Publications

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.
M. J. Ramos, Espinoza, D. N., Torres-Verd{\'ın, C., Spikes, K. T., Laubach, S. E., and others,Stress-Dependent Dynamic-Static Transforms of Anisotropic Mancos Shale,” in 51st US Rock Mechanics/Geomechanics Symposium, 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.
X. Liu, Ramos, M. J., Nair, S. D., Lee, H., Espinoza, N. D., van Oort, E., and others,True Self-Healing Geopolymer Cements for Improved Zonal Isolation and Well Abandonment,” in SPE/IADC Drilling Conference and Exhibition, 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.
H. T. M. Nguyen, Moy, A. J., Zhang, Y., Feng, X., Reichenberg, J. S., Fox, M., and Tunnell, J. W., “Tumor margin assessment in Mohs surgery using reflectance, fluorescence and Raman spectroscopy,” Proc. SPIE, vol. 10054. pp. 1005403-1005403-6, 2017. Publisher's VersionAbstract
Mohs surgery is the current gold standard to treat large, aggressive or high-risk non-melanoma skin cancer (NMSC) cases. While Mohs surgery is an effective treatment, the procedure is time-consuming and expensive for physicians as well as burdensome for patients as they wait for frozen section histology. Our group has recently demonstrated high diagnostic accuracy using a noninvasive “spectral biopsy” (combination of diffuse reflectance (DRS), fluorescence (FS) and Raman spectroscopy (RS)) to classify NMSC vs. normal lesion in a screening setting of intact tissue. Here, we examine the sensitivity of spectral biopsy to pathology in excised Mohs sections. The system is designed with three modalities integrated into one fiber probe, which is utilized to measure DRS, FS, and RS of freshly excised skin from patients with various NMSC pathologies including basal cell carcinoma (BCC) and squamous cell carcinoma (SCC), where each measurement location is correlated to histopathology. The spectral biopsy provides complimentary physiological information including the reduced scattering coefficient, hemoglobin content and oxygen saturation from DRS, NADH and collagen contribution from FS and information regarding multiple proteins and lipids from RS. We then apply logistic regression model to the extracted physiological parameters to classify NMSC vs. normal tissue. The results on the excised tissue are generally consistent with in vivo measurements showing decreased scattering within the tumor and reduced fluorescence. Due to the high sensitivity of RS to lipids, subcutaneous fat often dominates the RS signal. This pilot study demonstrates the potential for a spectral biopsy to classify NMSC vs. normal tissue, indicating the opportunity to guide Mohs excisions.
Ultraflexible nanoelectronic probes form reliable, glial scar-free neural integration
L. Luan, Wei, X., Zhao, Z., Siegel, J. J., Potnis, O., Tuppen, C. A., Lin, S., Kazmi, S., Fowler, R. A., Holloway, S., Dunn, A. K., Chitwood, R. A., and Xie, C., “Ultraflexible nanoelectronic probes form reliable, glial scar-free neural integration,” Science Advances, vol. 3, no. 2, pp. e1601966, 2017. Publisher's VersionAbstract
Implanted brain electrodes construct the only means to electrically interface with individual neurons in vivo, but their recording efficacy and biocompatibility pose limitations on scientific and clinical applications. We showed that nanoelectronic thread (NET) electrodes with subcellular dimensions, ultraflexibility, and cellular surgical footprints form reliable, glial scar–free neural integration. We demonstrated that NET electrodes reliably detected and tracked individual units for months; their impedance, noise level, single-unit recording yield, and the signal amplitude remained stable during long-term implantation. In vivo two-photon imaging and postmortem histological analysis revealed seamless, subcellular integration of NET probes with the local cellular and vasculature networks, featuring fully recovered capillaries with an intact blood-brain barrier and complete absence of chronic neuronal degradation and glial scar.
P. Jurney, Agarwal, R., Singh, V., Choi, D., Roy, K., Sreenivasan, S. V., and Shi, L., “Unique size and shape-dependent uptake behaviors of non-spherical nanoparticles by endothelial cells due to a shearing flow,” Journal of Controlled Release, vol. 245, pp. 170–176 , 2017. Publisher's Version
P. Jurney, Agarwal, R., Singh, V., Choi, D., Roy, K., Sreenivasan, S. V., and Shi, L., “Unique size and shape-dependent uptake behaviors of non-spherical nanoparticles by endothelial cells due to a shearing flow,” Journal of Controlled Release, vol. 245, pp. 170-176, 2017. DOIAbstract
The size and shape of nanoparticle (NP) drug carriers can potentially be manipulated to increase the drug delivery efficacy because of their effects on particle margination and interactions with various cells in vivo. It is found in this work that the presence of a physiologically relevant shearing flow rate results in very different size and shape-dependent uptake behavior of negatively charged, non-spherical polyethylene glycol (PEG) hydrogel NPs by endothelial cells (ECs) cultured in a microchannel compared to uptake of either identical NPs in static culture or spherical particles in a shear flow. In particular, larger rod- and disk-shaped PEG NPs show more uptake than smaller ones, opposite to the size effect observed for spherical particles in a flow. Moreover, the trend observed in this dynamic uptake experiment also differs from that reported for uptake of similar PEG NPs by ECs in a static culture, where the smaller disks were found to be uptaken the most. These differences suggest that the increasing rotational and tumbling motions of larger-size non-spherical NPs in the flow play a dominant role in NP margination and cell interaction, compared to Brownian motion, gravity, and cell membrane deformation energy. These findings suggest that the coupling between NP geometry and shear flow is an important factor that needs to be accounted for in the design of the size and shape of nanocarriers.
S. Ramos, Espinoza, D. N., and Torres-Verdín, C., “Use of shear-wave anisotropy to quantify the onset of stress-induced microfracturing,” Geophysics, vol. 82, no. 6, pp. MR201-MR212, 2017.
M. J. Ramos, Espinoza, N. D., Torres-Verd{\'ın, C., and Grover, T., “Use of S-wave anisotropy to quantify the onset of stress-induced microfracturingShear anisotropy and microfracturing,” Geophysics, vol. 82, pp. MR201–MR212, 2017.
C. E. Tinney, “Wall pressure unsteadiness on the aft deck of a planar multi-stream supersonic nozzle,” 55th AIAA Aerospace Sciences Meeting, AIAA Paper 2017-0525. Grapevine, Texas, USA, 2017.Abstract
The unsteady wall pressure on the aft deck of a multi-stream, planar supersonic nozzle is studied over a range of nozzle operating conditions corresponding to independent changes to the core and bypass stream pressure ratios. The data are processed using time-frequency analysis and reveal various tones corresponding to transonic resonance as wellunsteady interactions of both separation and reflection shocks with the developing boundary layer. The position of the separation shock is shown to experience significant hysteresis effects, which subside at pressure ratios well above the design pressure ratio of the nozzle. Shadowgraphy images of the exhaust plume are also presented, which are then analyzed using the snapshot form of proper orthogonal decomposition. The findings from this low-dimensional analysis demonstrates how the first most energetic mode highlights the shock cell patterns whereas the second most energetic mode elucidates turbulence motions in the plume.

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