Contact Information Email: Click to Mail Phone: (805) 893-4346 Office Location: 3321 Engineering II Address: Mail Code 5080 Chemical Engineering Dept. University of California Santa Barbara, CA 93106-5080 USA

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Course Pages ChE 210A Thermodynamics and Statistical Mechanics ChE 110A Chemical Engineering Thermodynamics ChE 210D Principles of Modern Molecular Simulation Methods ChE 170 Molecular and Cell Biology for Engineers

Education & Honors

BS: B.S. Chemical Engineering, Carnegie Mellon University, 2000

PhD: Ph.D. Chemical Engineering, Princeton University, 2005

Honors:
NSF CAREER Award, 2009
Camille and Henry Dreyfus New Faculty Award, 2007
Porter Ogbus Jacobus Honorific Fellowship (Princeton), 2004
Wu Fellowship (Princeton), 2000
Hertz Foundation Graduate Fellowship, 2000

Research

We use molecular simulation and theory to understand multi-scale, hierarchical interactions in complex biomolecular systems, with a specific focus on proteins and peptides. In particular, our group develops general methods for predicting peptide structure and self-assembly behavior, and is designing new approaches for linking simulations and theories across multiple length and time scales in fundamental, rigorous ways. These efforts are used to understand (1) folding and design principles in proteins; (2) peptide structure, association, self-assembly, and aggregation; and (3) the role of water and the hydrophobic interaction in driving biological recognition and self-assembly processes.

• protein biophysics
• condensed matter theory
• molecular simulation

Publications

Online Publication List

E. Lin and M. S. Shell, "Convergence and heterogeneity in replica exchange molecular dynamics peptide folding simulations," J. Chem. Theory Comput. 5, 2062 (2009).

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).

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).

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, 1 (2009).

M. S. Shell, "The relative entropy is fundamental to thermodynamic ensemble optimization," J. Chem. Phys. 129, 144108 (2008).

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).

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).

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, "Saddles in the energy landscape: extensivity and thermodynamic formalism," Phys. Rev. Lett. 92, 035506 (2004).

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).

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).