Publications by Type: Journal Article

2018
J. Zhao, Wang, G., del Mundo, I. M., McKinney, J. A., Lu, X., Bacolla, A., Boulware, S. B., Zhang, C., Zhang, H., Ren, P., and others,Distinct Mechanisms of Nuclease-Directed DNA-Structure-Induced Genetic Instability in Cancer Genomes,” Cell reports, vol. 22, pp. 1200–1210, 2018.
D. S. Choi, Poudel, N., Park, S., Akinwande, D., Cronin, S. B., Watanabe, K., Taniguchi, T., Yao, Z., and Shi, L., “Large Reduction of Hot Spot Temperature in Graphene Electronic Devices with Heat-Spreading Hexagonal Boron Nitride,” ACS Applied Materials & Interfaces, vol. 10 , pp. 11101–11107, 2018. Publisher's Version
S. Qu, Hu, M. - B., Wang, Y., and Song, T., “Modeling the influences of Ag or Au nanoparticles on the solar energy absorption and photocatalytic properties of N-TiO2,” Optics Communications, vol. 407, pp. 375-380, 2018. Publisher's VersionAbstract
Metallic nanoparticles have unique optical properties such as localized surface plasmon resonance (LSPR) effect, which can be used to improve the energy absorption and photocatalytic properties of semiconductor bases. In this paper, we construct a model to study the influence of Ag or Au nanoparticles (cubes or spheres) on the solar energy absorption and photocatalytic properties of nitrogen doped TiO2 (or N-TiO2). Effects of specific nanoparticle coupling parameters, such as particle shape, size, doping period (metal–metal distance) and separation distance (metal–semiconductor distance), on the properties of N-TiO2 are studied in detail. We show that the photocurrent improvement can be optimized by setting suitable geometric parameters. In particular, the separation distance between metallic nanoparticles and N-TiO2D should be around 6–7 nm, and the period of doping P should be around 360 nm. The silver cubes with edge length  show the best performance. The results can help the design of solar energy materials, in which metallic nanoparticles may play an important role.
L. Luan, Sullender, C. T., Li, X., Zhao, Z., Zhu, H., Wei, X., Xie, C., and Dunn, A. K., “Nanoelectronics enabled chronic multimodal neural platform in a mouse ischemic model,” Journal of neuroscience methods, vol. 295, pp. 68 - 76, 2018. Publisher's VersionAbstract
Background Despite significant advancements of optical imaging techniques for mapping hemodynamics in small animal models, it remains challenging to combine imaging with spatially resolved electrical recording of individual neurons especially for longitudinal studies. This is largely due to the strong invasiveness to the living brain from the penetrating electrodes and their limited compatibility with longitudinal imaging.
X. Wei, Luan, L., Zhao, Z., Li, X., Zhu, H., Potnis, O., and Xie, C., “Nanofabricated Ultraflexible Electrode Arrays for High-Density Intracortical Recording,” Advanced Science, pp. 1700625–n/a, 2018. Publisher's VersionAbstract
Understanding brain functions at the circuit level requires time-resolved simultaneous measurement of a large number of densely distributed neurons, which remains a great challenge for current neural technologies. In particular, penetrating neural electrodes allow for recording from individual neurons at high temporal resolution, but often have larger dimensions than the biological matrix, which induces significant damage to brain tissues and therefore precludes the high implant density that is necessary for mapping large neuronal populations with full coverage. Here, it is demonstrated that nanofabricated ultraflexible electrode arrays with cross-sectional areas as small as sub-10 µm2 can overcome this physical limitation. In a mouse model, it is shown that these electrodes record action potentials with high signal-to-noise ratio; their dense arrays allow spatial oversampling; and their multiprobe implantation allows for interprobe spacing at 60 µm without eliciting chronic neuronal degeneration. These results present the possibility of minimizing tissue displacement by implanted ultraflexible electrodes for scalable, high-density electrophysiological recording that is capable of complete neuronal circuitry mapping over chronic time scales.
E. Bakolas, “Distributed Partitioning Algorithms for Locational Optimization of Multi-Agent Networks in SE(2),” IEEE Transactions on Automatic Control, vol. 63, no. 1, pp. 101-116, 2018. Publisher's VersionPDF icon ieee_tac17_eb.pdf
E. Bakolas, “Constrained Minimum Variance Control for Discrete-Time Stochastic Linear Systems,” Systems & Control Letters, vol. 113, no. 3, pp. 109-116, 2018. Publisher's VersionPDF icon mvc_scl_fvrev_8.pdf
E. Bakolas, “Finite-Horizon Covariance Control for Discrete-Time Stochastic Linear Systems Subject to Input Constraints,” Automatica, vol. 91, no. 5, pp. 61-68, 2018. Publisher's VersionPDF icon bakauto2018_fv2.pdf
L. Lagardère, Jolly, L. - H., Lipparini, F., Aviat, F., Stamm, B., Jing, Z. F., Harger, M., Torabifard, H., Cisneros, A. G., Schnieders, M. J., and others,Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields,” Chemical Science, 2018.
2017
C. E. Schaefer, Ho, P., Gurr, C., Berns, E., and Werth, C. J., “Abiotic dechlorination of chlorinated ethenes in natural clayey soils: Impacts of mineralogy and temperature,” Journal of Contaminant Hydrology, 2017. Publisher's VersionAbstract
Laboratory batch experiments were performed to assess the impacts of temperature and mineralogy on the abiotic dechlorination of tetrachloroethene (PCE) or trichloroethene (TCE) due to the presence of ferrous minerals in natural aquifer clayey soils under anaerobic conditions. A combination of x-ray diffraction (XRD), magnetic susceptibility, and ferrous mineral content were used to characterize each of the 3 natural soils tested in this study, and dechlorination at temperatures ranging from 20 to 55 °C were examined. Results showed that abiotic dechlorination occurred in all 3 soils examined, yielding reduced gas abiotic dechlorination products acetylene, butane, ethene, and/or propane. Bulk first-order dechlorination rate constants (kbulk), scaled to the soil:water ratio expected for in situ conditions, ranged from 2.0 × 10−5 day−1 at 20 °C, to 32 × 10−5 day−1 at 55 °C in the soil with the greatest ferrous mineral content. For the generation of acetylene and ethene from PCE, the reaction was well described by Arrhenius kinetics, with an activation energy of 91 kJ/mol. For the generation of coupling products butane and propane, the Arrhenius equation did not provide a satisfactory description of the data, likely owing to the complex reaction mechanisms associated with these products and/or diffusional mass transfer processes associated with the ferrous minerals likely responsible for these coupling reactions. Although the data set was too limited to determine a definitive correlation, the two soils with elevated ferrous mineral contents had elevated abiotic dechlorination rate constants, while the one soil with a low ferrous mineral content had a relatively low abiotic dechlorination rate constant. Overall, results suggest intrinsic abiotic dechlorination rates may be an important long-term natural attenuation component in site conceptual models for clays that have the appropriate iron mineralogy.
B. S. Wendel, He, C. F., Qu, M. J., Wu, D., Hernandez, S. M., Ma, K. Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., Ren, P. Y., Chen, K. K., and Jiang, N., “Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature Communications, vol. 8, 2017.Abstract
Accurately measuring antibody repertoire sequence composition in a small amount of blood is challenging yet important for understanding repertoire responses to infection and vaccination. We develop molecular identifier clustering-based immune repertoire sequencing (MIDCIRS) and use it to study age-related antibody repertoire development and diversification before and during acute malaria in infants (<12 months old) and toddlers (12-47 months old) with 4-8ml of blood. Here, we show this accurate and high-coverage repertoire-sequencing method can use as few as 1000 naive B cells. Unexpectedly, we discover high levels of somatic hypermutation in infants as young as 3 months old. Antibody clonal lineage analysis reveals that somatic hypermutation levels are increased in both infants and toddlers upon infection, and memory B cells isolated from individuals who previously experienced malaria continue to induce somatic hypermutations upon malaria rechallenge. These results highlight the potential of antibody repertoire diversification in infants and toddlers.
X. Han, Jing, Z. F., Wu, W., Zou, B., Peng, Z. L., Ren, P. Y., Wikramanayake, A., Lu, Z. M., and Leblanc, R. M., “Biocompatible and blood-brain barrier permeable carbon dots for inhibition of A beta fibrillation and toxicity, and BACE1 activity,” Nanoscale, vol. 9, pp. 12862-12866, 2017.Abstract
Amyloid-beta peptide (A beta) fibrillation is pathologically associated with Alzheimer's disease (AD), and this has resulted in the development of an A beta inhibitor which is essential for the treatment of AD. However, the design of potent agents which can target upstream secretases, inhibit A beta toxicity and aggregation, as well as cross the blood-brain barrier remains challenging. In, this research carbon dots for AD treatment were investigated in vitro using experimental and computational methods for the first time. The results presented here demonstrate a novel strategy for the discovery of novel antiamyloidogenic agents for AD treatments.
C. Liu, Qi, R., Wang, Q., Piquemal, J. - P., and Ren, P., “Capturing Many-Body Interactions with Classical Dipole Induction Models,” Journal of Chemical Theory and Computation, vol. 13, pp. 2751–2761, 2017.
D. R. Bell, Cheng, S. Y., Salazar, H., and Ren, P., “Capturing RNA Folding Free Energy with Coarse-Grained Molecular Dynamics Simulations,” Scientific Reports, vol. 7, 2017.
W. Wu, Chai, Z., Gao, Y., Kong, D., He, F., Meng, X., and Wang, Y., “Carrier dynamics and optical nonlinearity of alloyed CdSeTe quantum dots in glass matrix,” Optical Materials Express, vol. 7, no. 5, pp. 1547-1556, 2017. Publisher's VersionAbstract
Size and pump-fluence dependent ultrafast carrier dynamics of CdSeTe QDs are investigated using femtosecond pump-probe techniques operating at two different repetition rates: 1 kHz (low-repetition rate), and 76 MHz (high-repetition rate). With a low-repetition rate laser and 3.1 eV excitation photon energy, multiple exciton generation (MEG) is observed and the optical responses of alloyed QDs clearly show three components: a fast decay ascribed to carrier recombination, an intermediate component associated with MEG decay, and a slow decay associated with radiative Auger recombination. With a high-repetition rate laser and excitation photon energy resonant with band-edge energy, obvious coherent phonon oscillations are observed in 4 nm CdSeTe QDs due to impulsive stimulated Raman scattering. Open-aperture Z-scan measurement is used to clarify the size and pump-fluence dependence of optical nonlinearity under femtosecond laser excitation. With increasing laser power, an evolution from saturable absorption to reverse saturable absorption in CdSeTe QDs is observed. The transition process is analyzed using a phenomenological model based on nonlinear absorption coefficient and saturation intensity. These results indicate that CdSeTe QDs in a glass matrix are a class of materials for potential application in all-optical switching devices.
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A. M. Bergquist, Bertoch, M., Gildert, G., Strathmann, T. J., and Werth, C. J., “Catalytic Denitrification in a Trickle Bed Reactor: Ion Exchange Waste Brine Treatment,” Journal-American Water Works Association, vol. 109, no. 5, pp. E129-E143, 2017. Publisher's VersionAbstract
Catalytic reduction of nitrate in ion exchange (IX) waste brine for reuse is a promising option for reducing IX costs and environmental impacts. A recycling trickle bed reactor (TBR) was designed and optimized using 0.5 percent byweight (wt%) palladium–0.05 wt% indium catalysts supported on US mesh size 12 × 14 or 12 × 30 activated carbon particles. Various liquid superficial velocities (Ur) and hydrogen gas superficial velocities (Ug-H2) were evaluated to assess performance in different flow regimes; catalyst activity increased with Ug-H2 at all Ur for both catalysts and was greatest for the 12 × 30 catalyst at thelowest Ur (8.9 m/h). The 12 × 30 catalyst demonstrated up to 100% higher catalytic activity and 280% higher mass transfer rate compared with the 12 × 14 catalyst. Optimal TBR performance was achieved with both catalysts in thetrickle flow regime. The results indicate that the TBR is a promising step forward, and continued improvements are possible to overcome remaining mass transfer limitations.
M. Bertoch, Bergquist, A. M., Gildert, G., Strathmann, T. J., and Werth, C. J., “Catalytic Nitrate Removal in a Trickle Bed Reactor: Direct Drinking Water Treatment,” Journal-American Water Works Association, vol. 109, no. 5, pp. E144, 2017. Publisher's VersionAbstract
Palladium (Pd)-based catalysts hold promise as an alternative water treatment technology for nitrate (NO3–), but practical application requires a flow-through reactor that efficiently delivers hydrogen (H2) from gas to water. A trickle bed reactor (TBR) packed with a 0.1 percent by weight (wt%) Pd–0.01 wt% In/γ-Al2O3 (indium and porous aluminum oxide) catalyst was evaluated to address this challenge. Catalytic activity generally increased with H2 superficial velocity (0.65–29.6 m/h) and liquid (deionized water) superficial velocities from 14.8 to 26.6 m/h before decreasing at 38.5 m/h. This decrease corresponded to a change in flow regime and suggests that optimal TBR performance occurs at the transition from pulse to bubble flow. An optimal TBR activity of 19.5 ± 1.3 mg NO3–/min-g Pd was obtained; this is only ~18% of the batch reactor activity as a result of H2 mass transfer limitations, but three to 15 times greater than activities obtained with previous flow-through reactors. Catalyst deactivation occurred in the TBR after 41 days of operation, motivating the need for improved fouling mitigation strategies.
R. Sitaram, Ros, T., Stoeckel, L., Haller, S., Scharnowski, F., Lewis-Peacock, J., Weiskopf, N., Blefari, M. L., Rana, M., Oblak, E., Birbaumer, N., and Sulzer, J., “Closed-loop brain training: the science of neurofeedback,” Nature Reviews Neuroscience, 2017.
A. J. Moy and Tunnell, J. W., “Combinatorial immunotherapy and nanoparticle mediated hyperthermia,” Advanced Drug Delivery Reviews, vol. 114, pp. 175 - 183, 2017. Publisher's VersionAbstract
Immune checkpoint therapy has become the first widely adopted immunotherapy for patients with late stage malignant melanoma, with potential for a wide range of cancers. While some patients can experience long term disease remission, this is limited only to a subset of patients and tumor types. The path forward to expand this therapy to more patients and tumor types is currently thought to be combinatorial treatments, the combination of immunotherapy with other treatments. In this review, the combinatorial approach of immune checkpoint therapy combined with nanoparticle-assisted localized hyperthermia is discussed, starting with an overview of the different nanoparticle hyperthermia approaches in development, an overview of the state of immune checkpoint therapy, recent reports of immune checkpoint therapy and nanoparticle-assisted hyperthermia in a combinatorial approach, and finally a discussion of future research topics and areas to be explored in this new combinatorial approach to cancer treatment.
W. F. Woodruff, Lewan, M. D., Revil, A., and Torres-Verdín, C., “Complex electrical conductivity changes associated with hydrous pyrolysis maturation of the Woodford Shale.,” Geophysics, vol. 82, no. 2, pp. D83-D104, 2017.

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