Publications:
journal articles
 M.
S. Shell, P. G. Debenedetti, and A. Z.
Panagiotopoulos,
“Molecular structural order and anomalies in liquid
silica,” Phys. Rev. E 66, 011202 (2002).
 M.
S. Shell, P. G. Debenedetti, and A. Z.
Panagiotopoulos,
“Generalization of the WangLaudau method for offlattice
simulations,” Phys. Rev. E 66, 056703 (2002).
 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).
 F.
Sciortino,
E. La Nave, P. Tartaglia, M. S. Shell,
and P.
G. Debenedetti, “Test of nonequilibrium thermodynamics in
glassy
systems: the softsphere case,” Phys. Rev. E 68, 032103
(2003).
 M.
S. Shell, P. G. Debenedetti, and A. Z.
Panagiotopoulos,
“An improved MonteCarlo method for direct calculation of the
density of states,” J. Chem. Phys. 119, 9406 (2003).
 P.
G. Debenedetti, F. H. Stillinger, and M. S. Shell,
“Model energy landscapes,” J. Phys. Chem. B 107,
14434 (2003).
 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).
 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).
 M. S.
Shell and P. G. Debenedetti,
“Thermodynamics
and the glass transition in model energy
landscapes,” Phys.
Rev. E 69, 051102 (2004).
 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).
 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 softsphere case,”
Phys.
Rev. E 71, 033102 (2005).
 M.
S. Shell, P. G. Debenedetti, and F. H. Stillinger,
“Novel computational probes of diffusive motion,”
J. Phys.
Chem. B 109, 21329 (2005).
 M.
S. Shell, P. G. Debenedetti, and F. H. Stillinger,
“Dynamic heterogeneity and nonGaussian diffusion in a model
supercooled liquid,” J. Phys.: Condens. Matter 17, S4035
(2005).
 M.
S. Shell, P. G. Debenedetti, and A. Z.
Panagiotopoulos,
“Computational characterization of the sequence landscape in
simple protein alphabets,” Proteins 62, 232 (2006).
 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).
 C.
Chipot, M. S. Shell, and A. Pohorille,
“Introduction,”
invited chapter in Free energy calculations: theory and applications in
chemistry and biology, Springer, 2006.
 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.
 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.
 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).
 K.
A.
Dill, S. B. Ozkan, M. S. Shell, and T. A. Weikl, "The protein folding
problem," Ann. Rev. Biophys. 37, 289 (2008).
 M.
S. Shell, “The relative entropy is
fundamental to thermodynamic ensemble optimization,” J. Chem.
Phys. 129, 144108 (2008).
 M.
S. Shell, S. B. Ozkan, V. Voelz, A. Wu, and
K. Dill, “Blind test of physicsbased prediction of protein
structures”, Biophys. J. 96, 917 (2009).
 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 MMP14 targeted
SPECT imaging probe”, Bioorganic and Medicinal Chemistry 17, 653
(2009).
 V.
Voelz, M. S. Shell, and K. Dill,
“Predicting native fragments from short peptide fragment
simulations”, PLoS Comput. Biol. 5, e1000281 (2009).
 A.
Chaimovich and M.S. Shell, “Anomalous waterlike behavior in
sphericallysymmetric water models optimized with the relative
entropy,” Phys. Chem. Chem. Phys 11, 1901 (2009).
 E.
Lin and M. S. Shell, “Convergence and heterogeneity in peptide
folding with replica exchange molecular dynamics,”J. Chem. Theory
Comput. 5, 2062 (2009).
 A.
Chaimovich and M. S. Shell, “The relative entropy as a universal
metric for multiscale errors,” Phys. Rev. E. 81, 060104 (2010).
 M.
S. Shell, “A replicaexchange approach to computing peptide
conformational free energies,” Mol. Simulation 36, 505 (2010).
 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).
 E. Lin
and M. S. Shell, “Can peptide folding simulations provide
predictive information for aggregation propensity?”, J. Phys.
Chem. B. 114, 11899 (2010).
 J. Gee
and M. S. Shell, “Twodimensional replica exchange approach to
peptidepeptide interactions,” J. Chem. Phys 134, 064112 (2011). Research Highlights Article in JCP
 A.
Chaimovich and M. S. Shell, “Coarsegraining errors and
optimization using a relative entropy framework,” J. Chem. Phys.
134, 094112 (2011). Research
Highlights Article in JCP
 A. PritchardBell
and M. S. Shell, “Smoothing protein energy landscapes by
integrating folding models with structure prediction,” Biophys.
J. 101, 2251 (2011).
 S.
Carmichael and M. S. Shell, “A New Multiscale Algorithm and its
Application to CoarseGrained Peptide Models for SelfAssembly,”
J. Phys. Chem. B 116, 8383 (2012). Invited article in special issue on
Multiscale Modeling
 J.
Jeon and M. S. Shell, “Charge effects on the fibril forming
peptide KTVIIE: a twodimensional replica exchange simulation
study,” Biophys. J. 102, 1952 (2012).
 C. C. Fu, P. M.
Kulkarni, M. S. Shell, and L. G. Leal, “A Test of Systematic
CoarseGraining of Molecular Dynamics Simulations: Thermodynamic
Properties,” J. Chem. Phys. 137, 164106 (2012).
 M. S. Shell,
“Systematic coarsegraining of potential energy landscapes and
dynamics in liquids,” J. Chem. Phys. 137, 084503 (2012).
 J. Jeon, C.
E. Mills, and M. S. Shell, "Molecular insights into diphenylalanine
nanotube assembly: allatom simulations of oligomerization," J. Phys.
Chem. B 117, 3935 (2013).
 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).
 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).
 C. C. Fu, P. M.
Kulkarni, M. S. Shell, and L. G. Leal, “A test of systematic
coarsegraining of molecular dynamics simulations: Transport
Properties,” J. Phys. Chem. 139, 094107 (2013).
 B. Giera, N.
Henson, E. M. Kober, T. M. Squires, and M. S. Shell, “Modelfree
test of localdensity meanfield behavior in electric double
layers,” Phys. Rev. E 88, 011301 (2013).
Publications: books and
book chapters
 C.
Chipot, M. S. Shell, and A. Pohorille,
“Introduction,” in Free energy
calculations: theory and applications in
chemistry and biology, Springer, 2006.
 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.
 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.

