Publications

2017
E. D. Maalouf and Torres-Verdín, C., “Interpretation of sonic measurements acquired in high-angle and horizontal wells using 3D fast forward modeling (Expanded Abstract),” Society of Petrophysicists and Well Log Analysts (SPWLA) 58th Ann. Logging Symposium. Oklahoma City, OK, June 17-21, 2017.
W. Goth, Sacks, M. S., and Tunnell, J. W., “Interpreting fiber structure from polarization dependent optical anisotropy,” Proc. SPIE, vol. 10068. pp. 100680P-100680P-8, 2017. Publisher's VersionAbstract
Polarized light is commonly used to detect optical anisotropies, such as birefringence, in tissues. This optical anisotropy is often attributed to underlying structural anisotropy in tissue, which may originate from regularly aligned collagen fibers. In these cases, the optical anisotropy, such as birefringence, is interpreted as a relative measure of the structural anisotropy of the collagen fibers. However, the relative amplitude of optical anisotropy depends on factors other than fiber orientation, and few models allow quantitative interpretation of absolute measures of true fiber orientation distribution from the optical signal. Our model uses the Mie solution to scattering of linearly polarized light from infinite cylindrical scatterers. The model is expanded to include populations of scatterers with physiologically relevant size and orientation distributions. We investigated the influences of fiber diameter, orientation distribution, and wavelength on the back-scattering signal with our computational model, and used these results to extract structural information from experimental fiber phantoms and bovine tendon. Our results demonstrated that by fitting our model to the experimental data using limited assumptions, we could extract fiber orientation distributions and diameters that were comparable to those found in scanning electron microscope images of the same fiber sample. We found a higher alignment of fibers in the bovine tendon sample, and the extracted fiber diameter was within the expected physiological range. Our model showed that the amplitude of optical anisotropy can vary widely due to factors other than the orientation distribution of fiber structures, including index of refraction, and therefore should not be taken as a sole indicator of structural anisotropy. This work highlights that the accuracy of model assumptions plays a crucial role in extracting quantitative structural information from optical anisotropy.
E. Maalouf and Torres-Verdín, C., “Inversion-based method to mitigate noise in borehole sonic logs,” Geophysics, vol. 83, no. 2, pp. D61-D71, 2017.
C. Wang, Ren, P., and Luo, R., “Ionic Solution: What Goes Right and Wrong with Continuum Solvation Modeling,” The Journal of Physical Chemistry B, vol. 121, pp. 11169–11179, 2017.
J. Zhang, Jia, S., Kholmanov, I., Dong, L., Er, D., Chen, W., Guo, H., Jin, Z., Shenoy, V. B., Shi, L., and Lou, J., “Janus Monolayer Transition Metal Dichalcogenides,” ACS Nano, vol. 11, pp. 8192 , 2017. Publisher's Version
E. Ortega, Luycx, M., Torres-Verdín, C., and Preeg, W. E., “Joint petrophysical interpretation of multi-detector nuclear measurements in the presence of invasion, shoulder-bed, and well-deviation effects,” Geophysics, vol. 82, no. 1, pp. D13-D30, 2017.
E. Ortega, Luycx, M., Torres-Verdín, C., and Preeg, W. E., “Joint petrophysical interpretation of multi-detector nuclear measurements in the presence of invasion, shoulder-bed, and well-deviation effects.,” Geophysics, vol. 82, no. 1, pp. D13-D30, 2017.
J. Liu, Su, X., Han, M., Wu, D., Gray, D. L., Shapley, J. R., Werth, C. J., and Strathmann, T. J., “Ligand Design for Isomer-Selective Oxorhenium(V) Complex Synthesis,” Inorganic Chemistry, vol. 56, no. 3, pp. 1757-1769, 2017. Publisher's VersionAbstract
Recently, N,N-trans Re(O)(LN–O)2X (LN–O = monoanionic N–O chelates; X = Cl or Br prior to being replaced by solvents or alkoxides) complexes have been found to be superior to the corresponding N,N-cis isomers in the catalytic reduction of perchlorate via oxygen atom transfer. However, reported methods for Re(O)(LN–O)2X synthesis often yield only the N,N-cis complex or a mixture of trans and cis isomers. This study reports a geometry-inspired ligand design rationale that selectively yields N,N-trans Re(O)(LN–O)2Cl complexes. Analysis of the crystal structures revealed that the dihedral angles (DAs) between the two LN–O ligands of N,N-cis Re(O)(LN–O)2Cl complexes are less than 90°, whereas the DAs in most N,N-trans complexes are greater than 90°. Variably sized alkyl groups (−Me, −CH2Ph, and −CH2Cy) were then introduced to the 2-(2′-hydroxyphenyl)-2-oxazoline (Hhoz) ligand to increase steric hindrance in the N,N-cis structure, and it was found that substituents as small as −Me completely eliminate the formation of N,N-cisisomers. The generality of the relationship between N,N-trans/cis isomerism and DAs is further established from a literature survey of 56 crystal structures of Re(O)(LN–O)2X, Re(O)(LO–N–N–O)X, and Tc(O)(LN–O)2X congeners. Density functional theory calculations support the general strategy of introducing ligand steric hindrance to favor synthesis of N,N-trans Re(O)(LN–O)2X and Tc(O)(LN–O)2X complexes. This study demonstrates the promise of applying rational ligand design for isomeric control of metal complex structures, providing a path forward for innovations in a number of catalytic, environmental, and biomedical applications.
M. Nole, Daigle, H., Cook, A. E., Hillman, J. I. T., and Malinverno, A., “Linking basin‐scale and pore‐scale gas hydrate distribution patterns in diffusion‐dominated marine hydrate systems,” Geochemistry, Geophysics, Geosystems, 2017.
J. M. Obliosca, Cheng, S. Y., Chen, Y. - A., Llanos, M. F., Liu, Y. - L., Imphean, D. M., Bell, D., Petty, J. T., Ren, P., and Yeh, H. - C., “LNA Thymidine Monomer Enables Differentiation of the Four Single-Nucleotide Variants by Melting Temperature,” Journal of the American Chemical Society, 2017.
K. Chen, Sheehan, N., He, F., Meng, X., Mason, S. C., Bank, S. R., and Wang, Y., “Measurement of Ambipolar Diffusion Coefficient of Photoexcited Carriers with Ultrafast Reflective Grating-Imaging Technique,” ACS Photonics, 2017. Publisher's VersionAbstract
A novel ultrafast reflective grating-imaging technique has been developed to measure ambipolar carrier diffusion in GaAs/AlAs quantum wells and bulk GaAs. By integrating a transmission grating and an imaging system into the traditional pump–probe setup, this technique can acquire carrier diffusion properties conveniently and accurately. The fitted results of the diffusion coefficient and diffusion length in bulk GaAs agree well with the literature values obtained by other techniques. The diffusion coefficient and diffusion length of GaAs/AlAs quantum wells are found to increase with the well layer thickness, which suggests that interface roughness scattering dominates carrier diffusion in GaAs/AlAs quantum wells. With the advantages of simple operation, sensitive detection, rapid and nondestructive measurement, and extensive applicability, the ultrafast reflective grating-imaging technique has great potential in experimental study of carrier diffusion in various materials.
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R. Victor, Prodanović, M., and Torres-Verdín, C., “Monte Carlo approach for estimating density and atomic number from dual-energy computed tomography images of carbonate rocks,” Journal of Geophysical Research – Solid Earth, vol. 122, pp. 9804-9824, 2017.
Z. Zhao, Luan, L., Wei, X., Zhu, H., Li, X., Lin, S., Siegel, J. J., Chitwood, R. A., and Xie, C., “Nanoelectronic coating enabled versatile multi-functional neural probes,” Nano Letters, 2017. Publisher's VersionAbstract
Brain function can be best studied by simultaneous measurements and modulation of the multifaceted signaling at the cellular scale. Extensive efforts have been made to develop multifunctional neural probes, typically involving highly specialized fabrication processes. Here, we report a novel multifunctional neural probe platform realized by applying ultra-thin nanoelectronic coating (NEC) on the surfaces of conventional microscale devices such as optical fibers and micropipettes. We fabricated the NECs by planar photolithography techniques using a substrate-less and multi-layer design, which host arrays of individually addressed electrodes with an overall thickness below 1 µm. Guided by an analytic model and taking advantage of the surface tension, we precisely aligned and coated the NEC devices on the surfaces of these conventional micro-probes, and enabled electrical recording capabilities on par with the state-of-the-art neural electrodes. We further demonstrated optogenetic stimulation and controlled drug infusion with simultaneous, spatially resolved neural recording in a rodent model. This study provides a low-cost, versatile approach to construct multifunctional neural probes that can be applied to both fundamental and translational neuroscience.
S. V. Sreenivasan, “Nanoimprint lithography steppers for volume fabrication of leading-edge semiconductor integrated circuits,” Microsystems & Nanoengineering, vol. 2017, no. 3, 2017. Publisher's VersionAbstract
This article discusses the transition of a form of nanoimprint lithography technology, known as Jet and Flash Imprint Lithography (J-FIL), from research to a commercial fabrication infrastructure for leading-edge semiconductor integrated circuits (ICs). Leading-edge semiconductor lithography has some of the most aggressive technology requirements, and has been a key driver in the 50-year history of semiconductor scaling. Introducing a new, disruptive capability into this arena is therefore a case study in a "highrisk-high-reward" opportunity. This article first discusses relevant literature in nanopatterning including advanced lithography options that have been explored by the IC fabrication industry, novel research ideas being explored, and literature in nanoimprint lithography. The article then focuses on the J-FIL process, and the interdisciplinary nature of risk, involving nanoscale precision systems, mechanics, materials, material delivery systems, contamination control, and process engineering. Next, the article discusses the strategic decisions that were made in the early phases of the project including: (i) choosing a step and repeat process approach; (ii) identifying the first target IC market for J-FIL; (iii) defining the product scope and the appropriate collaborations to share the risk-reward landscape; and (iv) properly leveraging existing infrastructure, including minimizing disruption to the widely accepted practices in photolithography. Finally, the paper discusses the commercial J-FIL stepper system and associated infrastructure, and the resulting advances in the key lithographic process metrics such as critical dimension control, overlay, throughput, process defects, and electrical yield over the past 5 years. This article concludes with the current state of the art in J-FIL technology for IC fabrication, including description of the high volume manufacturing stepper tools created for advanced memory manufacturing.
K. Michelson, Sanford, R. A., Valocchi, A. J., and Werth, C. J., “Nanowires of Geobacter sulfurreducens require redox cofactors to reduce metals in pore spaces too small for cell passage,” Environmental Science & Technology, 2017. Publisher's VersionAbstract
Members of the Geobacteraceae family are ubiquitous metal reducers that utilize conductive ‘nanowires’ to reduce Mn(IV) and Fe(III) oxides in anaerobic sediments. However, it is not currently known if and to what extent the Mn(IV) and Fe(III) oxides in soil grains and low permeability sediments that are sequestered in pore spaces too small for cell passage can be reduced by long-range extracellular electron transport via Geobacter nanowires, and what mechanisms control this reduction. We developed a microfluidic reactor that physically separates Geobacter sulfurreducens from the Mn(IV) mineral birnessite by a 1.4 μm thick wall containing <200 nm pores. Using optical microscopy and Raman spectroscopy, we show that birnessite can be reduced up to 15 μm away from cell bodies, similar to the reported length of Geobacter nanowires. Reduction across the nanoporous wall required reducing conditions, provided by Escherichia coli, and an exogenous supply of riboflavin. Our results discount electron shuttling by dissolved flavins, and instead support their role as bound redox cofactors in electron transport from nanowires to metal oxides. We also show that upon addition of a soluble electron shuttle (i.e., AQDS), reduction extends beyond the reported nanowire length up to 40 μm into a layer of birnessite.
B. Amoozgar, Wei, X., Lee, J. H., Bloomer, M., Zhao, Z., Coh, P., He, F., Luan, L., Xie, C., and Han, Y., “A novel flexible microfluidic meshwork to reduce fibrosis in glaucoma surgery,” PloS one, vol. 12, no. 3, 2017. Publisher's VersionAbstract
Fibrosis and hence capsule formation around the glaucoma implants are the main reasons for glaucoma implant failure. To address these issues, we designed a microfluidic meshwork and tested its biocompatibility in a rabbit eye model. The amount of fibrosis elicited by the microfluidic meshwork was compared to the amount elicited by the plate of conventional glaucoma drainage device
X. Xu, Zheng, X., He, F., Wang, Z., Subbaraman, H., Wang, Y., Jia, B., and Chen, R. T., “Observation of Third-order Nonlinearities in Graphene Oxide Film at Telecommunication Wavelength,” Scientific Reports, vol. 7, pp. 9646, 2017. Publisher's VersionAbstract
All-optical switches have been considered as a promising solution to overcome the fundamental speed limit of the current electronic switches. However, the lack of a suitable third-order nonlinear material greatly hinders the development of this technology. Here we report the observation of ultrahigh third-order nonlinearity about 0.45 cm2/GW in graphene oxide thin films at the telecommunication wavelength region, which is four orders of magnitude higher than that of single crystalline silicon. Besides, graphene oxide is water soluble and thus easy to process due to the existence of oxygen containing groups. These unique properties can potentially significantly advance the performance of all-optical switches.
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S. Sullivan, Vallabhaneni, A. K., Kholmanov, I., Ruan, X., Murthy, J., and Shi, L., “Optical generation and detection of local non-equilibrium phonons in suspended graphene,” Nano Letters, vol. 17, pp. 2049–2056 , 2017. Publisher's Version
J. A. Rackers, Wang, Q., Liu, C., Piquemal, J. - P., Ren, P., and Ponder, J. W., “An optimized charge penetration model for use with the AMOEBA force field,” Physical Chemistry Chemical Physics, vol. 19, pp. 276–291, 2017.
Y. J. Leong, Sanchez, N. P., Wallace, H. W., Cevik, K. B., Hernandez, C. S., Han, Y., Flynn, J. H., Massoli, P., Floerchinger, C., Fortner, E. C., Herndon, S., Bean, J. K., Ruiz, H. L., Jeon, W., Choi, Y., Lefer, B., and Griffin, R. J., “Overview of Surface Measurements and Spatial Characterization of Submicron Particulate Matter during the DISCOVER-AQ 2013 Campaign in Houston,” The Journal of the Air & Waste Management Association , vol. 67, no. 8, pp. 854-872, 2017.

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