Publications

2017
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.
PDF icon PDF
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
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.
S. Seraj, Kunal, P., Li, H., Henkelman, G., Humphrey, S. M., and Werth, C. J., “PdAu Alloy Nanoparticle Catalysts: Effective Candidates for Nitrite Reduction in Water,” ACS Catalysis, vol. 7, no. 5, pp. 3268-3276, 2017. Publisher's VersionAbstract
Well-defined palladium–gold nanoparticles (PdAuNPs) with randomly alloyed structures and broadly tunable compositions were studied in catalytic nitrite (NO2–) reduction. The catalysts were synthesized using a microwave-assisted polyol coreduction method. PdxAu100–xNPs with systematically varied compositions (x = 18–83) were supported on amorphous silica (SiO2) and studied as model catalysts for aqueous NO2– reduction in a batch reactor, using H2 as the electron donor. The reactions followed pseudo-first-order kinetics for ≥80% NO2– conversion. The PdxAu100–xNP-SiO2 catalysts showed a volcano-like correlation between NO2– reduction activity and x; the highest activity was observed for Pd53Au47, with an associated first-order rate constant of 5.12 L min–1 gmetal–1. Alloy NPs with greater proportions of Au were found to reduce the loss in catalytic activity due to sulfide fouling. Density functional theory calculations indicate that this is because Au weakens sulfur binding at PdAuNP surfaces due to atomic ensemble, electronic, and strain effects and thus reduces sulfur poisoning. The environmental relevance of the most active supported catalyst was evaluated by subjecting it to five cycles of catalytic NO2– reduction. The catalytic activity decreased over multiple cycles, but analysis of the postreaction PdxAu100–xNP-SiO2 materials using complementary techniques indicated that there were no significant structural changes. Most importantly, we show that PdxAu100–xNP-SiO2 alloys are significantly more active NO2– reduction catalysts in comparison to pure Pd catalysts.
Y. Zhang, Markey, M. K., and Tunnell, J. W., “Physiological basis for noninvasive skin cancer diagnosis using diffuse reflectance spectroscopy,” Proc. SPIE, vol. 10037. pp. 1003707-1003707-8, 2017. Publisher's VersionAbstract
Diffuse reflectance spectroscopy offers a noninvasive, fast, and low-cost alternative to visual screening and biopsy for skin cancer diagnosis. We have previously acquired reflectance spectra from 137 lesions in 76 patients and determined the capability of spectral diagnosis using principal component analysis (PCA). However, it is not well elucidated why spectral analysis enables tissue classification. To provide the physiological basis, we used the Monte Carlo look-up table (MCLUT) model to extract physiological parameters from those clinical data. The MCLUT model results in the following physiological parameters: oxygen saturation, hemoglobin concentration, melanin concentration, vessel radius, and scattering parameters. Physiological parameters show that cancerous skin tissue has lower scattering and larger vessel radii, compared to normal tissue. These results demonstrate the potential of diffuse reflectance spectroscopy for detection of early precancerous changes in tissue. In the future, a diagnostic algorithm that combines these physiological parameters could be enable non-invasive diagnosis of skin cancer.
C. Zhang, Bell, D., Harger, M., and Ren, P., “Polarizable Multipole-Based Force Field for Aromatic Molecules and Nucleobases,” J Chem Theory Comput, 2017.Abstract
Aromatic molecules with pi electrons are commonly involved in chemical and biological recognitions. For example, nucleobases play central roles in DNA/RNA structure and their interactions with proteins. The delocalization of the pi electrons is responsible for the high polarizability of aromatic molecules. In this work, the AMOEBA force field has been developed and applied to 5 regular nucleobases and 12 aromatic molecules. The permanent electrostatic energy is expressed as atomic multipole interactions between atom pairs, and many-body polarization is accounted for by mutually induced atomic dipoles. We have systematically investigated aromatic ring stacking and aromatic-water interactions for nucleobases and aromatic molecules, as well as base-base hydrogen-bonding pair interactions, all at various distances and orientations. van der Waals parameters were determined by comparison to the quantum mechanical interaction energy of these dimers and fine-tuned using condensed phase simulation. By comparing to quantum mechanical calculations, we show that the resulting classical potential is able to accurately describe molecular polarizability, molecular vibrational frequency, and dimer interaction energy of these aromatic systems. Condensed phase properties, including hydration free energy, liquid density, and heat of vaporization, are also in good overall agreement with experimental values. The structures of benzene liquid phase and benzene-water solution were also investigated by simulation and compared with experimental and PDB structure derived statistical results.
J. Selvakumar and Bakolas, E., “A pursuit-evasion game in the orbital plane,” in 27th AASAIAA Space Flight Mechanics Meeting, San Antonio, TX, 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.
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.
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.
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.
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.

Pages