physics, vol. 18, pp. 30261–30269, 2016.
C. Wang, Nguyen, P. H., Pham, K., Huynh, D., Le, T. - B. N., Wang, H., Ren, P., and Luo, R., “Calculating protein–ligand binding affinities with MMPBSA: Method and error analysis,” Journal of computational chemistry, vol. 37, pp. 2436–2446, 2016.
R. Fievet, Tinney, C. E., Baars, W. J., and Hamilton, M. F., “Coalescence in the sound field of a laboratory-scale supersonic jet,” AIAA Journal, DOI: 10.2514/1.J054252, vol. 54, no. 1, pp. 254-265, 2016.Abstract
The spatial evolution of acoustic waveforms produced by a laboratory-scale Mach 3 jet are investigated using both 1∕4 in. and 1∕8 in. pressure field microphones located along rays emanating from the postpotential core where the peak sound emission is found to occur. The measurements are acquired in a fully anechoic chamber, where ground or other large surface reflections are minimal. Various statistical metrics are examined along the peak emission path, where they are shown to undergo rapid changes within 2m from the source region. An experimentally validated wave-packet model is then used to confirm the location where the pressure amplitude along the peak emission path transitions from cylindrical to spherical decay. Various source amplitudes, provided by the wave-packet model, are then used to estimate shock formation distance and Gol’dberg numbers for diverging waves. The findings suggest that cumulative nonlinear distortion is likely to occur at laboratory scale near the jet flow, where the waveform amplitude decays cylindrically, but less likely to occur farther from the jet flow, where the waveform amplitude decays spherically. Direct inspection of the raw time series reveals how steepened waveforms are generated by rogue like waves that form from the constructive interference of waves from neighboring sources as opposed to classical cumulative nonlinear distortion.
B. Yang, Lesicko, J., Moy, A., Reichenberg, J., Sacks, M., and Tunnell, J. W., “Color structured light imaging of skin,” Journal of Biomedical Optics, vol. 21, pp. 050503, 2016. Publisher's VersionAbstract
Abstract.  We illustrate wide-field imaging of skin using a structured light (SL) approach that highlights the contrast from superficial tissue scattering. Setting the spatial frequency of the SL in a regime that limits the penetration depth effectively gates the image for photons that originate from the skin surface. Further, rendering the SL images in a color format provides an intuitive format for viewing skin pathologies. We demonstrate this approach in skin pathologies using a custom-built handheld SL imaging system.
H. Daigle and Johnson, A., “Combining mercury intrusion and nuclear magnetic resonance measurements using percolation theory,” Transport in Porous Media, vol. 111, no. 3, pp. 669-679, 2016.
J. K. Bean, Faxon, C. B., Leong, Y. J., Wallace, W. H., Cevik, B. K., Ortiz, S., Canagaratna, M. R., Usenko, S., Sheesley, R., Griffin, R. J., and Hildebrandt Ruiz, L., “Composition and sources of particulate matter measured near Houston, TX: Anthropogenic-biogenic interactions,” Atmosphere, vol. 7, 2016.
J. Liu, Wu, D., Su, X., Han, M., Kimura, S. Y., Gray, D. L., Shapley, J. R., Abu-Omar, M. M., Werth, C. J., and Strathmann, T. J., “Configuration Control in the Synthesis of Homo- and Heteroleptic Bis(oxazo/thiazolinylphenolato) Chelate Ligand Complexes of Oxorhenium(V): Isomer Effect on Ancillary Ligand Exchange Dynamics and Implications for Perchlorate Reduction Catalysis,” Inorganic Chemistry, vol. 55, no. 5, pp. 2597-2611, 2016. Publisher's VersionAbstract
This study develops synthetic strategies for N,N-trans and N,N-cis Re(O)(LO–N)2Cl complexes and investigates the effects of the coordination spheres and ligand structures on ancillary ligand exchange dynamics and catalytic perchlorate reduction activities of the corresponding [Re(O)(LO–N)2]+ cations. The 2-(2′-hydroxyphenyl)-2-oxazoline (Hhoz) and 2-(2′-hydroxyphenyl)-2-thiazoline (Hhtz) ligands are used to prepare homoleptic N,N-trans and N,N-cis isomers of both Re(O)(hoz)2Cl and Re(O)(htz)2Cl and one heteroleptic N,N-trans Re(O)(hoz)(htz)Cl. Selection of hoz/htzligands determines the preferred isomeric coordination sphere, and the use of substituted pyridine bases with varying degrees of steric hindrance during complex synthesis controls the rate of isomer interconversion. The five corresponding [Re(O)(LO–N)2]+ cations exhibit a wide range of solvent exchange rates (1.4 to 24,000 s–1 at 25 °C) and different LO–N movement patterns, as influenced by the coordination sphere of Re (trans/cis), the noncoordinating heteroatom on LO–N ligands (O/S), and the combination of the two LO–N ligands (homoleptic/heteroleptic). Ligand exchange dynamics also correlate with the activity of catalytic reduction of aqueous ClO4– by H2 when the Re(O)(LO–N)2Cl complexes are immobilized onto Pd/C. Findings from this study provide novel synthetic strategies and mechanistic insights for innovations in catalytic, environmental, and biomedical research.
K. Y. Yoon, Xue, Z., Fei, Y., Lee, J., Cheng, V., Bagaria, H. G., Huh, C., Bryant, S. L., Kong, S. D., and Ngo, V. W., “Control of magnetite primary particle size in aqueous dispersions of nanoclusters for high magnetic susceptibilities,” Journal of colloid and interface science, vol. 462, pp. 359-367, 2016. Publisher's VersionAbstract
Aqueous dispersions of iron oxide nanoparticles with a high initial magnetic susceptibility (χi) are of interest as contrast agents in electromagnetic tomography. Nanoclusters composed of iron oxide primary particles were formed by co-precipitation of Fe(II) and Fe(III) chlorides at alkaline conditions and high temperature of 95 °C. Two-step addition of citrate was used to produce large primary particles and then stabilize the nanoclusters. The size of the primary particles was tuned from 5 nm to 15 nm by varying the citrate/iron precursor ratio during the normal phase hydrolysis reaction, while the second iteration of citrate stabilized the nanoclusters with hydrodynamic diameters of 30–75 nm. The crystallinity of the iron oxide nanoparticles was promoted by annealing at 95 °C and systematically studied with Superconducting Quantum Interference Device (SQUID), Vibrating Sample Magnetometer (VSM), Transmission Electron Microscopy (TEM) and X-ray Diffraction (XRD). The dependence of χi was examined over a range of low volume fractions (0.005 < θ < 0.02) to understand the magnetic behavior of dispersions. The χi of the dispersions increased markedly with the size and concentration of the constituent primary particles, reaching an unusually high value of 0.85 at 1.6% v/v for 15 nm primary particles, which is 2–3 times higher than that for typical commercial ferrofluids. The high χi values are favored by the high crystallinity and the large magnetic diameter of 9.3 nm, indicating a relatively thin surface nonmagnetic layer where the spin orientations are disordered. Graphical abstract
T. S. Kaoud, WH Johnson, P. A., ND Ebelt, M Warthaka,, Micael Cano, S. R., Q Wang, Pengyu Ren, R. G., and Dalby, K. N., “Covalent inhibition of ERK docking interactions,” The FASEB Journal, vol. 30, no. 1, pp. 856.11-856.11, 2016.
R. Pour, Torres-Verdín, C., Sepehrnoori, K., and Nasizadeh, Z., “Depth variation of wettability alteration during oil-base mud-filtrate invasion and corresponding effects on resistivity logs.,” Journal of Petroleum Science and Engineering, vol. 147, no. November, pp. 593-604, 2016.
R. Pour, Torres-Verdín, C., Sepehrnoori, K., and Nasizadeh, Z., “Depth variation of wettability alteration during oil-base mud-filtrate invasion and corresponding effects on resistivity logs.,” Journal of Petroleum Science and Engineering, vol. 147, no. November, pp. 593-604, 2016.
K. Yang, Torres-Verdín, C., and Yilmaz, A. E., “Detection and quantification of 3D hydraulic fractures with vertical borehole induction resistivity measurements.,” Geophysics, vol. 81, no. 4, pp. E259-E264, 2016.
K. Yang, Torres-Verdín, C., and Yilmaz, A. E., “Detection and quantification of 3D hydraulic fractures with vertical borehole induction resistivity measurements.,” Geophysics, vol. 81, no. 4, pp. E259-E264, 2016.
F. He, Wu, W., and Wang, Y., “Direct measurement of coherent thermal phonons in Bi2Te3/Sb2Te3 superlattice,” Applied Physics A, vol. 122, pp. 777, 2016. Publisher's VersionAbstract
Coherent thermal phonons (CTPs) play an important role in thermal transport in superlattice (SL) structures. To have a profound understanding of CTP transport in SL, direct measurement of CTP properties is necessary. In this study, coherent phonon spectroscopy has been utilized to generate and detect CTP in Bi2Te3/Sb2Te3 SL. Phonon lifetimes have been extracted from experimental data, with which mode-wise thermal conductivities have been calculated. Comparing with bulk Bi2Te3, the estimated mode-wise thermal conductivity of longitudinal acoustic phonons shifts to higher frequencies, due to constructive coherent phonon interference. Our results suggest that it is possible to use SL structure to manipulate coherent phonon propagation and to tailor thermal conductivity.
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Z. Sun, Espinoza, N. D., and Balhoff, M. T., “Discrete element modeling of indentation tests to investigate mechanisms of CO2-related chemomechanical rock alteration,” Journal of Geophysical Research: Solid Earth, 2016.
Z. Ren, Jiang, S., Zeng, Q., Ding, X., Bai, S., Wang, J., Luo, Y., Su, Z., Xuan, Y., Yao, B., Cisneros, F., and Zhang, K., “Effect of dietary canthaxanthin and 25-hydroxycholecalciferol supplementation on the performance of duck breeders under two different vitamin regimens,” J Anim Sci BiotechnolJ Anim Sci Biotechnol, vol. 7, pp. 2, 2016.Abstract
BACKGROUND: Dietary canthaxanthin (CX), 25-hydroxycholecalciferol (25-OH-D 3 ) and vitamins have been widely reported to be involved in productive and reproductive performance of broiler breeders. However, limited information is available for duck breeders. In this study, a total of 1,560 Cherry Valley SM3 duck breeder females and 312 males were used to assess if the addition of CX and 25-OH-D3 could increase the performance of duck breeders under two different dietary vitamin regimens. Four diets were used under a 2 x 2 factorial arrangement with 2 kinds of vitamin premixes (REGULAR and HIGH; HIGH premix had higher levels of all vitamins except K3 than REGULAR premix), and with or without the supplementation of the mixture of CX (6 mg/kg) and 25-OH-D3 (0.069 mg/kg). The ducks were fed ad libitum with pelleted diets based on corn-soybean meal from 38 to 77 wk of age. RESULTS: HIGH vitamin premix decreased malondialdehyde (MDA) level (P < 0.001) of egg yolk, increased hatchability of fertile eggs (P = 0.029), increased hatchability of total eggs (P = 0.029), and decreased serum protein carbonyl level (P = 0.037) of breeder males. The mixture of CX and 25-OH-D3 increased serum calcium of breeder females (P = 0.010), decreased the cracked egg rate (P = 0.001), increased the pigmentation of egg yolk (P < 0.001) and male bill (P < 0.001), and decreased MDA level of egg yolk (P < 0.001) and male serum (P = 0.034). Interactive effects were observed in cracked egg rate (P = 0.038), shell thickness (P = 0.011) and serum phosphorus (P = 0.026) of breeder females. HIGH vitamin premix together with the mixture of CX and 25-OH-D3 decreased cracked egg rate and increased shell thickness of duck breeders. Serum phosphorus was decreased in duck breeder females fed REGULAR vitamin premix without the addition of the CX and 25-OH-D3 mixture. CONCLUSIONS: Dietary HIGH vitamin premix increased antioxidant status of eggs and breeder males, and increased hatchability. The mixture of CX and 25-OH-D3 enhanced egg shell quality, and promoted pigmentation and antioxidant status of eggs and breeder males.
R. Rojo, Tinney, C. E., and Ruf, J., “Effect of stagger on the vibroacoustic loads from clustered rockets,” AIAA Journal, vol. 54, no. 11, pp. 3588-3597, 2016.Abstract
The effect of stagger startup on the vibroacoustic loads that form during the end-effects regime of clustered rockets is studied using both full-scale (hot-gas) and laboratory-scale (cold-gas) data with vehicle geometry. Both configurations comprise three nozzles with thrust-optimized parabolic contours that undergo free-shock separated flow and restricted-shock separated flow as well as an end-effects regime before flowing full. Acoustic pressure waveforms recorded at the base of the nozzle cluster are analyzed using various statistical metrics as well as time-frequency analysis. The findings reveal a significant reduction in end-effects regime loads when engine startups are staggered. However, regardless of stagger, both the skewness and kurtosis of the acoustic pressure time derivative elevate to the same levels, thereby demonstrating the intermittence and impulsiveness of the acoustic waveforms during the end effects regime.
A. Qajar, Daigle, H., and Prodanović, M., “The effects of pore geometry on adsorption equilibrium in shale formations and coal-beds: Lattice density functional theory study,” Fuel, vol. 163, pp. 205-213, 2016.
T. Cantu, Rodier, B., Iszard, Z., Kilian, A., Pattani, V., Walsh, K., Weber, K., Tunnell, J., Betancourt, T., and Irvin, J., “Electroactive Polymer Nanoparticles Exhibiting Photothermal Properties,” no. 107, pp. e53631, 2016. Publisher's VersionAbstract
A method for the synthesis of electroactive polymers is demonstrated, starting with the synthesis of extended conjugation monomers using a three-step process that finishes with Negishi coupling. Negishi coupling is a cross-coupling process in which a chemical precursor is first lithiated, followed by transmetallation with ZnCl2. The resultant organozinc compound can be coupled to a dibrominated aromatic precursor to give the conjugated monomer. Polymer films can be prepared via electropolymerization of the monomer and characterized using cyclic voltammetry and ultraviolet-visible-near infrared (UV-Vis-NIR) spectroscopy. Nanoparticles (NPs) are prepared via emulsion polymerization of the monomer using a two-surfactant system to yield an aqueous dispersion of the polymer NPs. The NPs are characterized using dynamic light scattering, electron microscopy, and UV-Vis-NIR-spectroscopy. Cytocompatibility of NPs is investigated using the cell viability assay. Finally, the NP suspensions are irradiated with a NIR laser to determine their effectiveness as potential materials for photothermal therapy (PTT).
A. M. Bergquist, Choe, J. K., Strathmann, T. J., and Werth, C. J., “Evaluation of a hybrid ion exchange-catalyst treatment technology for nitrate removal from drinking water,” Water Research, vol. 96, pp. 177-187, 2016. Publisher's VersionAbstract
Ion exchange (IX) is the most common approach to treating nitrate-contaminated drinking water sources, but the cost of salt to make regeneration brine, as well as the cost and environmental burden of waste brine disposal, are major disadvantages. A hybrid ion exchange-catalyst treatment system, in which waste brine is catalytically treated for reuse, shows promise for reducing costs and environmental burdens of the conventional IX system. An IX model with separate treatment and regeneration cycles was developed, and ion selectivity coefficients for each cycle were separately calibrated by fitting experimental data. Of note, selectivity coefficients for the regeneration cycle required fitting the second treatment cycle after incomplete resin regeneration. The calibrated and validated model was used to simulate many cycles of treatment and regeneration using the hybrid system. Simulated waste brines and a real brine obtained from a California utility were also evaluated for catalytic nitrate treatment in a packed-bed, flow-through column with 0.5 wt%Pd–0.05 wt%In/activated carbon support (PdIn/AC). Consistent nitrate removal and no apparent catalyst deactivation were observed over 23 d (synthetic brine) and 45 d (real waste brine) of continuous-flow treatment. Ion exchange and catalyst results were used to evaluate treatment of 1 billion gallons of nitrate-contaminated source water at a 0.5 MGD water treatment plant. Switching from a conventional IX system with a two bed volume regeneration to a hybrid system with the same regeneration length and sequencing batch catalytic reactor treatment would save 76% in salt cost. The results suggest the hybrid system has the potential to address the disadvantages of a conventional IX treatment systems.

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