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

Journal Articles

  1. S. Najafi, S. Lobo, M.S. Shell, J.E. Shea “Context Dependency of Hydrophobicity in Intrinsically Disordered Proteins: Insights from a New Dewetting Free Energy-Based Hydrophobicity Scale” J. Physical. Chem. B (2025).
    https://doi.org/10.1021/acs.jpcb.4c06399
  2. C. Li, E.A. Murphy, S.J. Skala, K.T. Delaney, C.J. Hawker, M.S. Shell, G.H. Fredrickson “Accelerated Prediction of Phase Behavior for Block Copolymer Libraries Using a Molecularly Informed Field Theory” J. Am. Chem. Soc. 146, 43 (2024).
    https://doi.org/10.1021/jacs.4c11258
  3. T.C. Huang, R. Levenson, Y. Li, P. Kohl, D.E. Morse, M.S. Shell, M.E. Helgeson “A colloidal model for the equilibrium assembly and liquid-liquid phase separation of the reflectin A1 protein” Biophys. J. 123, 18 (2024).
    https://doi.org/10.1016/j.bpj.2024.07.004
  4. M.V.T. Nguyen, N. Sherck, S. Köhler, E. Schreiner, R. Gupta, G.H. Fredrickson, M.S. Shell, “Multiscale Computational Study of Cellulose Acetate–Water Miscibility: Insights from Molecularly Informed Field-Theoretic Modeling” Biomacromolecules 25, 9 (2024).
    https://doi.org/10.1021/acs.biomac.4c00474
  5. D.D. Mahanta, D.R. Brown, T. Webber, S. Pezzotti, G. Schwaab, S. Han, M.S. Shell, M. Havenith, “Bridging the Gap in Cryopreservation Mechanism: Unraveling the Interplay between Structure, Dynamics, and Thermodynamics in Cryoprotectant Aqueous Solutions” J. Physical. Chem. B 128, 15 (2024).
    https://doi.org/10.1021/acs.jpcb.4c00264
  6. S. Jiao and M.S. Shell, “Inverse design of pore wall chemistry and topology through active learning of surface group interactions” J. Chem. Physical 160, 12 (2024).
    https://doi.org/10.1063/5.0200900
  7. K. Yang, D.M. Rivera Mirabal, R.V. Garcia, N.W. Vlahakis, P.H. Nguyen, S.D. Mengel, M. Mecklenburg, J.A. Rodriguez, M.S. Shell, C.J. Hawker, R.A. Segalman, “Crystallization-Induced Flower-like Superstructures via Peptoid Helix Assembly”, ACS Macro Lett. 13, 4 (2024).
    https://doi.org/10.1021/acsmacrolett.4c00039
  8. K. M. Kidder, M.S. Shell, W.G. Noid, “Surveying the energy landscape of coarse-grained mappings”, J. Chem. Phys. 160, 5 (2024).
    https://doi.org/10.1063/5.0182524
  9. S. Jiao, D.C. Robinson Brown, M.S. Shell, “Relationships between Water’s Structure and Solute Affinity at Polypeptoid Brush Surfaces”, Langmuir 40, 761-771. (2024).
    https://doi.org/10.1021/acs.langmuir.3c02971
  10. J.D. Moon, T.R. Webber, D.R. Brown, P.M. Richardson, T.M. Casey, R.A. Segalman, M.S. Shell, S. Han, “Nanoscale water–polymer interactions tune macroscopic diffusivity of water in aqueous poly(ethylene oxide) solutions” Chem. Sci. (2024).
    https://doi.org/10.1039/d3sc05377f
  11. M. Nguyen, K. Dolph, K. T Delaney, K. Shen, N. Sherck, S. Köhler, R. Gupta, M. B. Francis, M.S. Shell, G.H. Fredrickson “Molecularly informed field theory for estimating critical micelle concentrations of intrinsically disordered protein surfactants” J. Chem. Phys. 159, 24 (2023).
    https://doi.org/10.1063/5.0178910
  12. E. Pretti and M.S. Shell, “Mapping the configurational landscape and aggregation phase behavior of the tau protein fragment PHF6”, PNAS 120, 48. (2023)
    https://doi.org/10.1073/pnas.2309995120
  13. M. Nguyen, K. Shen, N. Sherck, S. Köhler, R. Gupta, K.T. Delaney, M.S. Shell, G. H. Fredrickson, “A molecularly informed field-theoretic study of the complexation of polycation PDADMA with mixed micelles of sodium dodecyl sulfate and ethoxylated surfactants”, EPJE 46, 75. (2023)
    https://doi.org/10.1140/epje/s10189-023-00332-4
  14. D. D. Mahanta, D.C. Robinson Brown, S. Pezzotti, S. Han, G. Schwaab, MS. Shell, M. Havenith, “Local solvation structures govern the mixing thermodynamics of glycerol–water solutions”, Chem. Sci. 14,  7381-7392. (2023)
    https://doi.org/10.1039/D3SC00517H
  15. D.C. Robinson Brown, T. R. Webber, S. Jiao, D.M. Rivera Mirabal, S. Han, M.S. Shell, “Relationships between Molecular Structural Order Parameters and Equilibrium Water Dynamics in Aqueous Mixtures”, J. Phys. Chem. B. 127,  4577–4594 (2023).
    https://doi.org/10.1021/acs.jpcb.3c00826
  16. K. Shen, M. Nguyen, N. Sherck, B. Yoo, S. Köhler, J. Speros, K. T. Delaney , M.S. Shell, G. H. Fredrickson, “Predicting surfactant phase behavior with a molecularly informed field theory”, J. Colloid Interface Sci. 638, 84-98 (2023).
    https://doi.org/10.1016/j.jcis.2023.01.015
  17. S. Jiao, L.E. Katz, and M.S. Shell, “Inverse Design of Pore Wall Chemistry To Control Solute Transport and Selectivity”, ACS Cent. Sci. 8, 12, 1609–1617 (2022) .
    https://doi.org/10.1021/acscentsci.2c01011
  18. J.S. Straub, M.S. Nowotarski, J. Lu, T. Sheth, S. Jiao, M. PA Fisher, M.S. Shell, M.E. Helgeson, A. Jerschow, S. Han, “Phosphates form spectroscopically dark state assemblies in common aqueous solutions”, PNAS 120 (2022).
    https://doi.org/10.1073/pnas.2206765120
  19. M. Nguyen, N. Sherck, K. Shen, C.E.R. Edwards, B. Yoo, S. Köhler, J.C. Speros, M.E. Helgeson, K.T. Delaney, M.S. Shell, and G. H. Fredrickson, “Predicting Polyelectrolyte Coacervation from a Molecularly Informed Field-Theoretic Model”, Macromolecules. 55, 21, 9868–9879. (2022)
    https://doi.org/10.1021/acs.macromol.2c01759
  20. S. Jiao, D.M. Rivera Mirabal, A.J. DeStefano, R.A. Segalman, S. Han, M.S. Shell, “Sequence Modulates Polypeptoid Hydration Water Structure and Dynamics”, Biomacromolecules.  23, 4, 1745–1756. (2022).
    https://doi.org/10.1021/acs.biomac.1c01687
  21. H. Moon, R. P. Collanton, J. I. Monroe, T. M. Casey, M. S. Shell, S. Han, S. L. Scott, “Evidence for Entropically Controlled Interfacial Hydration in Mesoporous Organosilicas”, J. Am. Chem. Soc. 144, 4, 1766–1777. (2022).
    https://doi.org/10.1021/jacs.1c11342
  22. E. Pretti, M. S. Shell, “A microcanonical approach to temperature-transferable coarse-grained models using the relative entropy”, J. Chem. Phys. 155, 094102 (2021).
    https://doi.org/10.1063/5.0057104
  23. S. Jiao, A. DeStefano, J. I. Monroe, M. Barry, N. Sherck, T. Casey, R. A. Segalman, S. Han, M. S. Shell, “Quantifying Polypeptoid Conformational Landscapes through Integrated Experiment and Simulation”, Macromolecules. 54, 5011 (2021).
    https://doi.org/10.1021/acs.macromol.1c00550
  24. N. Sherck, K. Shen, M. Nguyen, B. Yoo, S. Köhler, J. C. Speros, K. T. Delaney, M. S. Shell, G. H. Fredrickson, “Molecularly Informed Field Theories from Bottom-up Coarse-Graining”, ACS Macro. Lett. 10, 576 (2021).
    https://doi.org/10.1021/acsmacrolett.1c00013
  25. J. I. Monroe, S. Jiao, R. J. Davis, D. Robinson-Brown, L. E. Katz, M. S. Shell, “Affinity of small-molecule solutes to hydrophobic, hydrophilic, and chemically patterned interfaces in aqueous solution”, PNAS, 118, e2020205118 (2021).
    https://doi.org/10.1073/pnas.2020205118
  26. R. Sujanani, M. R. Landsman, S. Jiao, J. D. Moon, M. S. Shell, D. F. Lawler, L. E. Katz, B. D. Freeman, “Designing solute-tailored selectivity in membranes: perspectives for water reuse and resource recovery”, ACS. Macro. Lett. 9, 1709 (2020).
    https://doi.org/10.1021/acsmacrolett.0c00710
  27. N. Sherck, T. Webber, D. Robinson Brown, T. Keller, M. Barry, A. DeStefano, S. Jiao, R. A. Segalman, G. H. Fredrickson,  M. S. Shell, S. Han, “End-to-End Distance Probability Distributions of Dilute Poly(ethylene oxide) in Aqueous Solution”, J. Am. Chem. Soc. 142, 19631 (2020).
    https://doi.org/10.1021/jacs.0c08709
  28. M. Giulini, R. Menichetti, M. S. Shell, R. Potestio, “An information-theory-based approach for optimal model reduction of biomolecules”, J. Chem. Theory Comput. 16, 6795 (2020).
    https://doi.org/10.1021/acs.jctc.0c00676
  29. K. Shen, N. Sherck, M. Nguyen, B. Yoo, S. Köhler, J. Speros, K. T. Delaney, G. H. Fredrickson, M. S. Shell, “Learning composition-transferable coarse-grained models: Designing external potential ensembles to maximize thermodynamic information”, J. Chem. Phys. 153, 154116 (2020).
    https://doi.org/10.1063/5.0022808
  30. J. I. Monroe, H. W. Hatch, N. A. Mahynski, M. S. Shell, V. K. Shen, “Extrapolation and interpolation strategies for efficiently estimating structural observables as a function of temperature and density”, J. Chem. Phys. 153, 144101 (2020). 
    https://doi.org/10.1063/5.0014282
  31. T. T. Foley, K. M. Kidder, M. S. Shell, W. G. Noid, “Exploring the landscape of model representations”, PNAS. 117, 24061 (2020).
    https://doi.org/10.1073/pnas.2000098117
  32. N. D. Petsev, L. G. Leal, M. S. Shell, “Universal gas adsorption mechanism for flat nanobubble morphologies”, Phys. Rev. Lett. 125, 146101 (2020).
    https://doi.org/10.1103/PhysRevLett.125.146101
  33. J. I. Monroe, M. Barry, A. DeStefano, P. A. Gokturk, S. Jiao, D. Robinson-Brown, T. Webber, E. J. Crumlin, S. Han, M. S. Shell, “Water structure and properties at hydrophilic and hydrophobic surfaces”, Annu. Rev. Chem. Biomol. Eng. 11, 523 (2020).
    https://doi.org/10.1146/annurev-chembioeng-120919-114657
  34. J. I. Monroe, M. S. Shell, “Decoding signatures of structure, bulk thermodynamics, and solvation in three-body angle distributions of rigid water models”, J. Chem. Phys. 151, 094501 (2019). https://doi.org/10.1063/1.5111545
  35. T. Sanyal, J. Mittal, M. S. Shell, “A hybrid, bottom-up, structurally accurate, G-like coarse-grained protein model”, J. Chem. Phys. 151, 044111 (2019).
    https://doi.org/10.1063/1.5108761
  36. D. Rosenberger, T. Sanyal, M. S. Shell, N. FA. van der Vegt, “Transferability of local density-assisted implicit solvation models for homogeneous fluid mixtures”, J. Chem. Theory Comput. 15, 2881 (2019)
    https://doi.org/10.1021/acs.jctc.8b01170
  37. 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
  38. 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, 209902 (2018). https://doi.org/10.1063/1.5043401
  39. 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
  40. 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
  41. 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
  42. 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
  43. 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 
  44. 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
  45. 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
  46. 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
  47. 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
  48. 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
  49. 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
  50. 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
  51. 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
  52. 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
  53. 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
  54. 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
  55. 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
  56. 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
  57. 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
  58. 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
  59. 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
  60. 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
  61. 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
  62. 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
  63. 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
  64. 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
  65. 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
  66. 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
  67. 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
  68. 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
  69. 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
  70. 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
  71. 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
  72. 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
  73. 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
  74. 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
  75. 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
  76. 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
  77. 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
  78. 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
  79. 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
  80. 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
  81. 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
  82. 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
  83. 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
  84. 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
  85. 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
  86. 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
  87. 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
  88. 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
  89. 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
  90. 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
  91. 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
  92. 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
  93. 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
  94. 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
  95. 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
  96. 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

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