Publications

2016
S. Kelly, El-Sobky, H., Torres-Verdín, C., and Balhoff, M., “Assessing the utility of FIB-SEM images for shale digital rock physics,” Advances in Water Research, vol. 95, no. September, pp. 302-316, 2016.
Y. Sun, Aman, M., and Espinoza, N. D., “Assessment of mechanical rock alteration caused by CO 2–water mixtures using indentation and scratch experiments,” International Journal of Greenhouse Gas Control, vol. 45, pp. 9–17, 2016.
G. Coloyan, Cultrara, N. D., Katre, A., Carrete, J., Heine, M., Ou, E., Kim, J., Jiang, S., Lindsay, L., Mingo, N., Broido, D., Heremans, J. P., Goldberger, J., and Shi, L., “Basal-plane thermal conductivity of nanocrystalline and amorphized thin germanane,” Applied Physics Letters, vol. 109, pp. 131907, 2016. Publisher's Version
C. Xu, Yang, Q., and Torres-Verdín, C., “Bayesian rock classification and petrophysical uncertainty characterization with fast well-log forward modeling in thin-bed reservoirs,” Interpretation, vol. 4, no. 2, pp. SF19-SF29, 2016.
C. Xu, Yang, Q., and Torres-Verdín, C., “Bayesian rock classification and petrophysical uncertainty characterization with fast well-log forward modeling in thin-bed reservoirs,” Interpretation, vol. 4, no. 2, pp. SF19-SF29, 2016.
X. Feng, Moy, A. J., Markey, M. K., Fox, M. C., Reichenberg, J. S., and Tunnell, J. W., “Biophysical basis for noninvasive skin cancer detection using Raman spectroscopy,” Proc. SPIE, vol. 9704. pp. 97040C-97040C-7, 2016. Publisher's VersionAbstract
Raman spectroscopy (RS) is proving to be a valuable tool for real time noninvasive skin cancer detection via optical fiber probe. However, current methods utilizing RS for skin cancer diagnosis rely on statistically based algorithms to provide tissue classification and do not elucidate the underlying biophysical changes of skin tissue. Therefore, we aim to use RS to explore skin biochemical and structural characteristics and then correlate the Raman spectrum of skin tissue with its disease state. We have built a custom confocal micro-Raman spectrometer system with an 830nm laser light. The high resolution capability of the system allows us to measure spectroscopic features from individual tissue components in situ. Raman images were collected from human skin samples from Mohs surgical biopsy, which were then compared with confocal laser scanning, two-photon fluorescence and hematoxylin and eosin-stained images to develop a linear model of skin tissue Raman spectra. In this model, macroscopic tissue spectra obtained from RS fiber probe were fit into a linear combination of individual basis spectra of primary skin constituents. The fit coefficient of the model explains the biophysical changes spanning a range of normal and various disease states. The model allows for determining parameters similar to that a pathologist is familiar reading and will be a significant guidance in developing RS diagnostic decision schemes.
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,” Phys Chem Chem PhysPhys Chem Chem Phys, vol. 18, pp. 30261-30269, 2016.Abstract
Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.
C. Wang, Nguyen, P. H., Pham, K., Huynh, D., Le, T. B., Wang, H., Ren, P., and Luo, R., “Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis,” J Comput Chem, vol. 37, pp. 2436-46, 2016.Abstract
Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) methods have become widely adopted in estimating protein-ligand binding affinities due to their efficiency and high correlation with experiment. Here different computational alternatives were investigated to assess their impact to the agreement of MMPBSA calculations with experiment. Seven receptor families with both high-quality crystal structures and binding affinities were selected. First the performance of nonpolar solvation models was studied and it was found that the modern approach that separately models hydrophobic and dispersion interactions dramatically reduces RMSD's of computed relative binding affinities. The numerical setup of the Poisson-Boltzmann methods was analyzed next. The data shows that the impact of grid spacing to the quality of MMPBSA calculations is small: the numerical error at the grid spacing of 0.5 A is already small enough to be negligible. The impact of different atomic radius sets and different molecular surface definitions was further analyzed and weak influences were found on the agreement with experiment. The influence of solute dielectric constant was also analyzed: a higher dielectric constant generally improves the overall agreement with experiment, especially for highly charged binding pockets. The data also showed that the converged simulations caused slight reduction in the agreement with experiment. Finally the direction of estimating absolute binding free energies was briefly explored. Upon correction of the binding-induced rearrangement free energy and the binding entropy lost, the errors in absolute binding affinities were also reduced dramatically when the modern nonpolar solvent model was used, although further developments were apparently necessary to further improve the MMPBSA methods. (c) 2016 Wiley Periodicals, Inc.
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.
R. Xu*, Mehmani, A., Qajar, A., Prodanović, M., Daigle, H., and Nguyen, S., “Combination of Lattice Density Functional Theory and a Multi-Scale Network Model for Sorption Isotherms Study in Tight Formations,” Unconventional Resources Technology Conference, San Antonio, Texas, 1-3 August 2016. Society of Exploration Geophysicists, American Association of Petroleum Geologists, Society of Petroleum Engineers, pp. 2255-2266, 2016.
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. Joseph and Tinney, C. E., “A combustion model for studying the effect of ideal gas properties on jet noise.,” Bulletin of the American Physical Society, vol. 61, no. 20. 2016.Abstract
A theoretical combustion model is developed to simulate the influence of ideal gas effects on various aeroacoustic parameters over a range of equivalence ratios. The motivation is to narrow the gap between laboratory and full-scale jet noise testing. The combustion model is used to model propane combustion in air and kerosene combustion in air. Gas properties from the combustion model are compared to real lab data acquired at the National Center for Physical Acoustics at the University of Mississippi as well as outputs from NASA’s Chemical Equilibrium Analysis code. Different jet properties are then studied over a range of equivalence ratios and pressure ratios for propane combustion in air, kerosene combustion in air and heated air. The findings reveal negligible differences between the three constituents where the density and sound speed ratios are concerned. Albeit, the area ratio required for perfectly expanded flow is shown to be more sensitive to gas properties, relative to changes in the temperature ratio.
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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.

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