Publications

The Research Computing Center support projects that result in published academic papers.

The following publications have resulted from work done in partnership with the RCC.

Publication List

  1. Methane Feedback on Atmospheric Chemistry: Methods, Models, and Mechanisms Holmes, CD Journal of Advances in Modeling Earth Systems (2018)
  2. Equilibrium, Metastability, and Hysteresis in a Model Spin-crossover Material with Nearest-neighbor Antiferromagnetic-like and P. A. Rikvold, G. Brown, S. Miyashita, C. Omand, and M. Nishino Physical Review B (2016)
  3. A Simple Gravitational Lens Model for Cosmic Voids Bin Chen, Ronald Kantowski, Xinyu Dai The Astrophysical Journal, (2015)
  4. Birnessite: A Layered Manganese Oxide to Capture Sunlight for Water-Splitting Catalysis Kevin Paul Lucht and Jose Luis Mendoza-Cortes J. Phys. Chem. C (2015)
  5. On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter Zheng, L. and Yang, W The Journal of Chemical Physics (2008)
  6. Cryoelectron tomography of HIV-1 envelope spikes: further evidence for tripod-like legs Ping Zhu, Hanspeter Winkler, Kenneth A. Taylor, and Kenneth H. Roux. PLoS Pathogens (2008)
  7. On-the-path random walk to efficiently optimize minimum free energy path Chen, M. and Yang, W. J. Comp. Chem. 30 (2009)
  8. A pseudoatomic model of the COPII cage obtained from cryo-electron microscopy and mass spectrometry Alex J Noble, Qian Zhang, Jason O'Donnell, Hanaa Hariri, Nilakshee Bhattacharya, Alan G Marshall & Scott M Stagg Nature Structural & Molecular Biology (2013)
  9. Conformational ladscape of platinum(II)-tetraamine complexes: DFT and NBO studies Yongye, A.; Giulianotti, M. A.; Nefzi, A.; Houghten, R. A.; Martinez-Mayorga, K. Journal of Computer Aided Molecular Design (2010)
  10. "Crash and Safety Assessment Program for Paratransit Buses" Leslaw Kwasniewski, Jeff Siervogel, Cezary Bojanowski, Jerry W. Wekezer, Krzysztof Cichocki International Journal of Impact Engineering (2009)
  11. Simulation of melting of two-dimensional Lennard-Jones solids Keola Wierschem and Efstratios Manousakis Physical Review B, Vol. 83 (2011)
  12. High Performance Computing at FSU Paul van der Mark, Daniel R. Voss, and Jeff E. McDonald SuperComputing 07 (2007)
  13. Roles of boundary conditions in DNA simulations: Analysis of ion distributions with the finite-difference Poisson-Boltzmann method Ye, X., Yang, W., Luo, R. Biophys. J. 97, (2009)
  14. Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics Clemens Lakner, Paul van der Mark, John P. Huelsenbeck, Bret Larget, and Fredrik Ronquist Systematic Biology, 57(1) (2008)
  15. Can geosynchronous imaging Fourier transform spectrometer capture vertical and temporal variability of a convective atmosphere? Haidao Lin and Xiaolei Zou J. Appl. Remote Sens., Vol. 2, 023534 (2008); DOI:10.1117/1.2980331 (2008)
  16. Parameter estimation by Density Functional Theory for a lattice-gas model of Br and Cl chemisorption on Ag(100) Tjipto Juwono, Ibrahim Abou Hamad, Per Arne Rikvold, Sanwu Wang Journal of Electroanalytical Chemistry Vol 662 (2011)
  17. A model-averaging method for assessing groundwater conceptual model uncertainty Ye, M., K.F. Pohlmann, J.B. Chapman, G.M. Pohll, and D.M. Reeves Ground Water (2010)
  18. On model selection criteria in multimodel analysis Ye, M., P.D. Meyer, and S.P. Neuman Water Resources Research (2008)
  19. Relative Stability of Peptide Sequence Ions Generated by Tandem Mass Spectrometry Bythell, B. J.; Hendrickson, C. L.; Marshall, A. G. J. Am. Soc. Mass Spectrom. (2012)
  20. An enzymatic atavist revealed in dual Min, D., Josephine, H., Li, H., Lakner, C., Swofford, D., Naylor, G. P.,Hedstrom, L.*, and Yang, W. PLoS Biology 6 (2008)
  21. A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations Donghong Min and Wei Yang The Journal of Chemical Physics Vol. 128, No. 9 (2008)
  22. On tidal resonance in the global ocean and the back effect of coastal tides upon open-ocean tides Arbic, B.K., Karsten, R.H., and C. Garrett Atmosphere-Ocean (2009)
  23. Simulation of the Hurricane Dennis storm surge and considerations for vertical resolution Dukhovskoy, D.S., and S.L. Morey Journal of Natural Hazards (2011)
  24. Modulation of African waves from the advection of upper level moisture from the Tropical Easterly Jet Mrinal K Biswas and T N Krishnamurti AMS 28th Conference on Hurricanes and Tropical Meteorology (2008)
  25. On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals Zheng, L. and Yang, W. Chem. Phys. 129 (2008)
  26. "Dynamic Response of a Highway Bridge Subjected to Moving Trucks" Hongyi Li, Leslaw Kwasniewski, Jerry W. Wekezer ASCE Journal of Bridge Engineering (2008)
  27. "Numerical Assessment of Dynamic Response of Highway Bridges Subjected to Heavy Vehicles" Jerzy Malachowski, Hongyi Li, Jerry W. Wekezer, Leslaw Kwasniewski Advances in Transportation Studies, An International Journal (2007)
  28. A hybrid recursion method to robustly ensure efficiency in the simulated scaling based free energy simulations. Zheng, L., I. O. Carbone, Berg, B. A., and Yang, W. J. Chem. Phys. 129 (2008)
  29. Conversion from Shear to Curvature Vorticity and Hurricane Evolution Benjamin A. Schenkel and T.N. Krishnamurti (2008)
  30. "Structural Response of Paratransit Buses in Rollover Accidents" Krzysztof Cichocki, Jerry W. Wekezer International Journal of Crashworthiness (2007)
  31. Algorithms And Programs For Strong Gravitational Lensing In Kerr Space-time Including Polarization Bin Chen, Ronald Kantowski, Xinyu Dai, Eddie Baron, Prasad Maddumage The Astrophysical Journal Supplement Series, (2015)
  32. Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening Jin Wang, Xiliang Zheng, Yongliang Yang, Dale Drueckhammer, Wei Yang, and Gennardy Verkhi Physical Review Letters Vol. 99, No. 19 (2007)
  33. Measurements and modeling of topographically trapped waves along the Sigsbee Escarpment Morey, S.L., D. S. Dukhovskoy, and C. Cooper Offshore Technology Conference, Houston, TX (2010)
  34. Embedded Lensing Time Delays, The Fermat Potential, And The Integrated Sachs–Wolfe Effect Bin Chen, Ronald Kantowski, Xinyu Dai Astrophysical Journal (2015)
  35. Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble conformational sampling Zheng, L., Chen, M., and Yang, W. J. Chem. Phys. 130 (2009)
  36. Conference Notebook: Potential Implications of Tropical Cyclone Passage Schenkel, B., and R. Hart Bulletin of the American Meteorological Society (2011)
  37. Conformationally Gated Fragmentations and Rearrangements Promoted by Interception of the Bergman Cyclization through Intramolecular H-Abstraction: A Possible Mechanism of Auto-Resistance to Natural... Abdulkader Baroudi, Justin Mauldin and Igor V. Alabugin Journal of the American Chemical Society (2010)
  38. Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations. Beerli, P., M. Palczewski Genetics (2010)
  39. On the Dielectric Boundary in Poisson-Boltzmann Calculations Harianto Tjong and Huan-Xiang Zhou J. Chem. Theory Comput Vol. 4, No. 3 (2008)