Publications

Please acknowledge the Florida State University shared High-Performance Computing facility and staff in publications (refereed, dissertations, theses, etc.), presentation, and reports, which have in any way benefited from the availability of these resources. One way to acknowledge the facility and staff is by including the following statement in your publications:

We acknowledge the Florida State University shared High-Performance Computing facility and staff for contributions to results presented in this paper.

Also, to better understand the breadth of research being served by FSU's shared HPC facility, please take few minutes to fill in a short form about your publications. The web-based form is available by clicking on the add a publication link.

Publications

  • Gopinath Subramanian and Sachin Shanbhag, Self-Diffusion in Binary Blends of Cyclic and Linear Polymers. Journal: Macromolecules, pages 7239–724, 2008.

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  • Nylander, J. A., J.C. Wilgenbusch, D. L. Warren, D. L. Swofford, AWTY (Are We There Yet): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Journal: Bioinformatics, pages 581–583, 2008.

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  • Van Dyke, Donald F., COAPS/FSU Real Time Gulf of Mexico 4 km WRF-ARW Atmospheric Model. Dissertation/Thesis 2008.

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  • Clemens Lakner, Paul van der Mark, John P. Huelsenbeck, Bret Larget, and Fredrik Ronquist, Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics. Journal: Systematic Biology, 57(1), pages 86-103, 2008.

  • Henry R. Winterbottom, Eric P. Chassignet, and Carol Anne Clayson, HYCOM North Atlantic Ocean Basin Forecasts. Dissertation/Thesis 2008.

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  • Isabel SanMartin, Paul van der Mark, and Fredrik Ronquist, Inferring dispersal: a Bayesian approach to phylogenetic-based island biogeography, with special reference to the Canary islands. Journal: Journal of Biogeography, 35, pages 428-449, 2008.

  • Haidao Lin and Xiaolei Zou, Can geosynchronous imaging Fourier transform spectrometer capture vertical and temporal variability of a convective atmosphere?. Journal: J. Appl. Remote Sens., Vol. 2, 023534 (2008); DOI:10.1117/1.2980331, pages 19, 2008.

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  • Paul van der Mark, Daniel R. Voss, and Jeff E. McDonald, High Performance Computing at FSU. Poster: SuperComputing 07, 2007.

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  • Harianto Tjong and Huan-Xiang Zhou, Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method. Journal: Journal of Chemical Theory and Computation, pages , 2008.

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  • Myunggi Yi, Hugh Nymeyer, Huan X Zhou, Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations. Journal: Physical Review Letters Vol. 101, No. 3, pages , 2008.

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  • Myunggi Yi, Timothy A. Cross, and Huan-Xiang Zhou, A Secondary Gate As a Mechanism for Inhibition of the M2 Proton Channel by Amantadine. Journal: Journal of Physical Chemistry B Vol. 112, No. 27, pages 7977-7979, 2008.

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  • Myunggi Yi, Harianto Tjong, and Huan-Xiang Zhou, Spontaneous conformational change and toxin binding in a7 acetylcholine receptor: Insight into channel activation and inhibition. Journal: Proc. Natl. Acad. Sci Vol 105, No. 34, pages 8280-8285, 2008.

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  • Harianto Tjong and Huan-Xiang Zhou, Prediction of Protein Solubility from Calculation of Transfer Free Energy. Journal: Biophysical Journal Vol 95, pages 2601-2609, 2008.

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  • Harianto Tjong and Huan-Xiang Zhou, On the Dielectric Boundary in Poisson-Boltzmann Calculations. Journal: J. Chem. Theory Comput Vol. 4, No. 3, pages 507-514, 2008.

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  • Hugh Nymeyer and Huan-Xiang Zhou, A Method to Determine Dielectric Constants in Nonhomogeneous Systems: Application to Biological Membranes. Journal: Biophysical Journal Vol 94, pages 1185-1193, 2008.

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  • Sanbo Qin and Huan-Xiang Zhou, Prediction of Salt and Mutational Effects on the Association Rate of U1A Protein and U1 Small Nuclear RNA Stem/Loop II. Journal: J. Phys. Chem. B Vol 112, N o. 19, pages 5955-5960, 2008.

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  • Ping Zhu, Hanspeter Winkler, Kenneth A. Taylor, and Kenneth H. Roux., Cryoelectron tomography of HIV-1 envelope spikes: further evidence for tripod-like legs. Journal: PLoS Pathogens, pages (in press), 2008.

  • Jason O'Donnel, Kenneth A. Taylor & Michael S. Chapman., Adeno-Associated Virus-2 and its primary cellular receptor ? cryo-EM structure of a heparin complex. Journal: J. Virology, pages submitted, 2008.

  • Mikolai I. Fajer, Hongzhi Li, Wei Yang, and Piotr G. Fajer, Mapping Electron Paramagnetic Resonance Spin Label Conformations by the Simulated Scaling Method. Journal: Journal of the American Chemical Society Vol. 129, No. 45, pages 13840-1384, 2007.

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  • Jin Wang, Xiliang Zheng, Yongliang Yang, Dale Drueckhammer, Wei Yang, and Gennardy Verkhi, Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening. Journal: Physical Review Letters Vol. 99, No. 19, pages , 2007.

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  • Bernd A. Berg and Wei Yang, Numerical calculation of the combinatorial entropy of partially ordered ice. Journal: The Journal of Chemical Physics Vol. 127, No. 22, pages , 2007.

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  • Donghong Min and Wei Yang, A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations. Journal: The Journal of Chemical Physics Vol. 128, No. 9, pages , 2008.

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  • Donghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang, fficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method. Journal: Chemical Physics Letters Volume 454, Issues 4-6, pages 391-395, 2008.

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  • Donghong Min and Wei Yang, Energy difference space random walk to achieve fast free energy calculations. Journal: The Journal of Chemical Physics Vol. 128, No. 19, pages , 2008.

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  • Lianqing Zheng and Wei Yang, Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy. Journal: The Journal of Chemical Physics Vol. 129, No. 1, pages , 2008.

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  • Lianqing Zheng, Irina O. Carbone and Alexey Lugovskoy, Bernd A. Berg, and Wei Yang, A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations. Journal: The Journal of Chemical Physics Vol. 129, No. 3, pages , 2008.

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  • D. Min, H. Josephine, H. Li, C. Lakner, I. Macpherson, G. Naylor, D. Swofford, L. Hedstrom, W. Yang, An Enzymatic Atavist Revealed in Dual Pathways for Water Activation. Journal: PLoS Biology, Vol. 6, No. 8, pages , 2008.

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  • Zheng, L. and Yang, W, On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter. Journal: The Journal of Chemical Physics, pages (in press), 2008.

  • Mrinal K Biswas and T N Krishnamurti, Modulation of African waves from the advection of upper level moisture from the Tropical Easterly Jet. Poster: AMS 28th Conference on Hurricanes and Tropical Meteorology, 2008.

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  • Benjamin A. Schenkel and T.N. Krishnamurti, Conversion from Shear to Curvature Vorticity and Hurricane Evolution. Dissertation/Thesis 2008.

  • Benjamin A. Schenkel and T.N. Krishnamurti, Conversion from Shear to Curvature Vorticity, Organization of Convection, and Hurricane Genesis. Poster: Tropical Meteorology Special Symposium, 2008.

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  • Dukhovskoy, D.S., S.L. Morey, P.J. Martin, J.J. O’Brien, C. Cooper, Application of a vanishing, quasi-sigma, vertical coordinate for simulation of high-speed, deep currents over the Sigsbee Escarpment in the Gulf of Mexico. Journal: Ocean Modelling, pages , 2008.

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  • O'Donnell J, Taylor KA, Chapman MS., Adeno-associated virus-2 and its primary cellular receptor-Cryo-EM structure of a heparin complex.. Journal: Virology, pages 434-443, 2009.

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  • S. H. Thompson, G. Brown, A. Kuhnle, P. A. Rikvold, and M. A. Novotny, Resolution-dependent Mechanisms for Bimodal Switching-time Distributions in Simulated Fe Nanopillars. Journal: Physical Review B, Vol. 79, pages 024429, 2009.

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  • # Sanbo Qin and Sanbo Qin and Huan-Xiang Zhou, Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Journal: Proc Natl Acad Sci U S A, pages 6974-6979, 2009.

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  • Austin Yongye, Yangmei Li, Marc Giulianotti, Yongping Yu, Richard Houghten, Karina Martinez-Mayorga, Modeling of Peptides Containing D-Amino Acids: Implications on Cyclization. Journal: Journal of Computer-Aided Molecular Design, pages DOI 10.100, 2009.

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  • Jianhua Lu & Ming Cai, Quantifying contributions to polar warming amplification in an idealized coupled general circulation model. Journal: Springer-Verlag 2009, pages 19, 2009.

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