HPCC Publications

2007

M.H. Shih, Adam Mock, M. Bagheri, N.K. Suh, S. Farrell, S.J. Choi, J.D. O'Brien, and P.D. Dapkus "Photonic crystal lasers in InGaAsP on a SiO2/Si substrate and its thermal impedance" Optics Express Vol.15 No.1, 8 January 2007

M.H. Shih, Mahmood Bagheri, Wan Kuang, Adam Mock, S.J. Choi, J.D. O'Brien, and P.D. Dapkus "Identification of modes and single mode operation of sapphire-bonded photonic crystal lasers under continuous-wave room temperature operation" Applied Physics Letters 90, 121116 2007

John O'Brien, Wan Kuang, Jiang-Rong Cao, Min-Hsiung Shih, Po-Tsung Lee, Mahmood Bagheri, Adam Mock and W K Marshall "Photonic crystal microcavity lasers" J. Phys. D: Appl. Phys. 40 (2007) 2671-2682

Stephens, P. J., J. J. Pan, F. J. Devlin, M. Urbanova and J. Hajicek, 2007. "Determination of the Absolute Configurations of Natural Products via Density Functional Theory Calculations of Vibrational Circular Dichroism, Electronic Circular Dichroism, and Optical Rotation: The Schizozygane Alkaloid Schizozygine" Journal of Organic Chemistry 2007, 72, 2508-2524

Stephens, P. J., J. J. Pan, F. J. Devlin, K. Krohn, and T. Kurtan, 2007. "Determination of the Absolute Configurations of Natural Products via Density Functional Theory Calculations of Vibrational Circular Dichroism, Electronic Circular Dichroism, and Optical Rotation: The Iridoids Plumericin and Isoplumericin" Journal of Organic Chemistry 2007, 72, 3521-3536

Sengupta, P., A. Raghavan and S. Haas, 2007. "Disorder-enhanced phase coherence in trapped bosons on optical lattices" New Journal of Physics 9 (2007) 103

2006

Wan Kuang, Woo Jun Kim, Adam Mock, and John O'Brien, 2006. "Propagation Loss of Line-Defect Photonic Crystal Slab Waveguides" IEEE journal of selected topics in quantum electronics, vol.12, no.6, 2006

A. Mock, W. Kuang, M.H. Shih, E.H. Hwang, W.J. Kim, J.D. O'Brien and P.D. Dapkus "Spectral Properties of Photonic Crystal Double-Heterostructure Resonant Cavities" IEEE 0-7803-9556-5/06 2006

M. H. Shih, Wan Kuang, Adam Mock, Mahmood Bagheri, E. H. Hwang J.D. O'Brien and P.D. Dapkus "High-quality-factor photonic crystal heterostructure laser" APPLIED PHYSICS LETTERS 89, 101104 2006

McCann, D. M., P. J. Stephens, 2006. "Determination of the Absolute Configurations Using Density Functional Theory Calculations of Optical Rotation and Electronic Circular Dichroism: Chiral Alkenes" Journal of Organic Chemistry 2006, 72, 6074-6098

Roscilde, T, S. Haas, 2006. "Mott glass in site-diluted S=1 antiferromagnets with single-ioN anisotropy" PACSnumbers: 75.10.Jm, 75.10.Nr, 75.40.Cx, 64.60.Ak

Schmidt, P., S. Haas and A. F. J. Levi, 2006. "Synthesis of electron transmission in nanoscale semiconductor devices" applied physics letter 88, 013502 2006

Yu, R., T. Roscildei, and S. Haas, 2006. "Quantum disorder and Griffiths singularities in bond-diluted two-dimensional Heisenberg" Physical Review B 73, 064406 2006.

Grigorenko, I., S. Haas and A. F. J. Levi, 2006. "Electromagnetic Response of Broken-Symmetry Nanoscale Clusters" PHYSICAL REVIEW LETTERS PRL 97, 036806 (2006).

2004

Borman, S., 2004. "Much Ado About Enzyme Mechanisms," C&EN. 82:35-39.

Cao, J.R., W. Kuang, Z. Wei, S. Choi, J. D. O'Brien, and P. D. Dapkus. 2004. "Far-Fields of Photonic Crystal Microcavity Lasers," CTuR, Conference on Laser and Electro-Optics (CLEO), San Francisco, California (2004).

Cao, J.R., Z. Wei, S. Choi, W. Kuang, J. D. O'Brien, P. D. Dapkus. 2004. "Sapphire-Bonded Photonic Crystal Lasers," TuA-3-2, the 6th International Conference on Indium Phosphide and Related Materials, (IPRM'04), Kagoshima, Japan (2004).

Firouzi M., T. T. Tsotsis, M. Sahimi. 2004. "Molecular dynamics simulations of transport and separation of carbon dioxide-alkane mixtures in carbon nanopores," Journal of Chemical Physics Volume120, pp8172 (2004).

Gheorma, I., S. Haas, and A.F.J. Levi. 2004. "A periodic Nano-Photonic Design," Journal of Applied Physics. 95, 1420-1426 (2004).

Kim, J., and Y. Gil. 2004. "Towards Interactive Composition of Semantic Web Services," AAAI Spring Symposium on Semantic Web Services, 2004.

Kuang W., and J. D. O'Brien. 2004. "Reducing the out-of-plane radiation loss of photonic crystal waveguides on high-index substrates," Optics Letters 29, 860-2 (2004).

Kuang, W., and J. D. O'Brien. 2004. "Strategy for Reducing the Out-of-Plane Radiation Loss in Photonic Crystal Waveguides on High-Index Substrates," CWG, Conference on Laser and Electro-Optics (CLEO), San Francisco, California (2004).

Kuang, W., J. R. Cao, T. Yang, S. Choi, J. D. O'Brien, P. D. Dapkus. 2004. "Classification of Modes in Multi-Moded Photonic Crystal Microcavities," CTuDD, Conference on Laser and Electro-Optics (CLEO), San Francisco, California (2004).

Normand, B., M. Matsumoto, O. Nohadani, S. Wessel, T.M. Rice, and M. Sigrist. 2004. "Pressure- and field-induced magnetic quantum phase transition," TlCuCl_3 J. Phys.: Cond. Matt. 16, S867 (2004).

Nohadani, O., S. Wessel, B. Normand, and S. Haas. 2004."Universal scaling at field-induced magnetic phase transitions,"Phys. Rev. B (2004)*.

Olsson, M. H. M., P. E. M. Siegbahn and A. Warshel. 2004. "Simulations of the large kinetic isotope effect and the temperature dependence of the hydrogen atom transfer in lipoxygenase," Journal of the American Chemical Society. 126:2820-2828.

Olsson, M. H. M., P. E. M. Siegbahn and A. Warshel. 2004. "Simulating large nuclear quantum mechanical corrections in hydrogen atom transfer reactions in metalloenzymes," Journal of Biological Inorganic Chemistry. 9:96-99.

Schutz, C. N. and A. Warshel. 2004. "Analyzing Free Energy Relationships for Proton Translocations in Enzymes; Carbonic Anhydrase Revisted," J. Phys. Chem. B. 108:2066-2075.

Schutz, C. N. and A. Warshel. 2004. "The Low Barrier Hydrogen Bond (LBHB) Proposal Revisited: The Case of the Asp-His Pair in Serine Proteases," Proteins: Struc., Func., and Bioinformatics*.

Shih, M. H., W. J. Kim, W. Kuang, J. R. Cao, H. Yukawa, S. J. Choi, J. D. O'Brien, P. D. Dapkus, and W. K. Marshall. 2004. "Two-Dimensional Photonic Crystal Mach-Zehnder Interferometers," Applied Physics Letters 84, 460-2 (2004).

Shurki, A., and A. Warshel. 2004. "Why does the Ras switch break by oncogenic mutations," Proteins: Struc., Func., and Bioinformatics. 55:1-10.

Stephens, P.J., D.M. McCann, E. Butkus, S. Stoncius, J.R. Cheeseman, and M.J. Frisch. 2004. "Determination of Absolute Configuration Using Concerted ab Initio DFT Calculations of Electronic Circular Dichroism and Optical Rotation:," Bicyclo[3.3.1]nonane Diones. Journal of Organic Chemistry, 69, 1948-1958.

Thalken, J., Y. Chen, A.F.J. Levi, S. Haas. 2004. "Adaptive quantum design of tight-binding clusters," Phys. Rev. B (2004)*.

Thalken, J., W. Li, S. Haas, and A.F.J. Levi. 2004. "Adaptive design of excitonic absorption in broken-symmetry quantum wells," Appl. Phys. Lett. (2004)*.

Yarnell, A., 2004. "Blockade in the cell's waterway," Chemical & Engineering News. 82:42-44.

* Papers that have been accepted but not yet published.

2003

Akcelik V., J. Bielak, G. Biros, I. Epanomeritakis, A. Fernandez, O.Ghattas, E. Kim, J. Lopez, D. O'Hallaron, T. Tu, and J. Urbanic. 2003. "High- resolution Forward and Inverse Earthquake Modeling on Terasacale Computers," Proceedings of ACM/IEEE SC2003, Phoenix, AZ, 2003.

Branicio, P.S., J. P. Rino, F. Shimojo, R. K. Kalia, A. Nakano, and P. Vashishta. 2003. "Molecular dynamics study of structural, mechanical, and vibrational properties of crystalline and amorphous Ga1-xInxAs alloy," Journal of Applied Physics 94, 3840-3848 (2003).

Branicio, P. S., R. K. Kalia, A. Nakano, J. P. Rino, F. Shimojo, and P. Vashishta. 2003. "Structural, mechanical, and vibrational properties of Ga1-xInxAs alloy: a molecular dynamics study," Applied Physics Letters 82, 1057-1059 (2003).

Burykin, A. and A. Warshel. 2003. "What Really Prevents Proton Transport Through Aquaporin Charge Self-Energy versus Proton Wire Proposals," Biophys. J. 85:3696-3706.

Burykin, A., M. Kato and A. Warshel. 2003. "Exploring The Origin Of The Ion Selectivity Of The KcsA Potassium Channel," PROTEINS. 52:412-426.

Cao, J.R., W. Kuang, S. Choi, P. Lee, J. D. O'Brien, and P. D. Dapkus. 2003. "Threshold dependence on the spectral alignment between the quantum-well gain peak and the cavity resonance in InGaAsP photonic crystal lasers," Applied Physics Letters 83, 4107-4109 (2003).

Chen, Y., R. Yu, W. Li, O. Nohadani, S. Haas, and A. F. J. Levi. 2003. "Adaptive design of nano-scale dielectric structures for photonics," J. Appl. Phys. 94, 6065-6068 (2003).

Deng, S., et al. 2003. "Plasma Wakefield Acceleration in Self-ionized Gas or Plasmas," Physical Review E 68, 04701 (2003).

Domaradzki, J.A., Z. Xiao, P.K. Smolarkiewicz. 2003. ``Effective eddy viscosities in implicit large eddy simulations of turbulent flows'', Phys. Fluids, vol. 15, 3890 (2003).

Field, E.H., T.H. Jordan, and C.A. Cornell. 2003. "OpenSHA: A Developing Community-modeling Environment for Seismic Hazard Analysis," Seism. Res. Lett. 74, 406-419.

Jordan, T.H., P.J. Maechling, and SCEC/CME Collaboration. 2003. "The SCEC Community Modeling Environment Ï An Information Infrastructure for System-Level Earthquake Science," Seism. Res. Lett. 74 No. 3, 44-46.

Kalia R. K., A. Nakano, P. Vashishta, C. L. Rountree, L. Van Brutzel, and S. Ogata. 2003. "Multiresolution atomistic simulations of dynamic fracture in nanostructured ceramics and glasses," International Journal of Fracture 121, 71-79 (2003).

Kim, E., J. Bielak, and O. Ghattas. 2003. "Large-scale Northridge Earthquake Simulation Using Octree-based Multiresolution Mesh Method," Proceedings of the 16th ASCE Engineering Mechanics Conference, Seattle, WA, 2003.

Kuang W., C. Kim, A. Stapleton, W. J. Kim, and J. D. O'Brien, "Calculated out-of-plane transmission loss for photonic-crystal slab waveguides," Optics Letters 28, 1781-3 (2003).

Marcinkovich, C., and K.B. Olsen. 2003. "On the Implementation of Perfectly Matched Layers in a 3D Fourth-Order Velocity-Stress Finite-Difference Scheme," JGR, 2002JB002235.

Moore, R., C. Baru, "Virtualization Services for Data Grids", Book chapter in "Grid Computing: Making the Global Infrastructure a Reality", John Wiley & Sons Ltd, 2003.

Ogata, S., T. J. Campbell, R. K. Kalia, A. Nakano, P. Vashishta, and S. Vemparala. 2003. "Scalable and portable implementation of the fast multipole method on parallel computers," Computer Physics Communications 153, 445-461 (2003).

Olsson, M. H. M., G. Y. Hong and A. Warshel. 2003. "Frozen density functional free energy simulations of redox proteins: Computational studies of the reduction potential of plastocyanin and rusticyanin." Journal of the American Chemical Society. 125:5025-5039.

Olsen, K.B., S.M. Day and C.R. Bradley. 2003. "Estimation of Q for long-period (>2 s) waves in the Los Angeles Basin," Bull. Seis. Soc. Am. 93, 627-638.

Rumolo, G., et al. 2003. "Electron Cloud Effects on Beam Evolution in a Circular Accelerator," Physical Review Special Topics Ï Acc. & Beams V5, No 1, p 011001 (2003).

Sharma A., A. Nakano, R. K. Kalia, P. Vashishta, S. Kodiyalam, P. Miller, W. Zhao, X. Liu, T. J. Campbell, and A. Haas. 2003. "Immersive and interactive exploration of billion-atom systems," Presence: Teleoperators and Virtual Environments 12, 85-95 (2003), Best Paper in IEEE Virtual Reality 2002, featured on the cover.

Sharma, A., R. K. Kalia, A. Nakano, and P. Vashishta. 2003. "Large multidimensional data visualization for materials science," IEEE Computing in Science and Engineering 5 (2), 26-33 (2003).

Strajbl, M., A. Shurki, M. Kato and A. Warshel. 2003. "Apparent NAC effect in chorismate mutase reflects electrostatic transition state stabilization," Journal of the American Chemical Society. 125:10228-10237.

Strajbl, M., A. Shurki and A. Warshel. 2003. "Converting conformational changes to electrostatic energy in molecular motors: The energetics of ATP synthase," Proceedings of the National Academy of Sciences of the United States of America. 100:14834-14839.

Su X., R. K. Kalia, A. Nakano, P. Vashishta, and A. Madhukar. 2003. "InAs/GaAs square nanomesas: multimillion-atom molecular dynamics simulations on parallel computers," Journal of Applied Physics 94, 6762-6773 (2003).

Tu, T., D. R. O'Hallaron, and J. Lopez. 2003. "The Etree Library: A System for Manipulating Large Octrees on Disk, Technical Report CMU-CS-03-174," School of Computer Science, Carnegie Mellon University, July, 2003.

Vashishta, P., R. K. Kalia, and A. Nakano. 2003. "Multimillion atom molecular dynamics simulations of nanoparticles on parallel computers," Journal of Nanoparticle Research 5, 119-135 (2003).

Walsh P., A. Omeltchenko, R. K. Kalia, A. Nakano, P. Vashishta, and S. Saini. 2003. "Nanoindentation of silicon nitride: a multi-million atom molecular dynamics study," Applied Physics Letters 82, 118-120 (2003), featured on the cover.