Recent Articles from UCSD Math Faculty

Recent publications from the UC San Diego Department of Math faculty:

BEJENARU, I., IONESCU, A., KENIG, C. & TATARU, D. 2013. Equivariant Schrödinger maps in two spatial dimensions. Duke Mathematical Journal, 162, 1967-2025.

BUSS, S. & MINNES, M. 2013. Probalistic algorithmic randomness. Journal of Symbolic Logic, 78, 579-601.

DODGE, J. & POPESCU, C. D. 2013. The refined Coates-Sinnott conjecture for characteristic p global fields. Journal of Number Theory, 133, 2047-2065.

DOWLA, A., PAPARODITIS, E. & POLITIS, D. N. 2013. Local block bootstrap inference for trending time series. Metrika, 76, 733-764.

DUANE, A., GARSIA, A. M. & ZABROCKI, M. 2013. A new “dinv” arising from the two part case of the shuffle conjecture. Journal of Algebraic Combinatorics, 37, 683-715.

EBENFELT, P. 2013. Partial rigidity of degenerate CR embeddings into spheres. Advances in Mathematics, 239, 72-96.

FIALKOW, L. & NIE, J. W. 2013. On the closure of positive flat moment matricies. Journal of Operator Theory, 69, 257-277.

GOUR, G. & WALLACH, N. R. 2013. Classification of Multipartite Entanglement of All Finite Dimensionality. Physical Review Letters, 111.

HAGLUND, J., MASON, S. & REMMEL, J. 2013. Properties of the nonsymmetric Robinson-Schensted-Knuth algorithm. Journal of Algebraic Combinatorics, 38, 285-327.

HOLST, M., SZYPOWSKI, R. & ZHU, Y. R. 2013. Two-grid methods for semilinear interface problems. Numerical Methods for Partial Differential Equations, 29, 1729-1748.

KOICHU, B., HAREL, G. & MANASTER, A. 2013. Ways of thinking associated with mathematics teachers’ problem posing in the context of division of fractions. Instructional Science, 41, 681-698.

MARIAN, A. & OPREA, D. 2013. Generic strange duality for K3 surfaces. Duke Mathematical Journal, 162, 1463-1501.

MATHER, W. H., HASTY, J., TSIMRING, L. S. & WILLIAMS, R. J. 2013. Translational Cross Talk in Gene Networks. Biophysical Journal, 104, 2564-2572.

MCLEAN, J. S., LOMBARDO, M. J., BADGER, J. H., EDLUND, A., NOVOTNY, M., YEE-GREENBAUM, J., VYAHHI, N., HALL, A. P., YANG, Y., DUPONT, C. L., ZIEGLER, M. G., CHITSAZ, H., ALLEN, A. E., YOOSEPH, S., TESLER, G., PEVZNER, P. A., FRIEDMAN, R. M., NEALSON, K. H., VENTER, J. C. & LASKEN, R. S. 2013. Candidate phylum TM6 genome recovered from a hospital sink biofilm provides genomic insights into this uncultivated phylum. Proceedings of the National Academy of Sciences of the United States of America, 110, E2390-E2399.

MEYER, D. A. & WONG, T. G. 2013. Nonlinear quantum search using the Gross-Pitaevskii equation. New Journal of Physics, 15, 063014.

POLITIS, D. N. 2013. Model-free model-fitting and predictive distributions. Test, 22, 183-221.

ZHAO, Y. X., KWAN, Y. Y., CHE, J. W., LI, B. & MCCAMMON, J. A. 2013. Phase-field approach to implicit solvation of biomolecules with Coulomb-field approximation. Journal of Chemical Physics, 139.

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Liangfang Zhang, One of “35 Innovators Under 35″

This week, Liangfang Zhang (NanoEngineering) was named one of “35 Innovators Under 35” by MIT Technology Review. As one of the “Pioneers,” he was recognized for his work with natural membranes in drug delivery systems:

Zhang derives red-blood-cell membranes from blood samples and uses them to coat polymer nanoparticles. Because these particles look like red blood cells on the surface, they can fool the immune system; loaded with drugs, they serve as robust and long-lived drug carriers. An unexpected bonus: they can also act like nanoscale sponges to suck up toxic proteins produced by infectious bacteria or introduced by snake or insect venom. If the particles flood the bloodstream, they will divert most of the toxin away from actual cells.

Jacobs School of Engineering press release: Liangfang Zhang Makes MIT Technology Review’s Annual Innovators Under 35 List

Some recent articles from the Zhang Research Group:

Fang, R.; Hu, C-M.; Chen, K.; Luk, B.; Carpenter, C.; Gao, W.; Li, S.; Zhang, D-E.; Lu, W.; Zhang, L.* ”Lipid-insertion enables targeting functionalization of erythocyte membrane-cloaked nanoparticles“, Nanoscale 2013, in press.  –OPEN ACCESS

Gao, W.; Hu, C-M.; Fang, R.; Luk, B.; Su, J.; Zhang, L.* ”Surface functionalization of gold nanoparticles with red blood cell membranes“, Advanced Materials 2013, 25, 3549-3553.

Hu, C-M.; Fang, R.; Copp, J.; Luk, B.; Zhang, L.* ”A biomimetic nanosponge that absorbs pore-forming toxins“, Nature Nanotechnology 2013, 8, 336-340.

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Recent UCSD NanoEngineering Publications

Recent articles from the UC San Diego Department of NanoEngineering:

Acharya, C. K., Jiang, F. C., Liao, C. H., Fitzgerald, P., Vecchio, K. S. & Cattolica, R. J. 2013. Tar and CO2 removal from simulated producer gas with activated carbon and charcoal. Fuel Processing Technology, 106, 201-208.

Gao, B., Alvi, Y., Rosen, D., Lav, M. & Tao, A. R. 2013. Designer nanojunctions: orienting shaped nanoparticles within polymer thin-film nanocomposites. Chemical Communications, 49, 4382-4384.

Gao, W., Feng, X. M., Pei, A., Gu, Y. E., Li, J. X. & Wang, J. 2013. Seawater-driven magnesium based Janus micromotors for environmental remediation. Nanoscale, 5, 4696-4700.

Han, J. K., Hannah, M. E., Piquette, A., Talbot, J. B., Mishra, K. C. & McKittrick, J. 2013. Europium-Activated KSrPO4-(Ba,Sr)(2)SiO4 Solid Solutions as Color-Tunable Phosphors for Near-UV Light-Emitting Diode Applications. Journal of the American Ceramic Society, 96, 1526-1532.

Hu, C. M. J., Fang, R. H., Copp, J., Luk, B. T. & Zhang, L. F. 2013. A biomimetic nanosponge that absorbs pore-forming toxins. Nature Nanotechnology, 8, 336-340.

Kong, S. D., Sartor, M., Hu, C. M. J., Zhang, W. Z., Zhang, L. F. & Jin, S. H. 2013. Magnetic field activated lipid-polymer hybrid nanoparticles for stimuli-responsive drug release. Acta Biomaterialia, 9, 5447-5452.

Lux, C. D. & Almutairi, A. 2013. Intramolecular Cyclization for Stimuli-Controlled Depolymerization of Polycaprolactone Particles Leading to Disassembly and Payload Release. ACS Macro Letters, 2, 432-435.

Meluzzi, D. & Arya, G. 2013. Recovering ensembles of chromatin conformations from contact probabilities. Nucleic Acids Research, 41, 63-75.

Meyers, M. A., Mckittrick, J. & Chen, P. Y. 2013. Structural Biological Materials: Critical Mechanics-Materials Connections. Science, 339, 773-779.

Sonnenberg, A., Marciniak, J. Y., Mccanna, J., Krishnan, R., Rassenti, L., Kipps, T. J. & Heller, M. J. 2013. Dielectrophoretic isolation and detection of cfc-DNA nanoparticulate biomarkers and virus from blood. Electrophoresis, 34, 1076-1084.

Verde, M. G., Carroll, K. J., Wang, Z. Y., Sathrum, A. & Meng, Y. S. 2013. Achieving high efficiency and cyclability in inexpensive soluble lead flow batteries. Energy & Environmental Science, 6, 1573-1581.

Xu, P. F., Hung, A. M., Noh, H. & Cha, J. N. 2013. Switchable Nanodumbbell Probes for Analyte Detection. Small, 9, 228-232.

Yoon, I., Baker, S. E., Kim, K., Wang, Y. M., Esener, S. C. & Sirbuly, D. J. 2013. Profiling the evanescent field of nanofiber waveguides using self-assembled polymer coatings. Nanoscale, 5, 552-555.

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Recent UCSD Bioengineering Articles

Some recent articles by faculty in the Department of Bioengineering

Chan, E. F.; Farnsworth, C. L.; Koziol, J. A.; Hosalkar, H. S.; Sah, R. L., Statistical shape modeling of proximal femoral shape deformities in Legg-Calve-Perthes disease and slipped capital femoral epiphysis. Osteoarthritis and Cartilage 2013, 21 (3), 443-449.

Chang, C. W.; Hwang, Y. S.; Brafman, D.; Hagan, T.; Phung, C.; Varghese, S., Engineering cell-material interfaces for long-term expansion of human pluripotent stem cells. Biomaterials 2013, 34 (4), 912-921.

DeLano, F. A.; Hoyt, D. B.; Schmid-Schonbein, G. W., Pancreatic Digestive Enzyme Blockade in the Intestine Increases Survival After Experimental Shock. Science Translational Medicine 2013, 5 (169).

Dutkowski, J.; Kramer, M.; Surma, M. A.; Balakrishnan, R.; Cherry, J. M.; Krogan, N. J.; Ideker, T., A gene ontology inferred from molecular networks. Nature Biotechnology 2013, 31 (1), 38-45.

Hightower, C. M.; Vazquez, B. Y. S.; Cabrales, P.; Tsai, A. G.; Acharya, S. A.; Intaglietta, M., Plasma expander and blood storage effects on capillary perfusion in transfusion after hemorrhage. Transfusion 2013, 53 (1), 49-59.

Hyduke, D. R.; Lewis, N. E.; Palsson, B. O., Analysis of omics data with genome-scale models of metabolism. Molecular Biosystems 2013, 9 (2), 167-174.

Mercola, M.; Colas, A.; Willems, E., Induced Pluripotent Stem Cells in Cardiovascular Drug Discovery. Circulation Research 2013, 112 (3), 534-548.

Metallo, C. M.; Vander Heiden, M. G., Understanding Metabolic Regulation and Its Influence on Cell Physiology. Molecular Cell 2013, 49 (3), 388-398.

Rao, N.; Evans, S.; Stewart, D.; Spencer, K. H.; Sheikh, F.; Hui, E. E.; Christman, K. L., Fibroblasts influence muscle progenitor differentiation and alignment in contact independent and dependent manners in organized co-culture devices. Biomedical Microdevices 2013, 15 (1), 161-169.

Sonnenberg, A.; Marciniak, J. Y.; McCanna, J.; Krishnan, R.; Rassenti, L.; Kipps, T. J.; Heller, M. J., Dielectrophoretic isolation and detection of cfc-DNA nanoparticulate biomarkers and virus from blood. Electrophoresis 2013, 34 (7), 1076-1084.

Vincent, L. G.; Choi, Y. S.; Alonso-Latorre, B.; del Alamo, J. C.; Engler, A. J., Mesenchymal stem cell durotaxis depends on substrate stiffness gradient strength. Biotechnology Journal 2013, 8 (4).

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Recent UCSD Chemistry & Biochemistry Publications

Recent publications from the Department of Chemistry and Biochemistry faculty, retrieved from Web of Science.

Cirera, J.; Paesani, F., Theoretical Prediction of Spin-Crossover Temperatures in Ligand-Driven Light-Induced Spin Change Systems. Inorganic Chemistry 2012, 51 (15), 8194-8201.

Garner, A. L.; Struss, A. K.; Fullagar, J. L.; Agrawal, A.; Moreno, A. Y.; Cohen, S. M.; Janda, K. D., 3-Hydroxy-1-alkyl-2-methylpyridine-4(1H)-thiones: Inhibition of the Pseudomonas aeruginosa Virulence Factor LasB. ACS Medicinal Chemistry Letters 2012, 3 (8), 668-672.

Moree, W. J.; Phelan, V. V.; Wu, C. H.; Bandeira, N.; Cornett, D. S.; Duggan, B. M.; Dorrestein, P. C., Interkingdom metabolic transformations captured by microbial imaging mass spectrometry. Proceedings of the National Academy of Sciences of the United States of America 2012, 109 (34), 13811-13816.

Ortiz-Sanchez, J. M.; Bucher, D.; Pierce, L. C. T.; Markwick, P. R. L.; McCammon, J. A., Exploring the Photophysical Properties of Molecular Systems Using Excited State Accelerated ab Initio Molecular Dynamics. Journal of Chemical Theory and Computation 2012, 8 (8), 2752-2761.

Rios, A. C.; Tor, Y., Refining the Genetic Alphabet: A Late-Period Selection Pressure? Astrobiology 2012, 12 (9), 884-891.

Schlamadinger, D. E.; Wang, Y.; McCammon, J. A.; Kim, J. E., Spectroscopic and Computational Study of Melittin, Cecropin A, and the Hybrid Peptide CM15. Journal of Physical Chemistry B 2012, 116 (35), 10600-10608.

Stout, E. P.; Yu, L. C.; Molinski, T. F., Antifungal Diterpene Alkaloids from the Caribbean Sponge Agelas citrina: Unified Configurational Assignments of Agelasidines and Agelasines. European Journal of Organic Chemistry 2012, (27), 5131-5135.

Taylor, S. S.; Keshwani, M. M.; Steichen, J. M.; Kornev, A. P., Evolution of the eukaryotic protein kinases as dynamic molecular switches. Philosophical Transactions of the Royal Society B-Biological Sciences 2012, 367 (1602), 2517-2528. [OPEN ACCESS]

VanWart, A. T.; Eargle, J.; Luthey-Schulten, Z.; Amaro, R. E., Exploring Residue Component Contributions to Dynamical Network Models of Allostery. Journal of Chemical Theory and Computation 2012, 8 (8), 2949-2961.

Wang, C.; Berg, C. J.; Hsu, C. C.; Merrill, B. A.; Tauber, M. J., Characterization of Carotenoid Aggregates by Steady-State Optical Spectroscopy. Journal of Physical Chemistry B 2012, 116 (35), 10617-10630.

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New UCSD Nanoengineering Articles

Recent articles from the UC San Diego Department of Nanoengineering:

Chen, I. H., Kiang, J. H., Correa, V., Lopez, M. I., Chen, P. Y., McKittrick, J. and Meyers, M. A. (2011) ‘Armadillo armor: Mechanical testing and micro-structural evaluation‘, Journal of the Mechanical Behavior of Biomedical Materials, 4(5), 713-722.

Fomina, N., McFearin, C. L., Sermsakdi, M., Morachis, J. M. and Almutairi, A. (2011) ‘Low Power, Biologically Benign NIR Light Triggers Polymer Disassembly‘, Macromolecules, 44(21), 8590-8597.

Fozdar, D. Y., Soman, P., Lee, J. W., Han, L. H. and Chen, S. C. (2011) ‘Three-Dimensional Polymer Constructs Exhibiting a Tunable Negative Poisson’s Ratio‘, Advanced Functional Materials, 21(14), 2712-2720.

Gao, W., Manesh, K. M., Hua, J., Sattayasamitsathit, S. and Wang, J. (2011a) ‘Hybrid Nanomotor: A Catalytically/Magnetically Powered Adaptive Nanowire Swimmer‘, Small, 7(14), 2047-2051.

Hu, C. M. J., Zhang, L., Aryal, S., Cheung, C., Fang, R. H. and Zhang, L. F. (2011) ‘Erythrocyte membrane-camouflaged polymeric nanoparticles as a biomimetic delivery platform‘, Proceedings of the National Academy of Sciences of the United States of America, 108(27), 10980-10985.

Hsu, S. W., On, K., Gao, B. and Tao, A. R. (2011) ‘Polyelectrolyte-Templated Synthesis of Bimetallic Nanoparticles‘, Langmuir, 27(13), 8494-8499.

Hung, A. M., Konopliv, N. A. and Cha, J. N. (2011) ‘Solvent-Based Assembly of CdSe Nanorods in Solution‘, Langmuir, 27(20), 12322-12328.

Khalifa, H. E. and Vecchio, K. S. (2011) ‘Thermal stability and crystallization phenomena of low cost Ti-based bulk metallic glass‘, Journal of Non-Crystalline Solids, 357(19-20), 3393-3398.

Orozco, J., Campuzano, S., Kagan, D., Zhou, M., Gao, W. and Wang, J. (2011) ‘Dynamic Isolation and Unloading of Target Proteins by Aptamer-Modified Microtransporters‘, Analytical Chemistry, 83(20), 7962-7969.

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Shu Chien Awarded National Medal of Science

President Barack Obama has named UC San Diego Bioengineering professor Shu Chien one of the 7 eminent researchers to receive the National Medal of Science, the highest honor bestowed by the United States government on scientists and engineers. Chien is the only engineer among the 7 medalists.

Shu Chien, a university professor of bioengineering and medicine and director of the UC San Diego Institute of Engineering in Medicine, is a world leader in the study of how blood flow and pressure affect blood vessels. He is one of only 11 renowned scholars who are members of all 3 U.S. national institutes — the National Academy of Sciences, National Academy of Engineering and the Institute of Medicine. MORE

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Recent UCSD Physics Articles

Recent articles from the UCSD Department of Physics faculty. Links go to abstracts; UCSD affiliates must use VPN, proxy or campus protected wifi to access the articles.

CHAPLER, B. C., MYERS, R. C., MACK, S., FRENZEL, A., PURSLEY, B. C., BURCH, K. S., SINGLEY, E. J., DATTELBAUM, A. M., SAMARTH, N., AWSCHALOM, D. D. & BASOV, D. N. 2011. Infrared probe of the insulator-to-metal transition in Ga(1-x)Mn(x)As and Ga(1-x)Be(x)As. Physical Review B, 84.

GOLDFLAM, M. D., DRISCOLL, T., CHAPLER, B., KHATIB, O., JOKERST, N. M., PALIT, S., SMITH, D. R., KIM, B. J., SEO, G., KIM, H. T., DI VENTRA, M. & BASOV, D. N. 2011. Reconfigurable gradient index using VO(2) memory metamaterials. Applied Physics Letters, 99.

JIANG, Z., LEE, D. R., NARAYANAN, S., WANG, J. & SINHA, S. K. 2011. Waveguide-enhanced grazing-incidence small-angle x-ray scattering of buried nanostructures in thin films. Physical Review B, 84.

KRITSUK, A. G., NORDLUND, A., COLLINS, D., PADOAN, P., NORMAN, M. L., ABEL, T., BANERJEE, R., FEDERRATH, C., FLOCK, M., LEE, D., LI, P. S., MULLER, W. C., TEYSSIER, R., USTYUGOV, S. D., VOGEL, C. & XU, H. 2011. Comparing numerical methods for isothermal magnetized supersonic turbulence. Astrophysical Journal, 737.

MENDEZ, A. J., COIL, A. L., LOTZ, J., SALIM, S., MOUSTAKAS, J. & SIMARD, L. 2011. AEGIS: The morphologies of green galaxies at 0.4 < z < 1.2. Astrophysical Journal, 736.

SCHAFGANS, A. A., PURSLEY, B. C., LAFORGE, A. D., SEFAT, A. S., MANDRUS, D. & BASOV, D. N. 2011. Phonon splitting and anomalous enhancement of infrared-active modes in BaFe(2)As(2). Physical Review B, 84.

STEWART, M. K., LIU, J., SMITH, R. K., CHAPLER, B. C., YEE, C. H., MEYERS, D., BAUMBACH, R. E., MAPLE, M. B., HAULE, K., CHAKHALIAN, J. & BASOV, D. N. 2011. Optical probe of strong correlations in LaNiO(3) thin films. Journal of Applied Physics, 110.

TORIGOE, S. E., URWIN, D. L., ISHII, H., SMITH, D. E. & KADONAGA, J. T. 2011. Identification of a Rapidly Formed Nonnucleosomal Histone-DNA Intermediate that Is Converted into Chromatin by ACF. Molecular Cell, 43, 638-648.

TRIPATHI, A., MOHANTY, J., DIETZE, S. H., SHPYRKO, O. G., SHIPTON, E., FULLERTON, E. E., KIM, S. S. & MCNULTY, I. 2011. Dichroic coherent diffractive imaging. Proceedings of the National Academy of Sciences of the United States of America, 108, 13393-13398.

WANG, S. S. & WOLYNES, P. G. 2011b. On the spontaneous collective motion of active matter. Proceedings of the National Academy of Sciences of the United States of America, 108, 15184-15189.

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5 UC San Diego Bioengineers Named Siebel Scholars

Five UC San Diego bioengineering Ph.D. students whose research is aimed at improving human health are among the 2012 recipients of the annual Siebel Scholars awards. Selected for their outstanding academic performance and leadership, each student receives a $35,000 fellowship during the final year of their studies.

The five new Siebel Scholars from the UC San Diego Jacobs School of Engineering are part of the Department of Bioengineering, which ranks 1st in the nation for biomedical engineering, according to the 2010 National Research Council (NRC) rankings.

UC San Diego Siebel Scholars: Class of 2012

  • Jessica DeQuach
  • Che-Ming Jack Hu
  • Dan Kagan
  • Lauren Hruby Jepson
  • Nathan Lewis

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Structural Engineering Articles, UCSD

Recent publications from faculty in the UC San Diego Department of Structural Engineering:

Akkerman, I., Bazilevs, Y., Kees, C. E., and Farthing, M. W. (2011). “Isogeometric analysis of free-surface flow.” Journal of Computational Physics, 230(11), 4137-4152.

Huson, P., Asaro, R. J., Stewart, L., and Hegemier, G. A. (2011). “Non-explosive methods for simulating blast loading of structures with complex geometries.” International Journal of Impact Engineering, 38(7), 546-557.

Lu, W., Kim, T., Han, A., Chen, X., and Qiao, Y. (2011). “Effects of electric field on confined electrolyte in a hexagonal mesoporous silica.” Journal of Chemical Physics, 134(20).

Luco, J. E., Ozcelik, O., Conte, J. P., and Mendoza, L. H. (2011). “Experimental study of the dynamic interaction between the foundation of the NEES/UCSD Shake Table and the surrounding soil: Reaction block response.” Soil Dynamics and Earthquake Engineering, 31(7), 954-973.

Okail, H. O., Shing, P. B., McGinley, W. M., Klingner, R. E., Jo, S., and McLean, D. I. (2011). “Shaking-table tests of a full-scale single-story masonry veneer wood-frame structure.” Earthquake Engineering & Structural Dynamics, 40(5), 509-530.

Raychowdhury, P., and Hutchinson, T. C. (2011). “Performance of seismically loaded shearwalls on nonlinear shallow foundations.” International Journal for Numerical and Analytical Methods in Geomechanics, 35(7), 846-858.

Shoele, K., Prowell, I., Zhu, Q., and Elgamal, A. (2011). “Dynamic and Structural Modeling of a Floating Wind Turbine.” International Journal of Offshore and Polar Engineering, 21(2), 155-160.

Xu, B., Qiao, Y., Li, Y., Zhou, Q., and Chen, X. (2011). “An electroactuation system based on nanofluids.” Applied Physics Letters, 98(22).

Zhu, Q. (2011). “Optimal frequency for flow energy harvesting of a flapping foil.” Journal of Fluid Mechanics, 675, 495-517.

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