Publications by Year: 2017

2017
A. Mehmani, Kelly, S., Torres-Verdín, C., and Balhoff, M., “Quantification of fracture-matrix fluid transport in unconventional rocks using two-scale microfluidic chips (Expanded Abstract),” Unconventional Resources Technology Conference (URTeC). Austin, Texas, July 24 – 26, 2017.
X. Feng, Moy, A. J., Nguyen, H. T. M., Zhang, J., Fox, M. C., Sebastian, K. R., Reichenberg, J. S., Markey, M. K., and Tunnell, J. W., “Raman active components of skin cancer,” Biomed. Opt. Express, vol. 8, pp. 2835–2850, 2017. Publisher's VersionAbstract
Raman spectroscopy (RS) has shown great potential in noninvasive cancer screening. Statistically based algorithms, such as principal component analysis, are commonly employed to provide tissue classification; however, they are difficult to relate to the chemical and morphological basis of the spectroscopic features and underlying disease. As a result, we propose the first Raman biophysical model applied to in vivo skin cancer screening data. We expand upon previous models by utilizing in situ skin constituents as the building blocks, and validate the model using previous clinical screening data collected from a Raman optical fiber probe. We built an 830nm confocal Raman microscope integrated with a confocal laser-scanning microscope. Raman imaging was performed on skin sections spanning various disease states, and multivariate curve resolution (MCR) analysis was used to resolve the Raman spectra of individual in situ skin constituents. The basis spectra of the most relevant skin constituents were combined linearly to fit in vivo human skin spectra. Our results suggest collagen, elastin, keratin, cell nucleus, triolein, ceramide, melanin and water are the most important model components. We make available for download (see supplemental information) a database of Raman spectra for these eight components for others to use as a reference. Our model reveals the biochemical and structural makeup of normal, nonmelanoma and melanoma skin cancers, and precancers and paves the way for future development of this approach to noninvasive skin cancer diagnosis.
R. Singh, Sivaguru, M., Fried, G. A., Fouke, B. W., Sanford, R. A., Carrera, M., and Werth, C. J., “Real rock-microfluidic flow cell: A test bed for real-time in situ analysis of flow, transport, and reaction in a subsurface reactive transport environment,” Journal of Contaminant Hydrology, vol. 204, pp. 28-39, 2017. Publisher's VersionAbstract
Physical, chemical, and biological interactions between groundwater and sedimentary rock directly control the fundamental subsurface properties such as porosity, permeability, and flow. This is true for a variety of subsurface scenarios, ranging from shallow groundwater aquifers to deeply buried hydrocarbon reservoirs. Microfluidic flow cells are now commonly being used to study these processes at the pore scale in simplified pore structures meant to mimic subsurface reservoirs. However, these micromodels are typically fabricated from glass, silicon, or polydimethylsiloxane (PDMS), and are therefore incapable of replicating the geochemical reactivity and complex three-dimensional pore networks present in subsurface lithologies. To address these limitations, we developed a new microfluidic experimental test bed, herein called the Real Rock-Microfluidic Flow Cell (RR-MFC). A porous 500 μm-thick real rock sample of the Clair Group sandstone from a subsurface hydrocarbon reservoir of the North Sea was prepared and mounted inside a PDMS microfluidic channel, creating a dynamic flow-through experimental platform for real-time tracking of subsurface reactive transport. Transmitted and reflected microscopy, cathodoluminescence microscopy, Raman spectroscopy, and confocal laser microscopy techniques were used to (1) determine the mineralogy, geochemistry, and pore networks within the sandstone inserted in the RR-MFC, (2) analyze non-reactive tracer breakthrough in two- and (depth-limited) three-dimensions, and (3) characterize multiphase flow. The RR-MFC is the first microfluidic experimental platform that allows direct visualization of flow and transport in the pore space of a real subsurface reservoir rock sample, and holds potential to advance our understandings of reactive transport and other subsurface processes relevant to pollutant transport and cleanup in groundwater, as well as energy recovery.
A. Menshov, Brick, Y., Torres-Verdín, C., and Yilmaz, A. E., “Recent progress in rigorous algorithms for the fast solution of 3-D EM frequency-domain integral equations (Expanded Abstract),” Sixth International Symposium on Three-Dimensional Electromagnetics. Berkeley, CA, March 28-30, 2017.
M. Luycx and Torres-Verdín, C., “Resolution and accuracy of neutron-gamma density measurements compared to conventional gamma-gamma density measurements (Expanded Abstract),” Society of Petroleum Engineers (SPE) 2017 Annual Technical Conference and Exhibition. San Antonio, TX, October 9-11, 2017.
D. Pylorof, Bettadpur, S., and Bakolas, E., “On the Robust Attitude Regulation for Earth Observation Spacecraft Under Hybrid Actuation,” in 27th AASAIAA Space Flight Mechanics Meeting, San Antonio, TX, 2017.
D.Pylorof and Bakolas, E., “Robust Control of Input Constrained Nonlinear Systems Subject to
Unknown Bounded Disturbances Based on Convex Optimization
,” American Control Conference. Seattle, WA, 2017.
D. Wang and Hildebrandt Ruiz, L., “Secondary organic aerosol from chlorine-initiated oxidation of isoprene,” Atmospheric Chemistry and Physics, vol. 17, pp. 13491–13508, 2017.
E. F. Oblak, Lewis-Peacock, J. A., and Sulzer, J. S., “Self-regulation strategy, feedback timing and hemodynamic properties modulate learning in a simulated fMRI neurofeedback environment,” PLoS computational biology, vol. 13, no. 7, pp. e1005681, 2017.
R. Wang, Herrera, W., and Torres-Verdín, C., “Simulation and interpretation of sonic waveforms in high-angle and horizontal wells,” Geophysics, vol. 82, no. 4, pp. D251-D263, 2017.
A. J. Moy, Feng, X., Nguyen, H. T. M., Zhang, Y., Sebastian, K. R., Reichenberg, J. S., and Tunnell, J. W., “Spectral biopsy for skin cancer diagnosis: initial clinical results,” Proc. SPIE, vol. 10037. pp. 1003704-1003704-6, 2017. Publisher's VersionAbstract
Skin cancer is the most common form of cancer in the United States and is a recognized public health issue. Diagnosis of skin cancer involves biopsy of the suspicious lesion followed by histopathology. Biopsies, which involve excision of the lesion, are invasive, at times unnecessary, and are costly procedures ( $2.8B/year in the US). An unmet critical need exists to develop a non-invasive and inexpensive screening method that can eliminate the need for unnecessary biopsies. To address this need, our group has reported on the continued development of a noninvasive method that utilizes multimodal spectroscopy towards the goal of a “spectral biopsy” of skin. Our approach combines Raman spectroscopy, fluorescence spectroscopy, and diffuse reflectance spectroscopy to collect comprehensive optical property information from suspicious skin lesions. We previously described an updated spectral biopsy system that allows acquisition of all three forms of spectroscopy through a single fiber optic probe and is composed of off-the-shelf OEM components that are smaller, cheaper, and enable a more clinic-friendly system. We present initial patient data acquired with the spectral biopsy system, the first from an extensive clinical study (n = 250) to characterize its performance in identifying skin cancers (basal cell carcinoma, squamous cell carcinoma, and melanoma). We also present our first attempts at analyzing this initial set of clinical data using statistical-based models, and with models currently being developed to extract biophysical information from the collected spectra, all towards the goal of noninvasive skin cancer diagnosis.
C. Griffith and Daigle, H., “Stability of polyvinyl alcohol-coated biochar nanoparticles in brine,” Journal of Nanoparticle Research, vol. 19, no. 1, pp. 23, 2017.
M. J. Ramos, Espinoza, D. N., Torres-Verdín, C., Spikes, K. T., and Laubach, S. E., “Stress-dependent dynamic-static transforms of anisotropic Mancos shale (Extended Abstract),” American Rock Mechanics Association (ARMA) 51st US Rock Mechanics/Geomechanics Symposium. San Francisco, California, June 25-28, 2017.
Z. Jing, Qi, R., Liu, C., and Ren, P., “Study of interactions between metal ions and protein model compounds by energy decomposition analyses and the AMOEBA force field,” The Journal of Chemical Physics, vol. 147, pp. 161733, 2017.
B. Smith, Vermeersch, B., Carrete, J., Ou, E., Kim, J., Mingo, N., Akinwande, D., and Shi, L., “Temperature and Thickness Dependences of the Anisotropic In-Plane Thermal Conductivity of Black Phosphorus,” Advanced Materials, vol. 29, pp. 1603756, 2017. Publisher's Version
K. S. Olsson, An, K., Ma, X., Sullivan, S., Venu, V., Tsoi, M., Zhou, J., Shi, L., and Li, X., “Temperature-dependent Brillouin light scattering spectra of magnons in yttrium iron garnet and permalloy,” Phys. Rev. B, vol. 96, pp. 024448, 2017. Publisher's Version
L. Lin, Peng, X., Wei, X., Mao, Z., Xie, C., and Zheng, Y., “Thermophoretic Tweezers for Low-Power and Versatile Manipulation of Biological Cells,” ACS nano, vol. 11, pp. 3147–3154, 2017. Publisher's VersionAbstract
Optical manipulation of biological cells and nanoparticles is significantly important in life sciences, early disease diagnosis, and nanomanufacturing. However, low-power and versatile all-optical manipulation has remained elusive. Herein, we have achieved light-directed versatile thermophoretic manipulation of biological cells at an optical power 100–1000 times lower than that of optical tweezers. By harnessing the permittivity gradient in the electric double layer of the charged surface of the cell membrane, we succeed at the low-power trapping of suspended biological cells within a light-controlled temperature gradient field. Furthermore, through dynamic control of optothermal potentials using a digital micromirror device, we have achieved arbitrary spatial arrangements of cells at a resolution of ∼100 nm and precise rotation of both single and assemblies of cells. Our thermophoretic tweezers will find applications in cellular biology, nanomedicine, and tissue engineering.
M. Harger, Li, D., Wang, Z., Dalby, K., Lagardere, L., Piquemal, J. P., Ponder, J., and Ren, P. Y., “Tinker-OpenMM: Absolute and Relative Alchemical Free Energies using AMOEBA on GPUs,” Journal of Computational Chemistry, vol. 38, pp. 2047-2055, 2017.Abstract
The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a similar to 200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. (C) 2017 Wiley Periodicals, Inc.
A. Frooqnia, Torres-Verdín, C., Sepehrnoori, K., and Abdhollah-Pour, R., “Transient coupled borehole/formation fluid-flow model for interpretation of oil/water production logs,” SPE Journal, vol. 22, no. 1, pp. 389-406, 2017.
F. Aviat, Levitt, A., Stamm, B., Maday, Y., Ren, P., Ponder, J. W., Lagardere, L., and Piquemal, J. P., “Truncated Conjugate Gradient: An Optimal Strategy for the Analytical Evaluation of the Many-Body Polarization Energy and Forces in Molecular Simulations,” J Chem Theory Comput, vol. 13, pp. 180-190, 2017.Abstract
We introduce a new class of methods, denoted as Truncated Conjugate Gradient(TCG), to solve the many-body polarization energy and its associated forces in molecular simulations (i.e. molecular dynamics (MD) and Monte Carlo). The method consists in a fixed number of Conjugate Gradient (CG) iterations. TCG approaches provide a scalable solution to the polarization problem at a user-chosen cost and a corresponding optimal accuracy. The optimality of the CG-method guarantees that the number of the required matrix-vector products are reduced to a minimum compared to other iterative methods. This family of methods is non-empirical, fully adaptive, and provides analytical gradients, avoiding therefore any energy drift in MD as compared to popular iterative solvers. Besides speed, one great advantage of this class of approximate methods is that their accuracy is systematically improvable. Indeed, as the CG-method is a Krylov subspace method, the associated error is monotonically reduced at each iteration. On top of that, two improvements can be proposed at virtually no cost: (i) the use of preconditioners can be employed, which leads to the Truncated Preconditioned Conjugate Gradient (TPCG); (ii) since the residual of the final step of the CG-method is available, one additional Picard fixed point iteration ("peek"), equivalent to one step of Jacobi Over Relaxation (JOR) with relaxation parameter omega, can be made at almost no cost. This method is denoted by TCG-n(omega). Black-box adaptive methods to find good choices of omega are provided and discussed. Results show that TPCG-3(omega) is converged to high accuracy (a few kcal/mol) for various types of systems including proteins and highly charged systems at the fixed cost of four matrix-vector products: three CG iterations plus the initial CG descent direction. Alternatively, T(P)CG-2(omega) provides robust results at a reduced cost (three matrix-vector products) and offers new perspectives for long polarizable MD as a production algorithm. The T(P)CG-1(omega) level provides less accurate solutions for inhomogeneous systems, but its applicability to well-conditioned problems such as water is remarkable, with only two matrix-vector product evaluations.

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