The Laboratory for Research on the Structure of Matter (LRSM)

2004 Publications

Primary Support, 2004

• Bermudez, H., Hammer, D.A. and Discher, D.E. “Effect of bilayer thickness on membrane bending rigidity,” Langmuir 20:540-543. (2004).

• Dalhaimer, P., Bermudez, H. and Discher, D. E. “Biopolymer mimickry with polymeric worm micelles: MW-scaled flexibility, locked-in curvature, and coexisting microphases ,” Journal of Polymer Science Part B – Polymer Physics 42: 168-176 (2004).

• Dogic, Z., Zhang, J., Lau, A.W.C., Aranda-Espinoza, H., P. Dalhaimer, Discher, D. E., Janmey, P.A. Kamien, R. D., Lubensky, T. C., Yodh, A. G. “Elongation and fluctuations of semi-flexible polymers in a nematic solvent,” Phys. Rev. Lett . 92, 125503/1-4 (2004).

• Islam, M. F., Alsayed, A. M, Dogic, Z., Zhang, J., Lubensky, T. C. and Yodh, A. G., “Nematic nanotube gels” Phys. Rev. Lett . 92 (8) 088303 (2004) *

• Rubtsov, I. V., Russo, R., Albers, T., Deria, P., Luzzi, D. E. and Therien, M. J., “Visible and near-infra red excited-state dynamics of single-walled carbon nanotubes” Appl. Phys. A. 79, 1747-1751 (2004).
  

*acknowledges use of Shared Experimental Facilities

Partial Support, 2004

• Ahmed, F. and Discher, D. E. “Self-porating polymersomes of PEG-PLA and PEG-PCL – hydrolysis-triggered controlled release vesicles,” Journal of Controlled Release 96, 37-53 (2004).

• Alsayed A.M., Dogic, Z., Yodh, A.G. “Melting of lamellar phases in temperature sensitive colloid-polymer suspensions” Physical Review Letters 93 (5): Art. No. 057801 JUL 30 2004 .

• Angiolillo, P. J. , Uyeda, H. T., Duncan, T. V. and Therien, M. J. “Impact of electronic asymmetry on photoexcited triplet-state spin distributions in conjugated porphyrin oligomers probed via EPR spectroscopy” J. Phys. Chem. B. 108, 11893-11903 (2004).

• Bermudez, H., Hammer, D.A. and Discher, D. E. “Effect of bilayer thickness on membrane bending rigidity” Langmuir 20: 540-543 (2004) .

• Borisevich, A., Davies, P.K., “1:3 Cation Order in aA(Li 1/3 (Nb,Ta) 2/3 O 3 Microwave Perovskites,” Appl. Phys. Lett ., 84, 1347-1349 (2004). *

• Cochran, F.V., Wu, S.P., Wang, W., Nanda, V., Saven, J.G., Therien, M. J., DeGrado, W.F.  “Computational De Novo design and characterization of a four-helix bundle protein that selectively binds a non-biological cofactor”  J. A. C. S . in press (2004).

• Dalhaimer, P., Bermudez, H. and Discher, D.E. “Biopolymer mimickry with polymeric worm micelles: MW-scaled flexibility, locked-in curvature, and coexisting microphases” Journal of Polymer Science B – Polymer Physics 42: 168-176 (2004).

• Dalhaimer, P., Engler, A., Parthasarthy, R. and Discher, D.E., “Targeted worm micelles” Biomacromolecules 5: 1714-1719 (2004).

• Discher, D.E. and Kamien, R., “Towards precision micelles” News and Views in Nature 430: 519-520 (2004).

• Discher, B.M, Noy, D., Lear, J.D., Moser, C.C. and Dutton, P.L. “Amphiphilic design strategy for assembly of membrane proteins and cofactor,” Biophysical Journal 86 (1): 366A-366A Part 2 Suppl. S, Jan 2004.

• Doerksen, R. J., Chen, B., Liu, D., Tew, G. N., DeGrado, W. F. & Klein, M. L. “Controlling the conformation of arylamides: Computational studies of intramolecular hydrogen bonds between amides and ethers or thioethers” Chemistry, A European Journal 10, 5008-5016 (2004).

• Dogic, Z., Zhang, J., Lau, A.W., Aranda-Espinoza, H., Dalhaimer, P., Discher, D. E., Janmey, P. A., Kamien, R. D., Lubensky, T. C., Yodh, A. G., “Elongation and fluctuations of semiflexible polymers in a nematic solvent” Physical Review Letters 92 (12), 125503 (2004).

• Duncan , T.V., Rubtsov, I.V., Uyeda, H.T. and Therien, M.J., “Highly conjugated (Polypyridyl)metal-(Porphinato)zinc(II) compounds: long-lived, high oscillator strength, excited-state absorbers having exceptional spectral coverage of the near-infrared” J. A. C. S. 126, 9474-9475 (2004).

• Engel, D. E. & DeGrado, W. F. “Amino acid propensities are position-dependent throughout the length of alpha-helices” J Mol Biol 337, 1195-205 (2004).

• Engler, A., Bacakova, L., Newman, C., Hategan, A., Griffin , M. and Discher, D.E., “Substrate compliance versus ligand density in cell on gel responses” Biophysical Journal 86: 617-628 (2004).

• Engler, A., Sheehan, M., Sen, S., Bonnemann, C., Sweeney, H.L. and Dische r, D.E. “Myotubes differentiate optimally on substrates with tissue-like stiffness: Pathological implications of stiff or soft microenvironments” Journal of Cell Biology 166 (6): 877-887 (2004). With accompanying Editor's Highlight.

• Engler, A., Richert, L., Wong, J., Picart, C. and Discher, D.E., “Surface probe measurements of the elasticity of sectioned tissue and thin gels: correlations between substrate stiffness and cell adhesion” Surface Science 570: 142-154 (2004).

• Ferris, J.H., Li, D. B., Kalinin, S. V., Bonnell, D. A., “Nanoscale domain patterning of lead zirconate titanate material using electron beams,” Appl. Phys. Lett ., 84, 774-776 (2004).

• Ghirlanda, G., Osyczka, A., Liu, W., Antolovich, M., Smith, K. M., Dutton, P. L., Wand, A. J. & DeGrado, W. F. “De Novo design of a D(2)-Symmetrical protein that reproduces the diheme four-helix bundle in cytochrome bc(1)” J. A. C. S. 126, 8141-8147 (2004).

• Ghoroghchian, P. P., Frail, P., Susumu, K., Blessington, D.; Bates, F. S.; Chance, B. Hammer, D.A., and Therien, M.J.(2004), "NIR-emissive Polymersomes: Soft matter self-assembly meets in vivo optical imaging" Proceedings of the National Academy of Sciences USA (2004).

• Griffin , M., Sen, S., Sweeney, H.L. and Discher, D.E., “Adhesion-contractile balance in myocyte differentiation” Journal of Cell Science 117: 5855-5863 (2004). With accompanying Editor's Highlight.

• Grinberg, I. and Rappe, A.M., “Silver solid solution ferroelectrics” Appl. Phys. Lett . 85, 1760 (2004).

• Grinberg, I. , Cooper, V.R. and Rappe, A.M., “Oxide chemistry and local structure of PbZr x Ti 1– x O 3 studied by density-functional theory supercell calculations” Physical Review B 69, 144118 (1-17) (2004).

• Hiddessen, A., Weitz, D.A., and Hammer, D.A., "Rheology of binary colloidal structures assembled via specific biological cross-linking" Langmuir 20:6788-6795 (2004)

• Hough, L. A., Islam, M. F., Janmey, P. A., Yodh, A. G., “Viscoelasticity of single wall carbon nanotube suspensions” Phys. Rev. Lett 93 (16): 168102 (2004).

• Huang S.S., Koder, R. L., Lewis, M., Wand, A.J., and Dutton, P.L. “The HP-1 Maquette: from an apoprotein structure to a structured hemoprotein designed to promote redox-coupled proton exchange” Proc. Natl. Acad. Sci . USA 101: 5536-5541 (2004).

• Islam, M.F., Alsayed, A.M., Dogic, Z., Zhang, J., Lubensky, T.C., and Yodh, A.G. “Nematic nanotube gels,” Physical Review Letters 92, 088303-1-088303-4 (2004).

• Islam, M.F., Milkie, D.E., Kane, C.L., et al. “Direct measurement of the polarized optical absorption cross section of single-wall carbon nanotubes” Physical Review Letters 93 (3): Art. No. 037404 (2004).

• Janmey, P. A. and Discher, D.E., “Holding it together in the eye” News and Views in Nature 431: 635-636 (2004).

• Janmey, P.A., Lindberg, U. "Cytoskeletal regulation: rich in lipids." Nat Rev Mol Cell Biol 5 (8):658-66 (2004).

• Janmey, P. A., Weitz, D. A., “Dealing with mechanics: mechanisms of force transduction in cells” Trends Biochem Sci . 29 (7): 364-70 (2004).

• Janmey, P.A. and Weitz, D.A. “Dealing with mechanics: mechanisms of force transduction in cells,” Trends in Biochemical Sciences 29, 364-370 (2004)

• Juhas, P., Davies, P.K. and Akbas, M., “Structure and Dielectric Properties of the Pb(Sc 2/3 W 1/3 )O 3 -PbMO 3 Systems (M=Zr, Ti)” Journal of the American Ceramic Society 87 (11), 2086-2092 (2004).

• Juhas, P., Grinberg, I. , Rappe, A.M., Dmowski, W., Egami , T. and Davies, P. K., “Correlations between the structure and dielectric properties of Pb(Sc 2/3 W 1/3 )O 3 –Pb(Ti/Zr)O 3 relaxors” Physical Review B 69, 214101 (1-13) (2004).

• Kaplan, J. & DeGrado, W. F. “De novo design of catalytic proteins” Proc Natl Acad Sci USA 101, 11566-70 (2004).

• Kundagrami, A. and Lubensky, T C. “Structure of TGB C Phases,” Phys. Rev. E 68, 060703 (2004).

• Lau, W. L., Ege, D. S., Lear, J. D., Hammer, D. A. & DeGrado, W. F. “Oligomerization of fusogenic peptides promotes membrane fusion by enhancing membrane destabilization” Biophysical J. 86, 272-84 (2004).

• Lichtenstein B.R, Koder R.L, Dutton P.L. “Model systems of co-factor chemistry,” Biophysical Journal 86 (1): 486A-486A Part 2 Suppl. S, Jan (2004).

• Lin, J. J., Silas, J.A., Bermudez, H., Milan , V.T., Bates, F. S., Hammer, D.A., "The effect of polymer chain length and density on the adhesiveness of functionalized polymersomes," Langmuir 20 (13):5493-5500 (2004).

• Liu, D., Choi, S., Chen, B., Doerksen, R. J., Clements, D. J., Winkler, J. D., Klein, M. L. & DeGrado, W. F. “Nontoxic membrane-active antimicrobial arylamide oligomers” Angew Chem Int Ed Engl 43, 1158-62 (2004).

• Mamchik, A., Dmowski, W., Egami , T. and Chen, I-W., “Magnetic Impurities in Conducting Oxides: II. (Sr 1- x La x )(Ru 1- x Co x )O 3 System,” Phys. Rev. B 70, 104410 (2004).

• Mamchik, A. and Chen, I-W., “Magnetic impurities in conducting Oxides: I. (Sr 1- x La x )(Ru 1- x Fe x )O 3 System,” Phys. Rev. B 70, 104409 (2004).

• Mason, S.E., Grinberg, I. and Rappe, A. M., “First principles extrapolation method for accurate CO adsorption energies on metal surfaces” Phys. Rev. B. Rapid Comm . 69, 161401 (1-4) (2004).

• McGill, S.A., Miller, R. I., Torrens, O.N., Mamchik, A., I-Wei Chen, I.W., Kikkawa, J.W., “Dynamic Kerr effect and spectral weight transfer of the manganites,” Phys. Rev. Lett . 93, 47402-47405 (2004).

• Nielsen, S.O., Lopez, C. F., Srinivas and Klein, M. L., “Coarse grain models and the computer simulation of soft materials” J. Phys. Condensed Matter 16, R481-R512 (2004).

• Osyczka, A., Moser, C. C., Daldal, F and Dutton, P. L., "Reversible redox energy coupling in electron transfer chains" Nature 427, 607-612 (2004).

• Park, S., Yang, X. and Saven, J.G., “Advances in computational protein design” Current Opinion in Structural Biology 14: 487-494 (2004).

• Pata, V., Ahmed, F., Discher, D.E. and Dan, N., “Membrane solubilization by detergent: Resistance conferred by thickness” Langmuir 20: 3888 - 3893 (2004).

• Peterson, R.W., Dutton, P. L. and Wand, A.J., “Improved side-chain prediction accuracy using an ab initio potential energy function and a very large rotamer library” Protein Science 13, 735-751 (2004).

• Richert, L., Engler, A., Discher, D.E. and Picart, C., “Elasticity of native and crosslinked polyelectrolyte multilayer films” Biomacromolecules 5: 1908-1916 (2004).

• Rubtsov, I. V., Redmore, N. P., Hochstrasser, R. M., and Therien, M. J., “Interrogating conformationally dependent electron transfer dynamics via ultrafast visible pump / IR probe spectroscopy” J. A. C. S. 126, 2684-2685 (2004).

• Rubtsov, I. V., Kang, Y. K., Redmore, N. P., Allen, R. M., Zheng, J., Beratan, D. N. and Therien, M. J., “The degree of charge transfer in ground and charge-separated states revealed by ultrafast visible pump / mid IR probe spectroscopy” J. A. C. S. 126, 5022-5023 (2004).

• Sapienza R, Mujumdar S, Cheung C, Yodh, A.G., Wiersma, D. “Anisotropic weak localization of light” Physical Review Letters 92 (3): Art. No. 033903 (2004).

• Slovic, A., Kono, H., Lear, J., Saven, J. G. and DeGrado, W. F. “Computational design and characterization of water-soluble analogues of the potassium channel KcsA,” Proceedings of the National Academy of Sciences 101, 1828-1833 (2004).

• Srinivas, G. and Klein, M. L., “Coarse-grain molecular dynamics simulations of diblock copolymer surfactants interacting with a lipid bilayer” Molecular Physics 102, 883-890 (2004).

• Srinivas, G. and Klein, M. L., “Computational approaches to nanobiotechnology: probing the interaction of synthetic molecules with phospholipid bilayers via a coarse grain model” Nanotechnology 15, 1289-1295 (2004).

• Srinivas, G., Discher, D.E. and Klein, M.L., “Self assembly and properties of diblock copolymers via coarse grain molecular dynamics” Nature Materials 3: 638-644 (2004). With accompanying News and Views by R. Lipowsky.

• Srinivas, G., Shelley, J. C., Nielsen, S. O., Discher, D. E. and Klein, M. L., “Simulation of diblock copolymer self-assembly using a coarse-grain model” J. Phys. Chem. B 108, 8153-8160 (2004).

• Staii, C., Pinto, N.J., Johnson, A.T. , “ Scanning Conductance Microscopy of Carbon Nanotubes and Polyethylene Oxide Nanofibers ” page 129-132, Proceedings of the XVIII International Winterschool on Electronic Properties of Novel Materials, Kirchberg, Austria, 2004, AIP Conference Proceedings 723 (Melville, New York, 2004).

• Staii, C., Pinto, N.J. and Johnson, A.T., “Quantitative analysis of scanning conductance microscopy” Nano Letters 4, 859-862 (2004).

• Stenull, O. and Lubensky, T.C. “Anomalous elasticity of nematic and critically soft elastomers,” Phys. Rev. E 69, 021807/1-11 (2004).

• Strzalka, J., Kneller, L.R., Gibney, B. R., Satija, S., Majkrzak, C. F. and Blasie, J. K., “Specular neutron reflectivity and structure of artificial protein maquettes vectorially oriented at interfaces” Phys. Rev. E . 70: 061905 (2004). *

• Strzalka, J. DiMasi, E., Kuzmenko, I. , Gog, T. and Blasie, J.K. “Resonant x-ray reflectivity from a bromine-labeled fatty-acid Langmuir monolayer” Phys. Rev. E 70: 051603-1-5 (2004). *

• Suchomel, M.R. and Davies, P.K., “Predicting the Position of the Morphotropic boundary in New High Temperature PbTiO 3 -Bi(B'B”)O 3 Based dielectric Ceramics” Journal of Applied Physics 96 (8), 4405-4410 (2004)

• Tsai, J.C. and Gollub, J. P., “Slowly sheared dense granular flows: crystallization and non unique final states” Phys. Rev. E 70, 031303 (2004).

• Tucker, M. J., Getahun, Z., Nanda, V., DeGrado, W. F. & Gai, F. “A new method for determining the local environment and orientation of individual side chains of membrane-binding peptides” J. A. C. S. 126, 5078-9 (2004.

• Walter, E.J. and Rappe, A. M., “Coadsorption of methyl radicals and oxygen on Rh(111)” Surface Science 549, 265-72 (2004).

• Wang, T., Zhu, Y., Getahun, Z., Du, D., Huang, C., DeGrado, W. & Gai, F. “Length dependent helix-coil transition kinetics of nine alanine-based peptides” J. Phys. Chem. B 108, 15301-10 (2004).

• Wang, T., Zhu, Y. J. and Gai, F., “Folding of a three-helix bundle at the folding speed limit” J. Phys. Chem B 108, 3694-3697 (2004).

• Yang, M. and Dai, H.-L. “Determination of molecular ordering at a buried interface and the effect of interfacial ordering on thin film crystallization by second harmonic generation,” Langmuir 20, 37-40 (2004).

• Yourdshahyan, Y., Cooper, V. R., Kolpak, A. M. and Rappe, A. M., “Catalytic behavior at the nanoscale: CO adsorption on Al 2 O 3 -supported Pt clusters” Proc. SPIE 5223, 223-32 (2004).

• Zhou, W, Islam, M.F., Wang, H., Yodh, A.G., Ho, D. L., Winey, K.I., Fische r, J.E., “Small angle neutron scattering from single-wall carbon nanotube suspensions: evidence for isolated rigid rods and rod networks” Chemical Physics Letters 384 (1-3): 185-189 (2004).

• Zhou, W., Winey, K.I., Fischer, J.E., Sreekumar, T.V., Kumar, S., Kataura, H. “Out-of-plane mosaic of single-wall carbon nanotube films,” Appl Phys Lett 84 (12): 2172-2174 MAR 22 (2004).

• Zhu, Y. J., Fu, X. R., Wang, T., Tamura, A., Takada, S., Saven, J. G. and Gai, F., “Guiding the search for a protein's maximum rate of folding” Chem. Phys . 307, 99-109 (2004).

*acknowledges use of Shared Experimental Facilities

Shared Experimental Facilities, 2004

• Borisevich A Y. and Davies, P. K. “1:2 Cation order in A(Li 1/3 (Nb,Ta) 2/3 )O 3 Microwave Perovskites”, Applied Physics Letters 84 (8), 1347-1349 (2004).

• Fisher, J.A.N., Civillico, E.F., Contreras, D., and Yodh, A.G. “ In vivo fluorescence microscopy of neuronal activity in three dimensions by use of voltage-sensitive dyes” Optics Letters 29, 71-73 (2004).

• Sapienza, R., Mujumdar, S., Cheung, C., Yodh, A.G., and Wiersma, D, “Anisotropic weak localization of light,” Physical Review Letters 92, 033903-1-033903-4 (2004).

• Tarvin, R. and Davies, P. K. “A- and B-Site Order in (Na 1/2 La 1/2 )(Mg 1/3 Nb 2/3 )O 3 Perovskites,” Journal of the American Ceramic Society 790, 87(5) (2004).