Publications by Type: Journal Article

2018
Z. Sun, Espinoza, N. D., and Balhoff, M. T., “Reservoir rock chemo-mechanical alteration quantified by triaxial tests and implications to fracture reactivation,” International Journal of Rock Mechanics and Mining Sciences, vol. 106, pp. 250–258, 2018. Publisher's Version
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
J. Selvakumar and Bakolas, E., “Robust Time-Optimal Guidance in a Partially Uncertain Time-Varying Flow-Field,” Journal of Optimization Theory and Applications, vol. 179, no. 1, pp. 240-264, 2018. Publisher's VersionPDF icon jota_jseb_2018.pdf
X. Chen and Espinoza, N. D., “Surface area controls gas hydrate dissociation kinetics in porous media,” Fuel, vol. 234, pp. 358–363, 2018. Publisher's Version
J. A. Rackers, Wang, Z., Lu, C., Laury, M. L., Lagardere, L., Schnieders, M. J., Piquemal, J. - P., Ren, P., and Ponder, J. W., “Tinker 8: software tools for molecular design,” Journal of chemical theory and computation, vol. 14, pp. 5273–5289, 2018.
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, vol. 9, pp. 956–972, 2018.
U. Herwig, Lutz, J., Scherpiet, S., Scheerer, H., Kohlberg, J., Opialla, S., Preuss, A., Steiger, V. R., Sulzer, J., and Weidt, S., “Training emotion regulation through real-time fMRI neurofeedback of amygdala activity,” NeuroImage, 2018.
F. Tian, Song, B., Chen, X., Ravichandran, N. K., Lv, Y., Chen, K., Sullivan, S., Kim, J., Zhou, Y., Liu, T. - H., Goni, M., Ding, Z., Sun, J., Gamage, G. A. G. U., Sun, H., Ziyaee, H., Huyan, S., Deng, L., Zhou, J., Schmidt, A. J., Chen, S., Chu, C. - W., Huang, P. Y., Broido, D., Shi, L., Chen, G., and Ren, Z., “Unusual high thermal conductivity in boron arsenide bulk crystals,” Science, vol. 361, pp. 582–585, 2018. Publisher's VersionAbstract
Conventional theory predicts that ultrahigh lattice thermal conductivity can only occur in crystals composed of strongly bonded light elements, and that it is limited by anharmonic three-phonon processes. We report experimental evidence that departs from these long-held criteria. We measured a local room-temperature thermal conductivity exceeding 1000 watts per meter-kelvin and an average bulk value reaching 900 watts per meter-kelvin in bulk boron arsenide (BAs) crystals, where boron and arsenic are light and heavy elements, respectively. The high values are consistent with a proposal for phonon-band engineering and can only be explained by higher-order phonon processes. These findings yield insight into the physics of heat conduction in solids and show BAs to be the only known semiconductor with ultrahigh thermal conductivity.
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.
B. S. Wendel, He, C., Qu, M., Wu, D., Hernandez, S. M., Ma, K. - Y., Liu, E. W., Xiao, J., Crompton, P. D., Pierce, S. K., and others,Accurate immune repertoire sequencing reveals malaria infection driven antibody lineage diversification in young children,” Nature communications, vol. 8, pp. 531, 2017.
A. S. Massaro, Espinoza, N. D., Frydman, M., Barredo, S., and Cuervo, S., “Analyzing a suitable elastic geomechanical model for Vaca Muerta Formation,” Journal of South American Earth Sciences, vol. 79, pp. 472–488, 2017.
L. A. Hernandez-Uribe, Aman, M., and Espinoza, N. D., “Assessment of Mudrock Brittleness with Micro-scratch Testing,” Rock Mechanics and Rock Engineering, vol. 50, pp. 2849–2860, 2017.
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.
X. Han, Jing, Z., Wu, W., Zou, B., Peng, Z., Ren, P., Wikramanayake, A., Lu, Z., 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.
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.
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.

Pages