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. Mapping Electron Paramagnetic Resonance Spin Label Conformations by the Simulated Scaling Method Mikolai I. Fajer, Hongzhi Li, Wei Yang, and Piotr G. Fajer Journal of the American Chemical Society Vol. 129, No. 45 (2007)
  2. A Markov chain model for characterizing medium heterogeneity and sediment layering structure Ye, M., and R. Khaleel Water Resources Research (2008)
  3. Quantum tunneling and scattering of a composite object reexamined Naureen Ahsan and Alexander Volya Physical Review C (2010)
  4. Quantification of uncertainty in pedotransfer function-based parameter estimation for unsaturated flow modeling Deng, H., M. Ye, M. G. Schaap, and R. Khaleel Water Resources Research (2009)
  5. Spontaneous conformational change and toxin binding in a7 acetylcholine receptor: Insight into channel activation and inhibition Myunggi Yi, Harianto Tjong, and Huan-Xiang Zhou Proc. Natl. Acad. Sci Vol 105, No. 34 (2008)
  6. A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations Lianqing Zheng, Irina O. Carbone and Alexey Lugovskoy, Bernd A. Berg, and Wei Yang The Journal of Chemical Physics Vol. 129, No. 3 (2008)
  7. Energy difference space random walk to achieve fast free energy calculations Donghong Min and Wei Yang The Journal of Chemical Physics Vol. 128, No. 19 (2008)
  8. Conformational heterogeneity of the M2 proton channel and a structural model for channel activation. Myunggi Yi, Timothy A. Cross, Huan-Xiang Zhou Proceedings of the National Academy of Sciences of the United States of America (2009)
  9. Resolution-dependent Mechanisms for Bimodal Switching-time Distributions in Simulated Fe Nanopillars S. H. Thompson, G. Brown, A. Kuhnle, P. A. Rikvold, and M. A. Novotny Physical Review B, Vol. 79 (2009)
  10. Energy difference space random walk to achieve fast free energy calculations Min, D. and Yang, W J. Chem. Phys. (Communication) 128 (2008)
  11. A Secondary Gate As a Mechanism for Inhibition of the M2 Proton Channel by Amantadine Myunggi Yi, Timothy A. Cross, and Huan-Xiang Zhou Journal of Physical Chemistry B Vol. 112, No. 27 (2008)
  12. Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy. Zheng, L. and Yang, W. J. Chem. Phys. 129 (2008)
  13. Integrated Sachs-Wolfe effect versus redshift test for the cosmological parameters Ronald Kantowski, Bin Chen, Xinyu Dai Physical Review D (2015)
  14. fficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method Donghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang Chemical Physics Letters Volume 454, Issues 4-6 (2008)
  15. Probing the integrated Sachs-Wolfe effect using embedded lens models Bin Chen, Ronald Kantowski Physical Review D (2015)
  16. Quantifying contributions to polar warming amplification in an idealized coupled general circulation model Jianhua Lu & Ming Cai Springer-Verlag 2009 (2009)
  17. A modeling study of the interaction between the Atlantic Warm Pool, the tropical Atlantic easterlies, and the Lesser Antilles Steven C. Chan, Vasubandhu Misra, and Henry Smith Journal of Geophysical Research - Atmospheres (2011)
  18. HYCOM North Atlantic Ocean Basin Forecasts Henry R. Winterbottom, Eric P. Chassignet, and Carol Anne Clayson (2008)
  19. A geologically based Markov chain model for simulating tritum transport with uncertain conditions in a nuclear-stimulated natural gas reservoir Ye, M., C.A. Cooper, J.B. Chapman, D. Gillespie, and Y. Zhang SPE Reservoir Evaluation & Engineering (2009)
  20. Self-Diffusion in Binary Blends of Cyclic and Linear Polymers Gopinath Subramanian and Sachin Shanbhag Macromolecules (2008)
  21. Quadrupole collectivity in the two-body random ensemble Volha Abramkina and Alexander Volya Physical Review C (2011)
  22. Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonion replica exchange strategy Min, D., Li, H., Berg, B. A., Fenley, M. O., and Yang, W. Chem. Phys. Lett. 454 (2008)
  23. Two modes of magnetization switching in a simulated iron nanopillar in an obliquely oriented field Thompson, S.H.; Brown, G.; Rikvold, P.A. and Novotny, M.A. Journal of Physics: Condensed Matter, Vol. 22 (2010)
  24. "Material and Structural Crashworthiness Characterization of Paratransit Buses" Mark F. Horstemeyer, Hongyi Li, Jeff Siervogel, Leslaw Kwasniewski, Jerry W. Wekezer, Brian Christia International Journal of Crashworthiness (2007)
  25. Prediction of Protein Solubility from Calculation of Transfer Free Energy Harianto Tjong and Huan-Xiang Zhou Biophysical Journal Vol 95 (2008)
  26. MMA: A computer code for multimodel analysis Ye, M. Ground Water (2010)
  27. Random walk in orthogonal space Zheng, L., Chen, M., and Yang, W Proc.Natl. Acad. Sci. USA 51, 20227-20232 (2008)
  28. Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations Myunggi Yi, Hugh Nymeyer, Huan X Zhou Physical Review Letters Vol. 101, No. 3 (2008)
  29. Adeno-Associated Virus-2 and its primary cellular receptor ? cryo-EM structure of a heparin complex Jason O'Donnel, Kenneth A. Taylor & Michael S. Chapman. J. Virology (2008)
  30. The overland reintensification of North Atlantic Tropical Cyclone Erin (2007): physical and dynamical characteristics Clark Evans, Russ S. Schumacher, and Thomas J. Galarneau, Jr. 29th Conference on Hurricanes and Tropical Meteorology (2010)
  31. Kinetic Monte Carlo simulations of a model for heat-assisted magnetization reversal in ultrathin films W.R. Deskins, G. Brown, S.H. Thompson, P.A. Rikvold Physical Review B Vol. 84 (2011)
  32. Modeling of Peptides Containing D-Amino Acids: Implications on Cyclization Austin Yongye, Yangmei Li, Marc Giulianotti, Yongping Yu, Richard Houghten, Karina Martinez-Mayorga Journal of Computer-Aided Molecular Design (2009)
  33. Dissection of the high rate constant for the binding of a ribotoxin to the ribosome # Sanbo Qin and Sanbo Qin and Huan-Xiang Zhou Proc Natl Acad Sci U S A (2009)
  34. Application of a vanishing, quasi-sigma, vertical coordinate for simulation of high-speed, deep currents over the Sigsbee Escarpment in the Gulf of Mexico Dukhovskoy, D.S., S.L. Morey, P.J. Martin, J.J. O’Brien, C. Cooper Ocean Modelling (2008)
  35. Tuning Selectivity of Anionic Cyclizations: Competition between 5-Exo and 6-Endo-dig Closures of Hydrazides of o-Acetylenyl Benzoic Acids and Based-catalyzed Fragmentation/Recyclization of the Initial S. F.Vasilevsky, T. F. Mikhailovskaya, V. I. Mamatyuk, G. A. Bogdanchikov, M. Manoharan, I. V. Alabu Joutnal of Organic Chemistry (2009)
  36. AWTY (Are We There Yet): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics Nylander, J. A., J.C. Wilgenbusch, D. L. Warren, D. L. Swofford Bioinformatics (2008)
  37. Molecular mechanisms of functional rescue mediated by p53 tumor. Tan, Y. H., Chen, Y. M., Ye, X., Lu, Q., Tretyachenko-Ladokhina, V., Yang, W., Senear, D. F., and Lu Biophys. Chem. 145 (2009)
  38. Inferring dispersal: a Bayesian approach to phylogenetic-based island biogeography, with special reference to the Canary islands Isabel SanMartin, Paul van der Mark, and Fredrik Ronquist Journal of Biogeography, 35 (2008)
  39. Molecular dynamics simulation of F-actin: Studying the mechanisms for semi-flexible filament assembly reveals the role of cross-linkers. Nguyen, L. T., Yang, W., Wang, Q., and Hirst, L. S. Soft Matter 5 (2009)