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Ken A. Dill
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Journal Articles

Building Markov state models using optimal transport theory

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Purushottam D. Dixit, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 150, 054105 (2019)
https://doi.org/10.1063/1.5086681
Published: February 2019
View articletitled, Building Markov state models using optimal transport theory
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Journal Articles

Perspective: Maximum caliber is a general variational principle for dynamical systems

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Purushottam D. Dixit, Jason Wagoner, Corey Weistuch, Steve Pressé, Kingshuk Ghosh, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 148, 010901 (2018)
https://doi.org/10.1063/1.5012990
Published: January 2018
View articletitled, Perspective: Maximum caliber is a general variational principle for dynamical systems
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Journal Articles

Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes

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Christian Holm, Gerhard Gompper, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 242901 (2015)
https://doi.org/10.1063/1.4938430
Published: December 2015
View articletitled, Preface: Special Topic on Coarse Graining of Macromolecules, Biopolymers, and Membranes
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Journal Articles

Constraint methods that accelerate free-energy simulations of biomolecules

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Alberto Perez, Justin L. MacCallum, Evangelos A. Coutsias, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 243143 (2015)
https://doi.org/10.1063/1.4936911
Published: December 2015
View articletitled, Constraint methods that accelerate free-energy simulations of biomolecules
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Journal Articles

Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics

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Michael J. Hazoglou, Valentin Walther, Purushottam D. Dixit, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 051104 (2015)
https://doi.org/10.1063/1.4928193
Published: August 2015
View articletitled, Communication: Maximum caliber is a general variational principle for nonequilibrium statistical mechanics
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Includes: Supplementary data
Journal Articles

Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion

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Libo Li, Christopher J. Fennell, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 141, 22D518 (2014)
https://doi.org/10.1063/1.4900890
Published: November 2014
View articletitled, Small molecule solvation changes due to the presence of salt are governed by the cost of solvent cavity formation and dispersion
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Includes: Supplementary data
Journal Articles

Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects

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Gabriel J. Rocklin, David L. Mobley, Ken A. Dill, Philippe H. Hünenberger
Journal: The Journal of Chemical Physics
J. Chem. Phys. 139, 184103 (2013)
https://doi.org/10.1063/1.4826261
Published: November 2013
View articletitled, Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: An accurate correction scheme for electrostatic finite-size effects
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Includes: Supplementary data
Journal Articles

Separated topologies—A method for relative binding free energy calculations using orientational restraints

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Gabriel J. Rocklin, David L. Mobley, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 138, 085104 (2013)
https://doi.org/10.1063/1.4792251
Published: February 2013
View articletitled, Separated topologies—A method for relative binding free energy calculations using orientational restraints
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Includes: Supplementary data
Journal Articles

Markov processes follow from the principle of maximum caliber

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Hao Ge, Steve Pressé, Kingshuk Ghosh, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 136, 064108 (2012)
https://doi.org/10.1063/1.3681941
Published: February 2012
View articletitled, Markov processes follow from the principle of maximum caliber
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Journal Articles

A statistical mechanical theory for a two-dimensional model of water

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Tomaz Urbic, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 132, 224507 (2010)
https://doi.org/10.1063/1.3454193
Published: June 2010
View articletitled, A statistical mechanical theory for a two-dimensional model of water
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Journal Articles

Theory for the three-dimensional Mercedes-Benz model of water

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Alan Bizjak, Tomaz Urbic, Vojko Vlachy, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 131, 194504 (2009)
https://doi.org/10.1063/1.3259970
Published: November 2009
View articletitled, Theory for the three-dimensional Mercedes-Benz model of water
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Journal Articles

The Second Law and Biology

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Ken A. Dill
Journal: AIP Conference Proceedings
AIP Conf. Proc. 1033, 90–110 (2008)
https://doi.org/10.1063/1.2979068
Published: August 2008
View articletitled, The Second Law and Biology
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Journal Articles

Maximum Caliber: A variational approach applied to two-state dynamics

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Gerhard Stock, Kingshuk Ghosh, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 128, 194102 (2008)
https://doi.org/10.1063/1.2918345
Published: May 2008
View articletitled, Maximum Caliber: A variational approach applied to two-state dynamics
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Journal Articles

Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics

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John D. Chodera, Nina Singhal, Vijay S. Pande, Ken A. Dill, William C. Swope
Journal: The Journal of Chemical Physics
J. Chem. Phys. 126, 155101 (2007)
https://doi.org/10.1063/1.2714538
Published: April 2007
View articletitled, Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics
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Journal Articles

On the use of orientational restraints and symmetry corrections in alchemical free energy calculations

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David L. Mobley, John D. Chodera, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 125, 084902 (2006)
https://doi.org/10.1063/1.2221683
Published: August 2006
View articletitled, On the use of orientational restraints and symmetry corrections in alchemical free energy calculations
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Journal Articles

Teaching the principles of statistical dynamics

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Kingshuk Ghosh, Ken A. Dill, Mandar M. Inamdar, Effrosyni Seitaridou, Rob Phillips
Journal: American Journal of Physics
Am. J. Phys. 74, 123–133 (2006)
https://doi.org/10.1119/1.2142789
Published: February 2006
View articletitled, Teaching the principles of statistical dynamics
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Journal Articles

Statistical mechanics of pseudoknot polymers

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Adam Lucas, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 119, 2414–2421 (2003)
https://doi.org/10.1063/1.1587129
Published: July 2003
View articletitled, Statistical mechanics of pseudoknot polymers
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Journal Articles

Predicting water’s phase diagram and liquid-state anomalies

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Thomas M. Truskett, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 117, 5101–5104 (2002)
https://doi.org/10.1063/1.1505438
Published: September 2002
View articletitled, Predicting water’s phase diagram and liquid-state anomalies
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Journal Articles

Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion

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Kevin A. T. Silverstein, Ken A. Dill, A. D. J. Haymet
Journal: The Journal of Chemical Physics
J. Chem. Phys. 114, 6303–6314 (2001)
https://doi.org/10.1063/1.1355997
Published: April 2001
View articletitled, Hydrophobicity in a simple model of water: Entropy penalty as a sum of competing terms via full, angular expansion
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Journal Articles

Symmetry and designability for lattice protein models

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Tairan Wang, Jonathan Miller, Ned S. Wingreen, Chao Tang, Ken A. Dill
Journal: The Journal of Chemical Physics
J. Chem. Phys. 113, 8329–8336 (2000)
https://doi.org/10.1063/1.1315324
Published: November 2000
View articletitled, Symmetry and designability for lattice protein models
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