PUBLICATIONS

Thrust One - 2009


Detcheverry, F. A.; Pike, D. Q.; Nagpal, U.; Nealey, P. F.; de Pablo, J. J., "Theoretically informed coarse grain simulations of block copolymer melts: method and applications", Soft Matter 5 (24), 4858-4865 (2009). Link

Detcheverry, F. A.; Pike, D. Q.; Nealey, P. F.; Muller, M.; de Pablo, J. J., "Monte Carlo Simulation of Coarse Grain Polymeric Systems", Physical Review Letters 102, 197801 (2009). Link

Han, E.; Stuen, K. O.; Leolukman, M.; Liu, C.-C.; Nealey, P. F.; Gopalan, P., "Perpendicular orientation of domains in cylinder-forming block copolymer thick films by controlled interfacial interactions", Macromolecules 42 (13), 4896-4901 (2009). Link

Hirai, T.; Leolukman, M.; Jin, S.; Goseki, R.; Ishida, Y.; Kakimoto, M. A.; Hayakawa, T.; Ree, M.; Gopalan, P., "Hierarchical Self-Assembled Structures from POSS-Containing Block Copolymers Synthesized by Living Anionic Polymerization", Macromolecules 42 (22), 8835-8843 (2009). Link

Hirai, T.; Leolukman, M.; Liu, C.-C.; Han, E.; Kim, Y. J.; Ishida, Y.; Hayakawa, T.; Kakimoto, M.; Nealey, P. F.; Gopalan, P., "One-step direct patterning template utilizing self-assembly of POSS containing block copolymers", Advanced Materials 21(43), 4334-4338 (2009). Link

Kang, H. M.; Kim, Y. J.; Gopalan, P.; Nealey, P. F., "Control of the critical dimensions and line edge roughness with pre-organized block copolymer pixelated photoresists", Journal of Vacuum Science & Technology B 27 (6), 2993-2997 (2009). Link

Kim, Y. J.; Kang, H. M.; Leolukman, M.; Nealey, P. F.; Gopalan, P., "Synthesis of Photoacid Generator-Containing Patternable Diblock Copolymers by Reversible Addition-Fragmentation Transfer Polymerization", Chemistry of Materials 21 (14), 3030-3032 (2009). Link

Liu, G. L.; Ji, S. X.; Stuen, K. O.; Craig, G. S. W.; Nealey, P. F.; Himpsel, F. J., "Modification of a polystyrene brush layer by insertion of poly(methyl methacrylate) molecules", Journal of Vacuum Science & Technology B 27 (6), 3038-3042 (2009). Link

Liu, G. L.; Stoykovich, M. P.; Ji, S. X.; Stuen, K. O.; Craig, G. S. W.; Nealey, P. F., "Phase Behavior and Dimensional Scaling of Symmetric Block Copolymer-Homopolymer Ternary Blends in Thin Films", Macromolecules 42 (8), 3063-3072 (2009). Link

Morin, S. A.; La, Y. H.; Liu, C.-C.; Streifer, J. A.; Hamers, R. J.; Nealey, P. F.; Jin, S., "Assembly of nanocrystal arrays via block copolymer directed nucleation", Angewandte Chemie International Edition 48 (12), 2135-2139 (2009). Link

Pike, D. Q.; Detcheverry, F. A.; Muller, M.; de Pablo, J. J., "Theoretically informed coarse grain simulations of polymeric systems", Journal of Chemical Physics 131 (8), (2009). Link

Son, J. G.; Bae, W. K.; Kang, H. M.; Nealey, P. F.; Char, K., "Placement Control of Nanomaterial Arrays on the Surface-Reconstructed Block Copolymer Thin Films", Acs Nano 3 (12), 3927-3934 (2009). Link

Stuen, K. O.; Thomas, C. F.; Liu, G.; Ferrier, N. J.; Nealey, P. F., "Dimensional scaling of cylinders in thin films of block copolymer-homo-polymer ternary blends", Macromolecules 42 (14), 5139-5145 (2009). Link

Thrust Two - 2009


Guiliano, M. A.; Horne, W. S.; Gellman, S. H., "An α/β-peptide helix bundle with pure β3-amino acid core and a distinctive quaternary structure", Journal of the American Chemical Society 131 (29), 9860-9861 (2009). Link

Karlsson, A.; Pomerantz, W. C.; Weisblum, B.; Gellman, S. H.; Palecek, S. P., "Effect of sequence and structural properties on 14-helical β-peptide activity against Candida albicans planktonic cells and biofilms", ACS Chemical Biology 4 (7), 567-579 (2009). Link

Lee, M. R.; Stahl, S. S.; Gellman, S. H.; Masters, K. S., "Nylon-3 Copolymers that Generate Cell-Adhesive Surfaces Identified by Library Screening", Journal of the American Chemical Society 131 (46), 16779-16789 (2009). Link

Liu, X. Y.; Abbott, N. L., "Electrochemical generation of gradients in surfactant concentration across microfluidic channels", Analytical Chemistry 81 (2), 772-781 (2009). Link

Miller, C. A.; Abbott, N. L.; de Pablo, J. J., "Surface activity of amphiphilic helical beta-peptides from molecular dynamics simulation", Langmuir 25 (5), 2811-2823 (2009). Link

Miller, C. A.; Gellman, S. H.; Abbott, N. L.; de Pablo, J. J., "Association of helical beta-peptides and their aggregation behavior from the potential of mean force in explicit solvent", Biophysical Journal 96 (11), 4349-4362 (2009). Link

Mondal, J.; Sung, B. J.; Yethiraj, A., "Sequence-Directed Organization of beta-Peptides in Self-Assembled Monolayers", Journal of Physical Chemistry B 113 (28), 9379-9385 (2009). Link

Mowery, B. P.; Lindner, A. M.; Weisblum, B.; Stahl, S. S.; Gellman, S. H., "Structure-activity relationships among random nylon-3 copolymers that mimic antibacterial host-defense peptides", Journal of the American Chemical Society 131 (28), 9735-9745 (2009). Link

Muller, M. M.; Windsor, M. A.; Pomerantz, W. C.; Gellman, S. H.; Hilvert, D., "A rationally designed aldolase foldamer", Angewandte Chemie International Edition 48 (5), 922-925 (2009). Link

Pomerantz, W. C.; Hadley, E. B.; Fry, C. G.; Gellman, S. H., "In situ monitoring of backbone thioester exchange by 19F NMR", ChemBioChem 10 (13), 2177-2181 (2009). Link

Sung, B.-J.; Mondal, J.; Yethiraj, A., "Coarse-grained model for the self-assembly of β-peptides: A Monte Carlo simulation study", (submitted), (2009).

Zhang, J.; Kissounko, D.; Lee, S. E.; Zhang, S. H.; Gellman, S. H.; Stahl, S. S., "Access to poly-β-peptides with functionalized side chains and end groups via controlled ring-opening polymerization of β-lactams", Journal of the American Chemical Society 131 (4), 1589-1597 (2009). Link

Thrust Three - 2009


Church, D. M.; Goodstadt, L.; Hillier, L. W.; Zody, M. C.; Goldstein, S.; She, X. W.; Bult, C. J.; Agarwala, R.; Cherry, J. L.; DiCuccio, M.; Hlavina, W.; Kapustin, Y.; Meric, P.; Maglott, D., et al., "Lineage-specific biology revealed by a finished genome assembly of the mouse", Plos Biology 7 (5), (2009). Link

Coleman, J. J.; Rounsley, S. D.; Rodriguez-Carres, M.; Kuo, A.; Wasmann, C. C.; Grimwood, J.; Schmutz, J.; Taga, M.; White, G. J.; Zhou, S. G.; Schwartz, D. C.; Freitag, M.; Ma, L. J.; Danchin, E. G. J., et al., "The genome of Nectria haematococca: Contribution of supernumerary chromosomes to gene expansion", Plos Genetics 5 (8), (2009). Link

Detcheverry, F. A.; Pike, D. Q.; Nagpal, U.; Nealey, P. F.; de Pablo, J. J., "Theoretically informed coarse grain simulations of block copolymer melts: method and applications", Soft Matter 5 (24), 4858-4865 (2009). Link

Detcheverry, F. A.; Pike, D. Q.; Nealey, P. F.; Muller, M.; de Pablo, J. J., "Monte Carlo Simulation of Coarse Grain Polymeric Systems", Physical Review Letters 102, 197801 (2009). Link

Haas, B. J.; Kamoun, S.; Zody, M. C.; Jiang, R. H. Y.; Handsaker, R. E.; Cano, L. M.; Grabherr, M.; Kodira, C. D.; Raffaele, S.; Torto-Alalibo, T.; Bozkurt, T. O.; Ah-Fong, A. M. V.; Alvarado, L.; Anderson, V. L., et al., "Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans", Nature 461 (7262), 393-398 (2009). Link

Hernandez-Ortiz, J. P.; Chopra, M.; Grier, S.; de Pablo, J. J., "Hydrodynamic effects on the translocation rate of a polymer through a pore", Journal of Chemical Physics 131, 044904 (2009). Link

Hernandez-Ortiz, J. P.; Underhill, P. T.; Graham, M. D., "Dynamics of confined suspensions of swimming particles", Journal of Physics-Condensed Matter 21 (20), (2009). Link

Jo, K.; Chen, Y. L.; de Pablo, J. J.; Schwartz, D. C., "Elongation and migration of single DNA molecules in microchannels using oscillatory shear flows", Lab on a Chip 9, 2348 - 2355 (2009). Link

Koenig, G. M.; de Pablo, J. J.; Abbott, N. L., "Characterization of the reversible interaction of pairs of nanoparticles dispersed in nematic liquid crystals", Langmuir 25 (23), 13318–13321 (2009). Link

Koenig, G. M.; Ong, R.; Cortes, A. D.; Moreno-Razo, J. A.; de Pablo, J. J.; Abbott, N. L., "Single nanoparticle tracking reveals influence of chemical functionality of nanoparticles on local ordering of liquid crystals and nanoparticle diffusion coefficients", Nano Letters 9 (7), 2794-2801 (2009). Link

Pike, D. Q.; Detcheverry, F. A.; Muller, M.; de Pablo, J. J., "Theoretically informed coarse grain simulations of polymeric systems", Journal of Chemical Physics 131 (8), (2009). Link

Sambriski, E. J.; Ortiz, V.; de Pablo, J. J., "Sequence effects in the melting and renaturation of short DNA oligonucleotides: Structure and mechanism pathways", Journal of Physics: Condensed Matter 21, 034105 (2009). Link

Sambriski, E. J.; Schwartz, D. C.; de Pablo, J. J., "Uncovering pathways in DNA oligonucleotide hybridization via transition state analysis", Proceedings of the National Academy of Sciences of the United States of America 106 (43), 18125-18130 (2009). Link

Sambriski, E. J.; Schwartz, D. C.; de Pablo, J. J., "A mesoscale model for DNA and its renaturation", Biophysical Journal 96 (5), 1675-1690 (2009). Link

Schnable, P. S.; Ware, D.; Fulton, R. S.; Stein, J. C.; Wei, F. S.; Pasternak, S.; Liang, C. Z.; Zhang, J. W.; Fulton, L.; Graves, T. A.; Minx, P.; Reily, A. D.; Courtney, L.; Kruchowski, S. S., et al., "The B73 maize genome: Complexity, diversity, and dynamics", Science 326 (5956), 1112-1115 (2009). Link

Staii, C.; Viesselmann, c.; Ballweg, J.; Shi, L.; Liu, G.-Y.; Williams, J. C.; Dent, E. W.; Coppersmith, S. N.; Eriksson, M. A., "Positioning and guidance of neurons on gold surfaces by directed assembly of proteins using atomic force microscopy", Biomaterials 30 (20), 3397-3404 (2009). Link

Tanaka, M.; Rastogi, A.; Toepperwein, G. N.; Riggleman, R. A.; Felix, N. M.; de Pablo, J. J.; Ober, C. K., "Fluorinated Quaternary Ammonium Salts as Dissolution Aids for Polar Polymers in Environmentally Benign Supercritical Carbon Dioxide", Chemistry of Materials 21 (14), 3125-3135 (2009). Link

Yu, H.; Kounovsky, K. L.; de Pablo, J. J.; Schwartz, D. C., "Molecular propulsion: chemical sensing and chemotaxis of DNA driven by RNA polymerase", Journal of the American Chemical Society 131 (16), 5722-5723 (2009). Link

Zhang, Y.; de Pablo, J. J.; Graham, M. D., "Multiple free energy minima in systems of confined tethered polymers-toward soft nanomechanical bistable elements", Soft Matter 5 (19), 3694-3700 (2009). Link

Zhang, Y.; Donev, A.; Weisgraber, T.; Alder, B. J.; Graham, M. D.; de Pablo, J. J., "Tethered DNA dynamics in shear flow", Journal of Chemical Physics 130 (23), (2009). Link

Zhou, S.; Wei, F.; Nguyen, J.; Bechner, M.; Potamousis, K.; Goldstein, S.; Pape, L.; Mehan, M.; Churas, C.; Paternak, S.; Forrest, D. K.; Wise, R.; Ware, D.; Wing, R., et al., "A single molecule scaffold for the maize genome", PloS Genetics 5 (11), e1000711 (2009). Link

Thrust Four - 2009


Bar-Ilan, O.; Albrecht, R. M.; Fako, V. E.; Furgeson, D. Y., "Toxicity assessments of multi-sized gold and silver nanoparticles in zebrafish embryos", Small 5 (16), 1897 - 1910 (2009). Link

King Heiden, T. C.; Wiecinski, P. N.; Mangham, A. N.; Metz, K. M.; Nesbit, D.; Pedersen, J. A.; Hamers, R. J.; Heideman, W.; Peterson, R. E., "Quantum dot nanotoxicity assessment using the zebrafish embryo", Environmental Science and Technology 43 (5), 1605-1611 (2009). Link

Metz, K. M.; Mangham, A. N.; Bierman, M. J.; Jin, S.; Hamers, R. J.; Pedersen, J. A., "Engineered nanomaterial transformation under oxidative environmental conditions: Development of an in vitro biomimetic assay", Environmental Science and Technology 43 (5), 1598-1604 (2009). Link

Wiecinski, P. N.; Heiden, T. C. K.; Metz, K. M.; Mangham, A. N.; Hamers, R. J.; Heideman, W.; Peterson, R. E.; Pedersen, J. A., "Developmental toxicity of oxidatively degraded quantum dots", Geochimica Et Cosmochimica Acta 73 (13), A1437-A1437 (2009).

Wiecinski, P. N.; Metz, K. M.; Mangham, A. N.; Jacobson, K. H.; Hamers, R. J.; Pedersen, J. A., "Gastrointestinal biodurability of engineered nanoparticles: Development of an in vitro assay", Nanotoxicology 3 (3), 202-214 (2009). Link

Societal Implications - 2009


Barben, D., "Analyzing acceptance politics: Towards an epistemological shift in the public understanding of science and technology", Public Understanding of Science (available online), (2009). Link

Powell, M.; Colin, M., "Participatory paradoxes: Facilitating citizen engagement in science and technology from the top-down?", Bulletin of Science, Technology & Society 29 (4), 325-342 (2009). Link

Rudd, J., "Regulating the Impacts of Engineered Nanoparticles under TSCA: Shifting Authority from Industry to Government", Columbia Journal for Environmental Law 33 (2), 215-282 (2009).

Seeds - 2009

Brossard, D.; Anderson, A. A.; Scheufele, D. A., "Tracking public interest in emerging technologies: Mapping the landscape", American Association for Public Opinion Research (AAPOR) 2009 Convention, Hollywood, FL, May 14-17.

Scheufele, D. A.; Brossard, D.; Dunwoody, S.; Corley, E. A.; Guston, D.; Peters, H. P., "Are scientists really out of touch?", The Scientist (published online), www.the-scientist.com/new/display/55875 (2009).

Education - 2009


Greenberg, A., "Integrating nanoscience into the classroom: Perspectives on nanoscience education projects", ACS Nano 3 (4), 762-769 (2009). Link

Tomasik, J. H.; Jin, S.; Hamers, R. J.; Moore, J. W., "Design and initial evaluation of an online nanoscience course for teachers", Journal of Nano Education 1, 48-67 (2009). Link

Facilities - 2009


Buzzi, F. L.; Ting, Y.-H.; Wendt, A. E., "Energy distributions of bombarding ions in plasma etching of dielectrics", Plasma Sources Science and Technology 18, 025009 (2009). Link

Chen, P.; Chen, W. V.; Yu, P. K. L.; Tang, C. W.; Lau, K. M.; Mawst, L. J.; Paulson, C.; Kuech, T. F.; Lau, S. S., "Effects of hydrogen implantation damage on the performance of InP/InGaAs/InP p-i-n photodiodes transferred on silicon", Applied Physics Letters 94, 012101 (2009). Link

Ding, R.; Klein, L. J.; Friesen, M. G.; Eriksson, M. A.; Wendt, A. E., "Sidewall damage in plasma etching of Si/SiGe heterostructures", Journal of Vacuum Science & Technology A 27 (4), 836-843 (2009). Link

Gomopoulos, N.; Cheng, W.; Efremov, M.; Nealey, P. F.; Fytas, G., "Out-of-Plane Longitudinal Elastic Modulus of Supported Polymer Thin Films", Macromolecules 42 (18), 7164-7167 (2009). Link

Horne, W. S.; Johnson, L. M.; Ketas, T. J.; Klasse, P. J.; Lu, M.; Moore, J. P.; Gellman, S. H., "Structural and biological mimicry of protein surface recognition by alpha/beta-peptide foldamers", Proceedings of the National Academy of Sciences of the United States of America 106 (35), 14751-14756 (2009). Link

Huang, J. Y. T.; Mawst, L. J.; Kuech, T. F.; Song, X.; Babcock, S. E.; Kim, C. S.; Vurgaftman, I.; Meyer, J. R.; Holmes, J., A. L., "Design and characterization of strained InGaAs/GaAsSb type-II 'W' quantum wells on InP substrates for mid-IR emission", Journal of Physics D: Applied Physics 42, 025108 (2009). Link

Jongpaiboonkit, L.; Franklin-Ford, T.; Murphy, W. L., "Mineral-coated polymer microspheres for controlled protein binding and release", Advanced Materials 21 (19), 1960-1963 (2009). Link

Kaufman, L.; Pereprezko, J. H.; Hildal, K.; Farmer, J.; Day, D.; Yang, N.; Branagan, D., "Transformation, stability and Pourbaix diagrams of high performance corrosion resistant (HPCRM) alloys", CALPHAD 33 (1), 89-99 (2009). Link

Koepsel, J. T.; Murphy, W. L., "Patterning Discrete Stem Cell Culture Environments via Localized Self-Assembled Monolayer Replacement", Langmuir 25 (21), 12825-12834 (2009). Link

Leolukman, M.; Paoprasert, P.; Mandel, I.; Diaz, S. J.; McGee, D. J.; Gopalan, P., "Linear-Dendritic Block Copolymer Hosts for the Encapsulation of Electro-Optic Chromophores via H-Bonding", Journal of Polymer Science Part a-Polymer Chemistry 47 (19), 5017-5026 (2009). Link

Marconnet, A. M.; He, M.; Sengele, S.; Ferrier, N. J.; van der Weide, D. W.; Madhaven, V.; Nelson, N.; Booske, J. H., "Microfabricated silicon high frequency waveguide couplers and antennas", IEEE Transactions on Electron Devices 56 (4), (2009). Link

Pallecchi, I.; Ferrando, V.; Tarantini, C.; Putti, M.; Ferdeghini, C.; Zhu, Y.; Voyles, P. M.; Xi, X. X., "Increased in-field critical current density in neutron irradiated MgB2 films", Superconductor Science and Technology 22, 015023 (2009). Link

Park, B.; Paoprasert, P.; Gopalan, P.; Kuech, T. F.; Evans, P. G., "Dynamics of photoinduced charge transfer between pentacene and a C60-terminated self assembled monolayer", Applied Physics Letters 94, 073302 (2009). Link

Park, J. H.; Liu, C.-C.; Rathi, M. K.; Mawst, L. J.; Nealey, P. F.; Kuech, T. F., "Nano-scale selective growth and optical characteristics of quantum dots on III-V substrates prepared by diblock copolymer nano-patterning", Journal of Nanophotonics 3, 031604 (2009). Link

Saurer, E. M.; Jewell, C. M.; Kuchenreuther, J. M.; Lynn, D. M., "Assembly of erodible, DNA-containing thin films on the surfaces of polymer microparticles: Toward a layer-by-layer approach to the delivery of DNA to antigen-presenting cells", Acta Biomaterialia 5 (3), 913-924 (2009). Link

Sengele, S.; Jiang, H.; Booske, J. H.; Kory, C. L.; van der Weide, D. W.; Ives, R. L., "Microfabrication and characterization of a selectively metalized w-band, meander-line TWT circuit", IEEE Transactions on Electron Devices 56 (4), (2009). Link

Simmons, C. B.; Thalakulam, M.; Rosemeyer, B. M.; Van Bael, B. J.; Sackmann, E. K.; Savage, D. E.; Lagally, M. G.; Joynt, R.; Friesen, M.; Coppersmith, S. N.; Eriksson, M. A., "Charge Sensing and Controllable Tunnel Coupling in a Si/SiGe Double Quantum Dot", Nano Letters 9 (9), 3234-3238 (2009). Link

Smith, C. I.; Bowfield, A.; Cuquerella, M. C.; Mansley, C. P.; Farrell, T.; Harrison, P.; Martin, D. S.; Fernig, D. G.; Edwards, C.; Butler, J. E.; Hamers, R. J.; Sun, B.; Wang, X.; Weightman, P., "Detection of DNA hybridisation on a functionalised diamond surfaces", Europhyics Letters 85, 18006 (2009). Link

Truitt, J. L.; Slinker, K. A.; Lewis, K. L. M.; Savage, D. E.; Tahan, C.; Klein, L. J.; Chu, J. O.; Mooney, P. M.; Tyryshkin, A. M.; van der Weide, D. W.; Joynt, R.; Coppersmith, S. N.; Friesen, M.; Eriksson, M. A., "Si/SiGe Quantum Devices, Quantum Wells, and Electron-Spin Coherence", Topics in Applied Physics, vol. 115: Electron Spin Resonance and Related Phenomena in Low-Dimensional Structures, Fanciulli, M.: Springer-Verlag, Berlin, 101-127 (2009). Link

Xiong, W.; Laaser, J. E.; Paoprasert, P.; Franking, R. A.; Hamers, R. J.; Gopalan, P.; Zanni, M. T., "Transient 2D IR Spectroscopy of Charge Injection in Dye-Sensitized Nanocrystalline Thin Films", Journal of the American Chemical Society 131 (50), 18040-+ (2009). Link