Publications

CSC research acknowledged in publications and presentations.

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Use was made of computational facilities purchased with funds from the National Science Foundation (CNS-1725797) and administered by the Center for Scientific Computing (CSC). The CSC is supported by the California NanoSystems Institute and the Materials Research Science and Engineering Center (MRSEC; NSF DMR 2308708) at UC Santa Barbara.

Selected Publications

2006

Effects of surface tethering on protein folding mechanisms
Friedel, M., Baumketner, A., & Shea, J. -E. (2006). Effects of surface tethering on protein folding mechanisms. Proc. Nat. Acad. Sci. Usa, 103, 8396-8401.
Electronic structure of nitride surfaces
Segev, D., & Van de Walle, C. G. (2006). Electronic structure of nitride surfaces. Journal Of Crystal Growth, First International Symposium On Growth Of Nitrides - Isgn-1, 300, 199-203.
Folding landscapes of the Alzheimer A\beta12-28 peptide from all-atom replica exchange molecular dynamics simulations in explicit solvent
Baumketner, A., & Shea, J. -E. (2006). Folding landscapes of the Alzheimer A\beta12-28 peptide from all-atom replica exchange molecular dynamics simulations in explicit solvent. J. Mol. Biol., 362, 567-579.
Kinematic Inversion of the 2004 Mw 6.0 Parkfield Earthquake
Liu, P., Custodio, S., & Archuleta, R. J. (2006). Kinematic Inversion of the 2004 Mw 6.0 Parkfield Earthquake. Bulletin Of The Seismological Society Of America, 96, Jan-37.
New insights into the role of native point defects in ZnO
Janotti, A., & Van de Walle, C. G. (2006). New insights into the role of native point defects in ZnO. Journal Of Crystal Growth, 287, 58-65.
Orbital magnetic field effects in spin liquid with spinon Fermi sea: Possible application to kappa-(ET)2 Cu2 (CN)3
Motrunich, O. I. (2006). Orbital magnetic field effects in spin liquid with spinon Fermi sea: Possible application to kappa-(ET)2 Cu2 (CN)3. Phys. Rev. B, 73, 155115.
Origins of Fermi-level pinning on GaN and InN polar and nonpolar surfaces
Segev, D., & Van de Walle, C. G. (2006). Origins of Fermi-level pinning on GaN and InN polar and nonpolar surfaces. Europhys. Lett., 76, 305.
Prediction of Broadband Ground-Motion Time Histories: Hybrid Low/High- Frequency Method with Correlated Random Source Parameters
Liu, P., Archuleta, R. J., & Hartzell, S. H. (2006). Prediction of Broadband Ground-Motion Time Histories: Hybrid Low/High- Frequency Method with Correlated Random Source Parameters. Bulletin Of The Seismological Society Of America, 96, 2118-2130.
Structure of the 21-30 fragment of amyloid Beta protein
Baumketner, A., Bernstein, S. L., Wyttenbach, T., Lazo, N. D., Teplow, D. B., Bowers, M. T., & Shea, J. -E. (2006). Structure of the 21-30 fragment of amyloid Beta protein. Protein Science, 15, 1239.
The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations
Baumketner, A., & Shea, J. -E. (2006). The thermodynamics of folding of a beta hairpin peptide probed through replica exchange molecular dynamics simulations. Theor. Chem. Acc., 116, 262.

2005

2004 Mw 6.0 Parkfield, California, earthquake: Inversion of Near-Source Ground Motion Using Different Datasets
Custodio, S., Liu, P., & Archuleta, R. J. (2005). 2004 Mw 6.0 Parkfield, California, earthquake: Inversion of Near-Source Ground Motion Using Different Datasets. Geophysical Research Letters, 32, L23312.
Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice beta-barrel protein
Griffin, M., Friedel, M., & Shea, J. E. (2005). Effects of frustration, confinement, and surface interactions on the dimerization of an off-lattice beta-barrel protein. J. Chem. Phys., 123, 174707.
The Equation of State for QCD with 2+1 Flavors of Quarks, The MILC Collaboration
Bernard, C., Burch, T., DeTar, C., Gottlieb, S., Heller, U. M., Hetrick, J., et al. (2005). The Equation of State for QCD with 2+1 Flavors of Quarks, The MILC Collaboration. Proceedings Of Science, (Lattice 2005), 156.
Free Energy Landscapes for Amyloidogenic Tetrapeptides Dimerization
Baumketner, A., & Shea, J. -E. (2005). Free Energy Landscapes for Amyloidogenic Tetrapeptides Dimerization. Biophysical Journal, 89, 1493-1503.
The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides
Baumketner, A., & Shea, J. -E. (2005). The influence of different treatments of electrostatic interactions on the thermodynamics of folding of peptides. J. Phys. Chem. B, 109, 21322.
Oxygen vacancies in ZnO
Janotti, A., & Van de Walle, C. G. (2005). Oxygen vacancies in ZnO. Applied Physics Letters, 87, 122102.
The Performance of LDPC codes with Large Girth
O\textquoterightSullivan, M. E., Brevik, J., & Wolski, R. (2005). The Performance of LDPC codes with Large Girth. Proc. 43Rd Allerton Conference On Communication, Control and Computing, Univ. Illinois, Aug.
Temperature Dependence of Order, Disorder, and Defects in Laterally Con?ned Diblock Copolymer Cylinder Monolayers
Hammond, M. R., Cochran, E. W., Fredrickson, G. H., & Kramer, E. J. (2005). Temperature Dependence of Order, Disorder, and Defects in Laterally Con?ned Diblock Copolymer Cylinder Monolayers. Macromolecules, 38(15), 6575ä\ o\~n6585.
Thermal equilibrium defects in laterally confined monolayers of block copolymer cylinders
Hammond, M. R., Cochran, E. W., Fredrickson, G. H., & Kramer, E. J. (2005). Thermal equilibrium defects in laterally confined monolayers of block copolymer cylinders. Polymer Preprints (American Chemical Society, Division Of Polymer Chemistry), 46(2), 576ä\ o\~n577.
Variational study of triangular lattice spin-1/2 model with ring exchanges and spin liquid state in kappa-(ET)2 Cu2 (CN)3
Motrunich, O. I. (2005). Variational study of triangular lattice spin-1/2 model with ring exchanges and spin liquid state in kappa-(ET)2 Cu2 (CN)3. Phys. Rev. B, 72, 45105.