Publications by Type: Journal Article

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.
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
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.
2016
A. Canchero, Tinney, C. E., Murray, N., and Ruf, J. H., “Acoustic imaging of clustered rocket nozzles undergoing end-effects.,” AIAA Journal, vol. 54, no. 12, pp. 3778-3786, 2016.Abstract
A nonintrusive measure of the exhaust plume and immediate sound field produced by a cluster of two thrust optimized parabolic contour nozzles is studied during two steady-state conditions. The first condition is at a nozzle pressure ratio of 25, at which point the flow is in a restricted-shock separated state. The second condition is at a nozzle pressure ratio of 37 and is when the flow and internal shock pattern transition rapidly between free-shock separated flow and the end-effects regime. These end-effects regime pulsations produce significant vibroacoustic loads due to the intermittent breathing of the last trapped annular separation bubble with the ambient. The exhaust plumes and surrounding sound field are first visualized by way of retroreflective shadowgraphy. Radon transforms of the spatially resolved shadowgraphy images are then used to characterize the statistical behavior of the acoustic wave fronts that reside within the hydrodynamic periphery of the nozzle flow. The findings reveal quantitative evidence of the sources of most intense vibroacoustic loads during the end-effects regime of clustered rockets.
D. N. Espinoza, Vandamme, M., Dangla, P., Pereira, J. - M., and Vidal-Gilbert, S., “Adsorptive-mechanical properties of reconstituted granular coal: Experimental characterization and poromechanical modeling,” International Journal of Coal Geology, 2016.
S. Kelly, Torres-Verdín, C., and Balhoff, M., “Anomalous liquid imbibition at the nanoscale: the critical role of interfacial deformations,” Nanoscale, vol. 8, no. 5, pp. 2751-2767, 2016.
S. Kelly, Torres-Verdín, C., and Balhoff, M., “Anomalous liquid imbibition at the nanoscale: the critical role of interfacial deformations.,” Nanoscale, vol. 8, no. 5, pp. 2751-2767, 2016.
H. Daigle, “Application of critical path analysis for permeability prediction in natural porous media,” Advances in Water Resources, vol. 96, pp. 43-54, 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.
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.

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