Google Scholar link

For the most recent list of our publications, please visit Prof. Shell’s Google Scholar page.

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).
    https://doi.org/10.1103/PhysRevE.66.011202
  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).
    https://doi.org/10.1103/PhysRevE.66.056703
  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).
    https://doi.org/10.1063/1.1566943
  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).
    https://doi.org/10.1103/PhysRevE.68.032103
  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).
    https://doi.org/10.1063/1.1615966
  6. P. G. Debenedetti, F. H. Stillinger, and M. S. Shell, “Model energy landscapes,” J. Phys. Chem. B107, 14434 (2003).
    https://doi.org/10.1021/jp030885b
  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).
    https://doi.org/10.1103/PhysRevLett.92.035506
  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).
    https://doi.org/10.1021/jp0372800
  9. M. S. Shell and P. G. Debenedetti, “Thermodynamics and the glass transition in model energy landscapes,”  Phys. Rev. E 69, 051102 (2004).
    https://doi.org/10.1103/PhysRevE.69.051102
  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).
    http://dx.doi.org/10.1021/jp047677j
  11. M. S. Shell, P. G. Debenedetti, and F. H. Stillinger, “Novel computational probes of diffusive motion,” J. Phys. Chem. B 109, 21329 (2005).
    https://doi.org/10.1021/jp0517145
  12. 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).
    http://dx.doi.org/10.1088/0953-8984/17/49/002
  13. M. S. Shell, P. G. Debenedetti, and A. Z. Panagiotopoulos, “Computational characterization of the sequence landscape in simple protein alphabets,” Proteins 62, 232 (2006).
    https://doi.org/10.1002/prot.20714
  14. 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).
    https://doi.org/10.1016/j.fluid.2005.11.002
  15. K. A. Dill, S. B. Ozkan, M. S. Shell, and T. R. Weikl, “The protein folding problem,” Ann. Rev. Biophys. Biomolec. Struct. 37, 289 (2008).
    https://doi.org/10.1146/annurev.biophys.37.092707.153558
  16. M. S. Shell, R. Ritterson, and K. Dill, “A test on peptide folding of AMBER force fields with implicit solvation” J. Phys. Chem. B 112, 6878 (2008).
    https://dx.doi.org/10.1021%2Fjp800282x
  17. M. S. Shell, “The relative entropy is fundamental to multiscale and inverse thermodynamic problems,” J. Chem. Phys. 129, 144108 (2008).
    https://doi.org/10.1063/1.2992060
  18. 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).
    https://doi.org/10.1016/j.bpj.2008.11.009
  19. 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).
    https://doi.org/10.1016/j.bmc.2008.11.078
  20. V. Voelz, M. S. Shell, and K. Dill, “Predicting peptide structures from native proteins in physical simulations of fragments”, PLoS Comput. Biol. 5, e1000218 (2009).
    https://dx.doi.org/10.1371%2Fjournal.pcbi.1000281
  21. 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).  ­– Invited article in special issue on Multiscale Modeling
    https://doi.org/10.1039/b818512c
  22. E. Lin and M. S. Shell, “Convergence and heterogeneity in peptide folding with replica exchange molecular dynamics,”J. Chem. Theory Comput. 5, 2062 (2009).
    https://doi.org/10.1021/ct900119n
  23. A. Chaimovich and M. S. Shell, “Relative entropy as a universal metric for multiscale errors,” Phys. Rev. E. 81, 060104 (2010). ­– Rapid Communication
    https://doi.org/10.1103/PhysRevE.81.060104
  24. M. S. Shell, “A replica-exchange approach to computing peptide conformational free energies,” Mol. Simulation 36, 505 (2010).  – Invited article
    https://doi.org/10.1080/08927021003720546
  25. 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).
    https://doi.org/10.1039/B926184B
  26. E. Lin and M. S. Shell, “Can peptide folding simulations provide predictive information for aggregation propensity?”, J. Phys. Chem. B. 114, 11899  (2010).
    https://doi.org/10.1021/jp104114n
  27. 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
    https://doi.org/10.1063/1.3551576
  28. 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
    https://doi.org/10.1063/1.3557038
  29. A. Pritchard-Bell and M. S. Shell, “Smoothing protein energy landscapes by integrating folding models with structure prediction,” Biophys. J. 101, 2251 (2011).
    https://dx.doi.org/10.1016%2Fj.bpj.2011.09.036
  30. 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
    https://doi.org/10.1021/jp2114994
  31. 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).
    https://dx.doi.org/10.1016%2Fj.bpj.2012.03.019
  32. M. S. Shell, “Systematic coarse-graining of potential energy landscapes and dynamics in liquids,” J. Chem. Phys. 137, 084503 (2012).  –Named among 80 seminal papers in JCP’s 80th Anniversary Collection, 2013
    https://doi.org/10.1063/1.4746391
  33. 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).
    https://doi.org/10.1063/1.4759463
  34. J. Jeon, C. Mills, and M. S. Shell, “Molecular insights into diphenylalanine nanotube assembly: all-atom simulations of oligomerization,” J. Phys. Chem. B 117, 3935 (2013).
    https://doi.org/10.1021/jp308280d
  35. 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).
    https://doi.org/10.1063/1.4810754
  36. 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). – Rapid Communication
    https://doi.org/10.1103/PhysRevE.88.010402
  37. 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).
    https://doi.org/10.1063/1.4819472
  38. 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). – Rapid Communication
    https://doi.org/10.1103/PhysRevE.88.011301
  39. S. P. Carmichael and M. S. Shell, “A simple mechanism for emergent chirality in achiral hard particle assembly,” J. Chem. Phys. 139, 164705 (2013).  ­– Editor’s Pick Article and Top Viewed Article
    https://doi.org/10.1063/1.4826466
  40. A. Chaimovich and M. S. Shell, “The length-scale crossover of the hydrophobic interaction in a coarse-grained water model,” Phys. Rev. E 88, 052313 (2013).
    https://doi.org/10.1103/PhysRevE.88.052313
  41. A. Chaimovich and M. S. Shell, “Tetrahedrality and structural order for hydrophobic interactions in a coarse-grained water model ,” Phys. Rev. E 89, 22140 (2014).
    https://doi.org/10.1103/PhysRevE.89.022140
  42. J. Jeon and M. S. Shell, “Self-assembly of cyclo-diphenylalanine peptides in vacuum,” J. Phys. Chem. B 118, 6644 (2014).
    https://doi.org/10.1021/jp501503x
  43. N. D. Petsev, L. G. Leal, and M. S. Shell, “Hybrid molecular-continuum simulations using smoothed dissipative particle dynamics,” J. Chem. Phys 142, 044101 (2015).
    https://doi.org/10.1063/1.4905720
  44. B. Giera, N. Henson, E. M. Kober, M. S. Shell, and T. M. Squires, “Electric Double-Layer Structure in Primitive Model Electrolytes: Comparing Molecular Dynamics with Local-Density Approximations,” Langmuir 31, 3553 (2015).
    https://doi.org/10.1021/la5048936
  45. S. P. Carmichael and M. S. Shell, “Entropic (de)stabilization of surface-bound peptides conjugated with polymers,” J. Chem. Phys. 143, 243103 (2015).
    https://doi.org/10.1063/1.4929592
  46. T. T. Foley, M. S. Shell, and W. G. Noid, “The impact of resolution upon entropy and information in coarse-grained models,” J. Chem. Phys. 143, 243104 (2015).
    https://doi.org/10.1063/1.4929836
  47. N. D. Petsev, L. G. Leal, and M. S. Shell, “Multiscale Simulation of Ideal Mixtures Using Smoothed Dissipative Particle Dynamics,” J. Chem. Phys 144, 084155 (2016).
    https://doi.org/10.1063/1.4942499
  48. M. S. Shell, “Coarse-graining with the relative entropy,” invited chapter in Advances in Chemical Physics, A. Dinner and S. A. Rice, editors, volume 161, 395-442(2016).  – Invited Review
    https://doi.org/10.1002/9781119290971.ch5
  49. T. Sanyal and M. S. Shell, “Coarse-Grained Models Using Local-Density Potentials Optimized with the Relative Entropy: Application to Implicit Solvation,” J. Chem. Phys. 145, 034109 (2016).
    https://doi.org/10.1063/1.4958629
  50. J. Jeon and M. S. Shell, “Peptide binding landscapes: specificity and homophilicity across sequence space in a lattice model,” Phys. Rev. E 94, 042405 (2016).
    https://doi.org/10.1103/PhysRevE.94.042405
  51. M. Robinson, J. I. Monroe, and M. S. Shell, “Are modern protein force fields and implicit solvation models additive?” J. Chem. Theory & Computation 12, 5631 (2016).
    https://doi.org/10.1021/acs.jctc.6b00788
  52. P. Stock, J. I. Monroe, T. Utzig, D. J. Smith, M. S. Shell, and M. Valtiner, “Unraveling hydrophobic interactions at the molecular scale using force spectroscopy and molecular dynamics simulations,” ACS Nano 11, 2586 (2017).
    https://doi.org/10.1021/acsnano.6b06360
  53. D. J. Smith and M. S. Shell, “Can Simple Interaction Models Predict Sequence-Dependent Effects in Peptide Homodimerization?” J. Chem. Phys. 121, 5928 (2017).
    https://doi.org/10.1021/acs.jpcb.7b03186
  54. N. D. Petsev, L. G. Leal, and M. S. Shell, “Coupling Discrete and Continuum Concentration Particle Models for Multiscale and Hybrid Molecular-Continuum Simulations,” J. Chem. Phys 147, 234112 (2017).  – JCP Editor’s Choice for 2017
    https://doi.org/10.1063/1.5001703 
  55. A. M. Schrader, J. I. Monroe, R. Sheil, H. A. Dobbs, T. J. Keller, Y. Li, S. Jain, M. S. Shell, J. N. Israelachvili, S. Han, “Surface chemical heterogeneity modulates silica surface hydration,” Proceedings of the National Academy of Sciences USA 115, 2890 (2018).
    https://doi.org/10.1073/pnas.1722263115
  56. T. Sanyal and M. S. Shell, “Transferable coarse-grained models of liquid-liquid equilibrium using local density potentials optimized with the relative entropy,” J. Phys. Chem. B 122, 5678 (2018).  https://doi.org/10.1021/acs.jpcb.7b12446
  57. D. J. Smith, L. G. Leal, S. Mitragotri, and M. S. Shell, “Nanoparticle Transport Across Model Cellular Membranes: When Do Solubility-Diffusion Models Break Down?”, J. Physics D: Appl. Physics 51, 29400 (2018).
    https://doi.org/10.1088/1361-6463/aacac9
  58. J. I. Monroe and M. S. Shell, “Computational discovery of chemically patterned surfaces that effect unique hydration water dynamics,” Proceedings of the National Academy of Sciences USA 115, 8093 (2018).
    https://doi.org/10.1073/pnas.1807208115
  59. M. P. Howard, W. F. Reinhart, T. Sanyal, M. S. Shell, A. Nikoubashman, and A. Z. Panagiotopoulos, “Evaporation induced assembly of colloidal crystals,” J. Chem. Phys. 149, 094901 (2018).
    https://doi.org/10.1063/1.5043401
  60. N. D. Petsev, L. G. Leal, and M. S. Shell, “An Integrated Boundary Approach for Colloidal Suspensions Simulated Using Smoothed Dissipative Particle Dynamics,” Computers and Fluids 179, 672 (2019).
    https://doi.org/10.1016/j.compfluid.2018.11.025

Book Chapters

  1. C. Chipot, M. S. Shell, and A. Pohorille, “Introduction,” invited chapter in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
    https://www.springer.com/us/book/9783540384472
  2. 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.
    https://www.springer.com/us/book/9783540384472
  3. M. S. Shell and A. Z. Panagiotopoulos, “Methods for examining phase equilibria,” invited chapter in Free energy calculations: theory and applications in chemistry and biology, Springer, 2006.
    https://www.springer.com/us/book/9783540384472

Book

  1. M. S. Shell, Thermodynamics and Statistical Mechanics: An Integrated Approach, Cambridge, 2015.
    http://www.cambridge.org/9781107656789

Other Publications

  1. 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).
    https://doi.org/10.1103/PhysRevE.71.033102