Research group of M Scott Shell
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Publications: journal articles
  1. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “Molecular structural order and anomalies in liquid silica,” Phys. Rev. E 66, 011202 (2002).
  2. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “Generalization of the Wang-Laudau method for off-lattice simulations,” Phys. Rev. E 66, 056703 (2002).
  3. M. S. Shell, P. G. Debenedetti, F. Sciortino, and E. La Nave, “Energy landscapes, ideal glasses, and their equation of state,” J. Chem. Phys. 118, 8821 (2003).
  4. F. Sciortino, E. La Nave, P. Tartaglia, M. S. Shell, and P. G. Debenedetti, “Test of non-equilibrium thermodynamics in glassy systems: the soft-sphere case,” Phys. Rev. E 68, 032103 (2003).
  5. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “An improved Monte-Carlo method for direct calculation of the density of states,” J. Chem. Phys. 119, 9406 (2003).
  6. P. G. Debenedetti, F. H. Stillinger, and M. S. Shell, “Model energy landscapes,” J. Phys. Chem. B 107, 14434 (2003).
  7. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “Saddles in the energy landscape: extensivity and thermodynamic formalism,” Phys. Rev. Lett. 92, 035506 (2004).
  8. M. S. Shell, P. G. Debenedetti, and F. H. Stillinger, “Inherent structure view of self diffusion in liquids,”  Journal of Physical Chemistry B 108, 6772 (2004).
  9. M. S. Shell and P. G. Debenedetti, “Thermodynamics and the glass transition in model energy landscapes,”  Phys. Rev. E 69, 051102 (2004).
  10. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “Flat histogram dynamics and optimization in density of states simulations of fluids,” J. Phys. Chem. B 108, 19748 (2004).
  11. E. La Nave, F. Sciortino, P. Tartaglia, M. S. Shell, and P. G. Debenedetti, Reply to comment on “Test of nonequilibrium thermodynamics in glassy systems: the soft-sphere case,” Phys. Rev. E 71, 033102 (2005).
  12. M. S. Shell, P. G. Debenedetti, and F. H. Stillinger, “Novel computational probes of diffusive motion,” J. Phys. Chem. B 109, 21329 (2005).
  13. M. S. Shell, P. G. Debenedetti, and F. H. Stillinger, “Dynamic heterogeneity and non-Gaussian diffusion in a model supercooled liquid,” J. Phys.: Condens. Matter 17, S4035 (2005).
  14. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “Computational characterization of the sequence landscape in simple protein alphabets,” Proteins 62, 232 (2006).
  15. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “A conformal solution theory for the energy landscape and glass transition of mixtures,” Fluid Phase Equilibria 241, 147 (2006).
  16. C. Chipot, M. S. Shell, and A. Pohorille, “Introduction,” invited chapter in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
  17. M. S. Shell, A. Z. Panagiotopoulos, and A. Pohorille, “Methods based on probability distributions and histograms,” invited chapter in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
  18. M. S. Shell and A. Z. Panagiotopoulos, “Simulation methods for free energy calculations of fluids,” invited chapter in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
  19. M. S. Shell, R. Ritterson, and K. Dill, “A test on peptide stability of AMBER force fields with implicit solvation” J. Phys. Chem. B (2008).
  20. K. A. Dill, S. B. Ozkan, M. S. Shell, and T. A. Weikl, "The protein folding problem," Ann. Rev. Biophys. 37, 289 (2008).
  21. M. S. Shell, “The relative entropy is fundamental to thermodynamic ensemble optimization,” J. Chem. Phys. 129, 144108 (2008).
  22. M. S. Shell, S. B. Ozkan, V. Voelz, A. Wu, and K. Dill, “Blind test of physics-based prediction of protein structures”, Biophys. J. 96, 917 (2009).
  23. G. A. Watkins, E. F. Jones, M. S. Shell, H. F. VanBrocklin, M. H. Pan, S. M. Hanrahan, J. J. Feng, J. He, N. E. Sounni, K. A. Dill, C. H. Contag, L. M. Coussens and B. L. Franc, “Development of an optimized activatable MMP-14 targeted SPECT imaging probe”, Bioorganic and Medicinal Chemistry 17, 653 (2009).
  24. V. Voelz, M. S. Shell, and K. Dill, “Predicting native fragments from short peptide fragment simulations”, PLoS Comput. Biol. 5, e1000281 (2009).
  25. A. Chaimovich and M.S. Shell, “Anomalous waterlike behavior in spherically-symmetric water models  optimized with the relative entropy,” Phys. Chem. Chem. Phys 11, 1901 (2009).
  26. E. Lin and M. S. Shell, “Convergence and heterogeneity in peptide folding with replica exchange molecular dynamics,”J. Chem. Theory Comput. 5, 2062 (2009).
  27. A. Chaimovich and M. S. Shell, “The relative entropy as a universal metric for multiscale errors,” Phys. Rev. E. 81, 060104 (2010).
  28. M. S. Shell, “A replica-exchange approach to computing peptide conformational free energies,” Mol. Simulation 36, 505 (2010).
  29. M. U. Hammer, T. H. Anderson, A. Chaimovich, M. S. Shell, and J. Israelachvili, “The search for the hydrophobic force law,” Faraday Discussions 146, 299 (2010).
  30. E. Lin and M. S. Shell, “Can peptide folding simulations provide predictive information for aggregation propensity?”, J. Phys. Chem. B. 114, 11899  (2010).
  31. J. Gee and M. S. Shell, “Two-dimensional replica exchange approach to peptide-peptide interactions,” J. Chem. Phys 134, 064112 (2011).  Research Highlights Article in JCP
  32. A. Chaimovich and M. S. Shell, “Coarse-graining errors and optimization using a relative entropy framework,” J. Chem. Phys. 134, 094112 (2011). Research Highlights Article in JCP
  33. A. Pritchard-Bell and M. S. Shell, “Smoothing protein energy landscapes by integrating folding models with structure prediction,” Biophys. J. 101, 2251 (2011).
  34. S. Carmichael and M. S. Shell, “A New Multiscale Algorithm and its Application to Coarse-Grained Peptide Models for Self-Assembly,” J. Phys. Chem. B 116, 8383 (2012).  Invited article in special issue on Multiscale Modeling
  35. J. Jeon and M. S. Shell, “Charge effects on the fibril forming peptide KTVIIE: a two-dimensional replica exchange simulation study,” Biophys. J. 102, 1952 (2012).
  36. C. C. Fu, P. M. Kulkarni, M. S. Shell, and L. G. Leal, “A Test of Systematic Coarse-Graining of Molecular Dynamics Simulations: Thermodynamic Properties,” J. Chem. Phys. 137, 164106  (2012).
  37. M. S. Shell, “Systematic coarse-graining of potential energy landscapes and dynamics in liquids,” J. Chem. Phys. 137, 084503 (2012).
  38. J. Jeon, C. E. Mills, and M. S. Shell, "Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization," J. Phys. Chem. B 117, 3935 (2013).
  39. P. M. Kulkarni, C.-C. Fu, M. S. Shell, and L. G. Leal, “Multiscale modeling with smoothed dissipative particle dynamics,” J. Chem. Phys. 138, 234105 (2013).
  40. N. D. Petsev, M. S. Shell, and L. G. Leal, “Dynamic equilibrium explanation for nanobubbles’ unusual temperature and saturation dependence,” Phys. Rev. E 88, 010402 (2013). 
  41. C. C. Fu, P. M. Kulkarni, M. S. Shell, and L. G. Leal, “A test of systematic coarse-graining of molecular dynamics simulations: Transport Properties,” J. Phys. Chem. 139, 094107 (2013).
  42. B. Giera, N. Henson, E. M. Kober, T. M. Squires, and M. S. Shell, “Model-free test of local-density mean-field behavior in electric double layers,” Phys. Rev. E 88, 011301 (2013). 



Publications: books and book chapters
  1. C. Chipot, M. S. Shell, and A. Pohorille, “Introduction,” in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
  2. M. S. Shell, A. Z. Panagiotopoulos, and A. Pohorille, “Methods based on probability distributions and histograms,” in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
  3. M. S. Shell and A. Z. Panagiotopoulos, “Simulation methods for free energy calculations of fluids,” in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.

Department of Chemical Engineering  |  University of California Santa Barbara