Selected Publications of Ken A. Dill - The Journal of Physical

Special Issue Preface Cite This: J. Phys. Chem. B 2018, 122, 5269−5277

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Selected Publications of Ken A. Dill 299. E. Brini, S.S. Paranahewage, C.J. Fennell, K.A. Dill, Adapting the Semi-Explicit Assembly Solvation Model for Estimating Water-Cyclohexane Partitioning with the SAMPL5 Molecules. J. Comput.-Aided Mol. Des., 30 (11): 1067−1077 (2016). 298. K. Ghosh, A.M.R. de Graff, L. Sawle, K.A. Dill, Role of Proteome Physical Chemistry in Cell Behavior. J. Phys. Chem. B, 120 (36): 9549−9563 (2016). 297. J.A. Wagoner, K.A. Dill, Molecular Motors: Power Strokes Outperform Brownian Ratchets. J. Phys. Chem. B, 120 (26): 6327−6336 (2016). 296. A. Maitra, K.A. Dill, Modeling the Overproduction of Ribosomes When Antibacterial Drugs Act on Cells. Biophys. J., 110 (3): 743−748 (2016). 295. A. Perez, J.A. Morrone, C. Simmerling, K.A. Dill, Advances in Free-Energy-Based Simulations of Protein Folding and Ligand Binding. Curr. Opin. Struct. Biol., 36: 25−31 (2016). 294. A.M.R de Graff, M.J. Hazoglou, K.A. Dill, Highly Charged Proteins: The Achilles’ Heel of Aging Proteomes. Structure, 24 (2): 329−336 (2016). 293. A. Perez, J.L. MacCallum, E.A. Coutsias, K.A. Dill, Constraint Methods That Accelerate Free-Energy Simulations of Biomolecules. J. Chem. Phys., 143 (24): 243143 (2015). 292. P.D. Dixit, A. Jain, G. Stock, K.A. Dill, Inferring Transition Rates of Networks from Populations in Continuous-Time Markov Processes. J. Chem. Theory Comput., 11 (11): 5464−5472 (2015). 291. A. Perez, J.L. MacCallum, E. Brini, C. Simmerling, K.A. Dill, Grid-Based Backbone Correction to the ff12SB Protein Force Field for Implicit-Solvent Simulations. J. Chem. Theory Comput., 11 (10): 4770−4779 (2015). 290. M.J. Hazoglou, V. Walther, P.D. Dixit, K.A. Dill, Communication: Maximum Caliber Is a General Variational Principle for Nonequilibrium Statistical Mechanics. J. Chem. Phys., 143 (5): 51104 (2015). 289. S. Pressé, K. Ghosh, J. Lee, K.A. Dill, Reply to C. Tsallis’ “Conceptual Inadequacy of the Shore and Johnson Axioms for Wide Classes of Complex Systems”. Entropy, 17 (7): 5043−5046 (2015). 288. A. Perez, J.L. MacCallum, K.A. Dill, Accelerating Molecular Simulations of Proteins Using Bayesian Inference on Weak Information. Proc. Natl. Acad. Sci. U.S.A., 112 (38): 11846−11851 (2015). 287. J.L. MacCallum, A. Perez, K.A. Dill, Determining Protein Structures by Combining Semireliable Data with Atomistic Physical Models by Bayesian Inference. Proc. Natl. Acad. Sci. U.S.A., 112 (22): 6985−6990 (2015).

312. P.D. Dixit, J. Wagoner, C. Weistuch, S. Pressé, K. Ghosh, K.A. Dill, Perspective: Maximum Caliber Is a General Variational Principle for Dynamical Systems. J. Chem. Phys., 148 (1): 010901 (2018). 311. P.D. Dixit, K.A. Dill, Caliber Corrected Markov Modeling (C2M2): Correcting Equilibrium Markov Models. J. Chem. Theory Comput., 14 (2), 1111−1119 (2018). 310. M. Kastelic, K.A. Dill, Y.V. Kalyuzhnyi, V. Vlachy, Controlling the Viscosities of Antibody Solutions through Control of Their Binding Sites. J. Mol. Liq. (in press), online 2017.11.106 (2017) 309. E. Brini, C.J. Fennell, M. Fernandez-Serra, B. Hribar-Lee, M. Lukšič, K.A. Dill, How Water’s Properties Are Encoded in Its Molecular Structure and Energies. Chem. Rev., 117 (19): 12385−12414 (2017). 308. M. Szenk, K.A. Dill, A.M.R. de Graff, Why Do FastGrowing Bacteria Enter Overflow Metabolism? Testing the Membrane Real Estate Hypothesis. Cell Syst., 5 (2): 95−104 (2017). 307. T. Urbič, K.A. Dill, Analytical Theory of the Hydrophobic Effect of Solutes in Water. Phys. Rev. E, 96: 32101 (2017). 306. E. Guseva, R.N. Zuckermann, K.A. Dill, Foldamer Hypothesis for the Growth and Sequence Differentiation of Prebiotic Polymers. Proc. Natl. Acad. Sci. U.S.A., 114 (36): E7460−E7468 (2017). 305. A. Perez, J.A. Morrone, K.A. Dill, Accelerating Physical Simulations of Proteins by Leveraging External Knowledge. Wiley Interdiscip. Rev.: Comput. Mol. Sci., 7 (5): e1309 (2017). 304. M. Santra, D.W. Farrell, K.A. Dill, Bacterial Proteostasis Balances Energy and Chaperone Utilization Efficiently. Proc. Natl. Acad. Sci. U.S.A., 114 (13): E2654−E2661 (2017). 303. J.A. Morrone, A. Perez, Q. Deng, S.N. Ha, M.K. Holloway, T.K. Sawyer, B.S. Sherborne, F.K. Brown, K.A. Dill, Molecular Simulations Identify Binding Poses and Approximate Affinities of Stapled α-Helical Peptides to MDM2 and MDMX. J. Chem. Theory Comput., 13 (2): 863−869 (2017). 302. J.A. Morrone, A. Perez, J.L. MacCallum, K.A. Dill, Computed Binding of Peptides to Proteins with MELDAccelerated Molecular Dynamics. J. Chem. Theory Comput., 13 (2): 870−876 (2017). 301. I. Bahar, R. Jernigan, K.A. Dill, Protein Actions: Principles and Modeling; Garland Science, Taylor & Francis Group, LLC, New York, NY (2017). 300. A. Perez, J.A. Morrone, E. Brini, J.L. MacCallum, K.A. Dill, Blind Protein Structure Prediction Using Accelerated Free-Energy Simulations. Sci. Adv., 2 (11): e1601274 (2016). © 2018 Ken A. Dill

Special Issue: Ken A. Dill Festschrift Published: May 31, 2018 5269

DOI: 10.1021/acs.jpcb.8b02467 J. Phys. Chem. B 2018, 122, 5269−5277

Special Issue Preface

The Journal of Physical Chemistry B 286. A. Maitra, K.A. Dill, Bacterial Growth Laws Reflect the Evolutionary Importance of Energy Efficiency. Proc. Natl. Acad. Sci. U.S.A., 112 (2): 406−411 (2015). 285. M. Kastelic, Y.V. Kalyuzhnyi, B. Hribar-Lee, K.A. Dill, V. Vlachy, Protein Aggregation in Salt Solutions. Proc. Natl. Acad. Sci. U.S.A., 112 (10): 6766−6770 (2015). 284. L. Li, K.A. Dill, C.J. Fennell, Testing the Semi-Explicit Assembly Model of Aqueous Solvation in the SAMPL4 Challenge. J. Comput.-Aided Mol. Des., 28 (3): 259−264 (2014). 283. L. Li, C. J. Fennell, K.A. Dill, Small Molecule Solvation Changes Due to the Presence of Salt Are Governed by the Cost of Solvent Cavity Formation and Dispersion. J. Chem. Phys., 141 (22): 22D518 (2014). 282. V.K. Sharma, T.W. Patapoff, B. Kabakoff, S. Pai, E. Hilario, B. Zhang, C. Li, O. Borisov, R.F. Kelley, I. Chorny, J.Z. Zhou, K.A. Dill, T.E. Swartz, In Silico Selection of Therapeutic Antibodies for Development: Viscosity, Clearance, Chemical Stability. Proc. Natl. Acad. Sci. U.S.A., 111 (52): 18601−18606 (2014). 281. S. Pressé, J. Peterson, J. Lee, P. Elms, J.L. MacCallum, S. Marqusee, C.J. Bustamante, K.A. Dill, Single Molecule Conformational Memory Extraction: P5ab RNA Hairpin. J. Phys. Chem. B, 118 (24): 6597−6603 (2014). 280. G.C. Rollins, K.A. Dill, General Mechanism of Two-State Protein Folding Kinetics. J. Am. Chem. Soc., 136 (32): 11420−11427 (2014). 279. P.D. Dixit, K.A. Dill, Inferring Microscopic Kinetic Rates from Stationary State Distributions. J. Chem. Theory Comput., 10 (8): 3002−3005 (2014). 278. M. Lukšič, C.J. Fennell, K.A. Dill, Using Interpolation for Fast and Accurate Calculation of Ion−Ion Interactions. J. Phys. Chem. B, 118 (28): 8017−8025 (2014). 277. G.J. Rocklin, D.L. Mobley, K.A. Dill, P.H. Hunenberger, 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. J. Chem. Phys., 139 (18): 184103 (2013). 276. S. Pressé, K. Ghosh, J. Lee, K.A. Dill, Principles of Maximum Entropy and Maximum Caliber in Statitistical Physics. Rev. Mod. Phys., 85 (3): 1115−1141 (2013). 275. S. Pressé, K. Ghosh, J. Lee, K.A. Dill, Nonadditive Entropies Yield Probability Distributions with Biases Not Warranted by the Data. Phys. Rev. Lett., 111 (18): 180604 (2013). 274. S. Pressé, J. Lee, K.A. Dill, Extracting Conformational Memory from Single-Molecule Kinetic Data. J. Phys. Chem. B, 117 (2): 495−502 (2013). 273. A. Roy, A. Perez, K.A. Dill, J. MacCallum, Computing the Relative Stabilities and the Per-Residue Components in Protein Conformational Changes. Structure, 22 (1): 168−175 (2013). 272. G.J. Rocklin, D.L. Mobley, K.A. Dill, Calculating the Sensitivity and Robustness of Binding Free Energy Calculations to Force Field Parameters. J. Chem. Theory Comput., 9 (7): 3072−3083 (2013). 271. G.J. Rocklin, D.L. Mobley, K.A. Dill, Separated TopologiesA Method for Relative Binding Free Energy Calculations Using Orientational Restraints. J. Chem. Phys., 138 (8): 085104 (2013). 270. G.J. Rocklin, S.E. Boyce, M. Fischer, I. Fish, D.L. Mobley, B.K. Shoichet, K.A. Dill, Blind Prediction of Charged

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Ligand Binding Affinities in a Model Binding Site. J. Mol. Biol., 425 (22): 4569−4583 (2013). J. Peterson, P. Dixit, K.A. Dill, A Maximum Entropy Framework for Nonexponential Distributions. Proc. Natl. Acad. Sci. U.S.A., 110 (51): 20380−20385 (2013). E. Kortkhonjia, R. Brandman, J.Z. Zhou, V.A. Voelz, I. Chorny, B. Kabakoff, T.W. Patapoff, K.A. Dill, T.E. Swartz, Probing Antibody Internal Dynamics with Fluorescence Anisotropy and Molecular Dynamics Simulations. mAbs, 5 (2): 306−322 (2013). K.A. Dill, J.L. MacCallum, The Protein Folding Problem, 50 Years On. Science, 338 (6110): 1042−1046 (2012). A. Perez, Z. Yang, I. Bahar, K.A. Dill, J.L. MacCallum, FlexE: Using Elastic Network Models to Compare Models of Protein Structure. J. Chem. Theory Comput., 8 (10): 3985−3991 (2012). C.W. Kehoe, C.J. Fennell, K.A. Dill, Testing the SemiExplicit Assembly Solvation Model in the SAMPL3 Community Blind Test. J. Comput. Aided Mol. Des., 26 (5): 563−568 (2012). C.J. Fennell, L. Li, K.A. Dill, Simple Liquid Models with Corrected Dielectric Constants. J. Phys. Chem. B, 116 (23): 6936−6944 (2012). G.L. Butterfoss, B. Yoo, J.N. Jaworski, I. Chorny, K.A. Dill, R.N. Zuckermann, R. Bonneau, K. Kirshenbaum, V.A. Voelz, De Novo Structure Prediction and Experimental Characterization of Folded Peptoid Pligomers. Proc. Natl. Acad. Sci. U.S.A., 109 (1): 14320−14325 (2012). J.D. Schmit, K.A. Dill, Growth Rates of Protein Crystals. J. Am. Chem. Soc., 134 (9): 3934−3937 (2012). G.J. Peterson, S. Pressé, K.S. Peterson, K.A. Dill, Simulated Evolution of Protein−Protein Interaction Networks with Realistic Topology. PLOS One, 7 (6): e39052 (2012). M. Lukšič, T. Urbič, B. Hribar-Lee, K.A. Dill, Simple Model of Hydrophobic Hydration. J. Phys. Chem. B, 116 (21): 6177−6186 (2012). H. Ge, S. Pressé, K. Ghosh, K.A. Dill, Markov Processes Follow from the Principle of Maximum Caliber. J. Chem. Phys., 136 (6): 064108 (2012). V.A. Voelz, K.A. Dill, I. Chorny, Peptoid Conformational Free Energy Landscapes from Implicit-Solvent Molecular Simulations in AMBER. Biopolymers, 96 (5): 639−650 (2011). K.A. Dill, K. Ghosh, J.D. Schmit, Physical Limits of Cells and Proteomes. Proc. Natl. Acad. Sci. U.S.A., 108 (44): 17876−17882 (2011). K.A. Dill, America Needs More Deep Innovation. ASBMB Today, (2012). http://www.asbmb.org/ asbmbtoday/asbmbtoday_article.aspx?id=15438 J.D. Schmit, S. Whitelam, K.A. Dill, Electrostatics and Aggregation: How Charge Can Turn a Crystal into a Gel. J. Chem. Phys., 135 (8): 085103 (2011). S. Pressé, K. Ghosh, K.A. Dill, Modeling Stochastic Dynamics in Biochemical Systems with Feedback Using Maximum Caliber. J. Phys. Chem. B, 115 (19): 6202− 6212 (2011). C.J. Fennell, K.A. Dill, Physical Modeling of Aqueous Solvation. J. Stat. Phys., 145 (2): 209−266 (2011). C.J. Fennell, C.W. Kehoe, K.A. Dill, Modeling Aqueous Solvation with Semi-Explicit Assembly. Proc. Natl. Acad. Sci. U.S.A., 108 (8): 3234−3239 (2011). DOI: 10.1021/acs.jpcb.8b02467 J. Phys. Chem. B 2018, 122, 5269−5277


The Journal of Physical Chemistry B 251. J. Schmit, K. Ghosh, K.A. Dill, What Drives Amyloid Molecules to Assemble into Oligomers and Fibrils? Biophys. J., 100 (2): 450−458 (2011). 250. K.A. Dill, S. Bromberg, Molecular Driving Forces: Statistical Thermodynamics in Biology, Chemistry, Physics, and Nanoscience; Garland Science, New York, NY (2nd ed. 2011). 249. Y.V. Kalyuzhnyi, V. Vlachy, K.A. Dill, Aqueous Alkali Halide Solutions: Can Osmotic Coefficients Be Explained on the Basis of the Ionic Sizes Alone? Phys. Chem. Chem. Phys., 12 (23): 6260−6266 (2010). 248. K. Ghosh, K.A. Dill, Cellular Proteomes Have Broad Distributions of Protein Stability. Biophys. J., 99 (12): 3996−4002 (2010). 247. B. Hribar-Lee, K.A. Dill, V. Vlachy, Receptacle Model of Salting-In by Tetramethylammonium Ions. J. Phys. Chem. B, 114 (46): 15085−15091 (2010). 246. S. Pressé, K. Ghosh, R. Phillips, K.A. Dill, Dynamical Fluctuations in Biochemical Reactions and Cycles. Phys. Rev. E, 82 (3): 031905 (2010). 245. G.J. Peterson, S. Pressé, K.A. Dill, Nonuniversal Power Law Scaling in the Probability Distribution of Scientific Citations. Proc. Natl. Acad. Sci. U.S.A., 107 (37): 16023− 16027 (2010). 244. T. Urbič, K.A. Dill, A Statistical Mechanical Theory for a Two-Dimensional Model of Water. J. Chem. Phys., 132 (22): 224507 (2010). 243. J.D. Schmit, K.A. Dill, The Stabilities of Protein Crystals. J. Phys. Chem. B, 114 (11): 4020−4027 (2010). 242. C.J. Fennell, C. Kehoe, K.A. Dill, Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Just Size. J. Am. Chem. Soc., 132 (1): 234−240 (2010). 241. M. Druchok, V. Vlachy, K.A. Dill, Computer Simulations of Ionenes, Hydrophobic Ions with Unusual Solution Thermodynamic Properties. The Ion-Specific Effects. J. Phys. Chem. B, 113 (43): 14270−14276 (2009). 240. D.L. Mobley, C.I. Bayly, M.D. Cooper, K.A. Dill, Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations. J. Phys. Chem. B, 113 (14): 4533−4537 (2009). 239. J.L. MacCallum, L. Hua, M.J. Schnieders, V.J. Pande, M.P. Jacobson, K.A. Dill, Assessment of the ProteinStructure Refinement Category in CASP8. Proteins, 77 (S9): 66−80 (2009). 238. A. Bizjak, T. Urbič, V. Vlachy, K.A. Dill, Theory for the Three-Dimensional Mercedes-Benz Model of Water. J. Chem. Phys., 131 (19): 194504 (2009). 237. S.E. Boyce, D.L. Mobley, G.J. Rocklin, A.P. Graves, K.A. Dill, B.K. Shoichet, Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site. J. Mol. Biol., 394 (4): 747−763 (2009). 236. C.J. Fennell, A. Bizjak, V. Vlachy, K.A. Dill, S. Sarupria, S. Rajamani, S. Garde, Additions and Corrections to Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions. J. Phys. Chem. B, 113 (44): 14837− 14838 (2009). 235. M. Druchok, V. Vlachy, K.A. Dill, Explicit-Water Molecular Dynamics Study of a Short-Chain 3,3 Ionene in Solutions with Sodium Halides. J. Chem. Phys., 130 (13): 134903 (2009). 234. K. Ghosh, K.A. Dill, Computing Protein Stabilities from Their Chain Lengths. Proc. Natl. Acad. Sci. U.S.A., 106 (26): 10649−10654 (2009).

233. D. Wu, K. Ghosh, M. Inamdar, H.J. Lee, S. Fraser, K.A. Dill, R. Phillips, Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes. Phys. Rev. Lett., 103 (5): 050603 (2009). 232. C.J. Fennell, A. Bizjak, V. Vlachy, K.A. Dill, Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions. J. Phys. Chem. B, 113 (19): 6782−6791 (2009). 231. D.L. Mobley, C.L. Bayly, M.D. Cooper, M.R Shirts, K.A. Dill, Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. J. Chem. Theory Comput., 5 (2): 350−358 (2009). 230. M.S. Shell, S.B. Ozkan, V. Voelz, G.A. Wu, K.A. Dill, Blind Test of Physics-Based Prediction of Protein Structures. Biophys. J., 96 (3): 917−924 (2009). 229. K. Ghosh, K.A. Dill, Theory for Protein Folding Cooperativity: Helix Bundles. J. Am. Chem. Soc., 131 (6): 2306−2312 (2009). 228. D.L. Mobley, K.A. Dill, Binding of Small-Molecule Ligands to Proteins: “What You See” Is Not Always “What You Get”. Structure, 17 (4): 489−498 (2009). 227. B. Hribar-Lee, V. Vlachy, K.A. Dill, Modeling Hofmeister Effects. Acta Chim. Slov., 56 (1): 196−202 (2009). 226. V.A. Voelz, M.S. Shell, K.A. Dill, Predicting Peptide Structures in Native Proteins from Physical Simulations of Fragments. PLOS Comput. Biol., 5 (2): e1000281 (2009). 225. M.S. Shell, R. Ritterson, K.A. Dill, A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation. J. Phys. Chem. B, 112 (22): 6878−6886 (2008). 224. G. Albert Wu, E.A. Coutsias, K.A. Dill, Iterative Assembly of Helical Proteins by Optimal Hydrophobic Packing. Structure, 16 (8): 1257−1266 (2008). 223. B.-C. Lee, T.K. Chu, K.A. Dill, R.N. Zuckermann, Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer. J. Am. Chem. Soc., 130 (27): 8847−8855 (2008). 222. T. Urbič, T. Urbič, F. Avbelj, K.A. Dill, Molecular Simulations Find Stable Structures in Fragments of Protein G. Acta Chim. Slov., 55: 385−395 (2008). 221. G. Stock, K. Ghosh, K.A. Dill, Maximum Caliber: A Variational Approach Applied to Two-State Dynamics. J. Chem. Phys., 128 (19): 194102 (2008). 220. K.A. Dill, S.B. Ozkan, M.S. Shell, T.R. Weikl, The Protein Folding Problem. Annu. Rev. Biophys., 37: 289−316 (2008). 219. D.L. Mobley, A.E. Barber II, C.J. Fennell, K.A. Dill, Charge Asymmetries in Hydration of Polar Solutes. J. Phys. Chem. B, 112 (8): 2405−2414 (2008). 218. D.L. Mobley, J.D. Chodera, K.A. Dill, Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules. J. Phys. Chem. B, 112 (3): 938−946 (2008). 217. K. Ghosh, S.B. Ozkan, K.A. Dill, The Ultimate Speed Limit to Protein Folding Is Conformational Searching. J. Am. Chem. Soc., 129 (39): 11920−11927 (2007). 216. T. Urbič, V. Vlachy, Y.V. Kalyuzhnyi, K.A. Dill, An Improved Thermodynamic Perturbation Theory for Mercedes-Benz Water. J. Chem. Phys., 127 (17): 174511 (2007). 5271



The Journal of Physical Chemistry B 215. T. Urbič, V. Vlachy, Y.V. Kalyuzhnyi, K.A. Dill, Theory for the Solvation of Nonpolar Solutes in Water. J. Chem. Phys., 127 (17): 174505 (2007). 214. D.L. Mobley, J.D. Chodera, K.A. Dill, The Confine and Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. J. Chem. Theory Comput., 3 (4): 1231−1235 (2007). 213. A. Bizjak, T. Urbič, V. Vlachy, K.A. Dill, The ThreeDimensional “Mercedes Benz” Model of Water. Acta Chim. Slov., 54 (3): 532−537 (2007). 212. A. Lucas, L. Huang, A. Joshi, K.A. Dill, Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach. J. Am. Chem. Soc., 129 (14): 4272−4281 (2007). 211. D.L. Mobley, A.P. Graves, J.D. Chodera, A.C. McReynolds, B.K. Shoichet, K.A. Dill, Predicting Absolute Ligand Binding Free Energies to a Simple Model Site. J. Mol. Biol., 371 (4): 1118−1134 (2007). 210. S.B. Ozkan, G.A. Wu, J.D. Chodera, K.A. Dill, Protein Folding by Zipping and Assembly. Proc. Natl. Acad. Sci. U.S.A., 104 (29): 11987−11992 (2007). 209. K.A. Dill, S.B. Ozkan, T.R. Weikl, J.D. Chodera, V.A. Voelz, The Protein Folding Problem: When Will It Be Solved? Curr. Opin. Struct. Biol., 17 (3): 342−346 (2007). 208. J.D. Chodera, N. Singhal, V.S. Pande, K.A. Dill, W.C. Swope, Automatic Discovery of Metastable States for the Construction of Markov Models of Macromolecular Conformational Dynamics. J. Chem. Phys., 126 (15): 155101 (2007). 207. J.A. Bradford, K.A. Dill, Stochastic Innovation as a Mechanism by which Catalysts Might Self-Assemble into Chemical Reaction Networks. Proc. Natl. Acad. Sci. U.S.A., 104 (24): 10098−10103 (2007). 206. K.A. Dill, A. Lucas, J. Hockenmaier, L. Huang, D. Chiang, A. Joshi, Computational Linguistics: A New Tool for Exploring Biopolymer Structures and Statistical Mechanics. Polymer, 48 (15): 4289−4300 (2007). 205. V.A. Voelz, K.A. Dill, Exploring Zipping and Assembly as a Protein Folding Principle. Proteins, 66 (4): 877−888 (2007). 204. E. Seitaridou, M.M. Inamdar, R. Phillips, K. Ghosh, K.A. Dill, Measuring Flux Distributions for Diffusion in the Small-Numbers Limit. J. Phys. Chem. B, 111 (9): 2288− 2292 (2007). 203. D.L. Mobley, E. Dumont, J.D. Chodera, K.A. Dill, Comparison of Charge Models for Fixed-Charge Force Fields: Small-Molecule Hydration Free Energies in Explicit Solvent. J. Phys. Chem. B, 111 (9): 2242−2254 (2007). 202. T.R. Weikl, K.A. Dill, Transition States in ProteinFolding Kinetics: The Structural Interpretation of Φ Values. J. Mol. Biol., 365 (5): 1578−1586 (2007). 201. J. Hockenmaier, A.K. Joshi, K.A. Dill, Routes Are Trees: The Parsing Perspective on Protein Folding. Proteins, 66 (1): 1−15 (2007). 200. J.D. Chodera, W.C. Swope, J.W. Pitera, C. Seok, K.A. Dill, Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations. J. Chem. Theory Comput., 3 (1): 26−41 (2007). 199. J.D. Chodera, W.C. Swope, J.W. Pitera, K.A. Dill, LongTime Protein Folding Dynamics from Short-Time

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Substrate Interactions. NATO ASI Series (Series B: Physics), vol. 325, S. Doniach (Ed.), Springer, Boston, MA, pp 109−113 (1994). H.S. Chan, K.A. Dill, Solvation: Effects of Molecular Size and Shape. J. Chem. Phys., 101 (8): 7007−7026 (1994). D.P. Yee, H.S. Chan, T.F. Havel, K.A. Dill, Does Compactness Induce Secondary Structure in Proteins? A Study of Poly-Alanine Chains Computed by Distance Geometry. J. Mol. Biol., 241 (4): 557−573 (1994). H.S. Chan, K.A. Dill, Transition States and Folding Dynamics of Proteins and Heteropolymers. J. Chem. Phys., 100 (12): 9238−9257 (1994). S. Bromberg, K.A. Dill, Side-Chain Entropy and Packing in Proteins. Protein Sci., 3 (7): 997−1009 (1994). E.E. Lattman, K.M. Fiebig, K.A. Dill, Modeling Compact Denatured States of Proteins. Biochemistry, 33 (20): 6158−6166 (1994). L.R. De Young, A.L. Fink, K.A. Dill, Aggregation of Globular Proteins. Acc. Chem. Res., 26 (12): 614−620 (1993). H.S. Chan, K.A. Dill, Energy Landscapes and the Collapse Dynamics of Homopolymers. J. Chem. Phys., 99 (3): 2116−2127 (1993). D. Stigter, K.A. Dill, Theory for Second Virial Coefficients of Short DNA. J. Chem. Phys., 97 (49): 12995−12997 (1993). K. Yue, K.A. Dill, Sequence-Structure Relationships in Proteins and Copolymers. Phys. Rev. E, 48 (3): 2267− 2278 (1993). P.D. Thomas, K.A. Dill, Local and Nonlocal Interactions in Globular Proteins, and Mechanisms of Alcohol Denaturation. Protein Sci., 2 (12): 2050−2065 (1993). D. Baker, H.S. Chan, K.A. Dill, Coordinate-Space Formulation of Polymer Lattice Cluster Theory. J. Chem. Phys., 98 (12): 9951−9962 (1993). D. Stigter, K.A. Dill, Theory for Protein Solubilities. Fluid Phase Equilib., 82: 237−249 (1993). D.P. Yee, K.A. Dill, Families and the Structural Relatedness Among Globular Proteins. Protein Sci., 2 (6): 884−899 (1993). L.R. De Young, K.A. Dill, A.L. Fink, Aggregation and Denaturation of Apomyoglobin in Aqueous Urea Solutions. Biochemistry, 32 (15): 3877−3886 (1993). K.M. Fiebig, K.A. Dill, Protein Core Assembly Processes. J. Chem. Phys., 98 (4): 3475−3487 (1993). K.A. Dill, Folding Proteins: Finding a Needle in a Haystack. Curr. Opin. Struct. Biol., 3 (1): 99−103 (1993). K.A. Dill, K.M. Fiebig, H.S. Chan, Cooperativity in Protein-Folding Kinetics. Proc. Natl. Acad. Sci. U.S.A., 90 (5): 1942−1946 (1993). H.S. Chan, K.A. Dill, The Protein Folding Problem. Phys. Today, 46 (2): 4−32 (1993). D.F. Stickle, L.G. Presta, K.A. Dill, G.D. Rose, Hydrogen Bonding in Globular Proteins. J. Mol. Biol., 226 (4): 1143−1159 (1992). G.B. Fields, D.O.V. Alonso, D. Stigter, K.A. Dill, Theory for the Aggregation of Proteins and Copolymers. J. Phys. Chem., 96 (10): 3974−3981 (1992). D. Stigter, J. Mingins, K.A. Dill, Phospholipid Interactions in Model Membrane Systems. II. Theory. Biophys. J., 61 (6): 1616−1629 (1992). DOI: 10.1021/acs.jpcb.8b02467 J. Phys. Chem. B 2018, 122, 5269−5277



46. L.R. DeYoung, K.A. Dill, Partitioning of Nonpolar Solutes into Bilayers and Amorphous n-Alkanes. J. Phys. Chem., 94 (2): 801−809 (1990). 45. H.S. Chan, K.A. Dill, Compact Polymers. Macromolecules, 22 (12): 4559−4573 (1989). 44. D. Stigter, K.A. Dill, Free Energy of Electrical Double Layers: Entropy of Adsorbed Ions and the Binding Polynomial. J. Phys. Chem., 93 (18): 6737−6743 (1989). 43. K.F. Lau, K.A. Dill, A Lattice Statistical Mechanics Model of the Conformational and Sequence Spaces of Proteins. Macromolecules, 22 (10): 3986−3997 (1989). 42. J.G. Dorsey, K.A. Dill, The Molecular Mechanism of Retention in Reversed-Phase Liquid Chromatography. Chem. Rev., 89 (2): 331−346 (1989). 41. K.A. Dill, D.O.V. Alonso, K. Hutchinson, Thermal Stabilities of Globular Proteins. Biochemistry, 28 (13): 5439−5449 (1989). 40. H.S. Chan, K.A. Dill, Intrachain Loops in Polymers: Effects of Excluded Volume. J. Chem. Phys., 90 (1): 492− 509 (1989). 39. P.T. Ying, J.G. Dorsey, K.A. Dill, Retention Mechanisms of Reversed Phase Liquid Chromatography: Determination of Solute−Solvent Interaction Free Energies. Anal. Chem., 61 (22): 2540−2546 (1989). 38. K.A. Dill, D.O.V. Alonso, Conformational Entropy and Protein Stability. In Protein Structure and Protein Engineering. Colloquium der Gesellschaf t für Biologische Chemie, 14.−16. April 1988 in Mosbach/Baden, vol. 39, E.L. Winnacker, R. Huber (Eds.), Springer, Berlin, Heidelberg, pp 51−58 (1988). 37. K.A. Dill, J. Naghizadeh, J.A. Marqusee, Chain Molecules at High Densities at Interfaces. Annu. Rev. Phys. Chem., 39 (1): 425−461 (1988). 36. L.R. DeYoung, K.A. Dill, Solute Partitioning into Lipid Bilayer Membranes. Biochemistry, 27 (14): 5281−5289 (1988). 35. K.A. Dill, D. Stigter, Lateral Interactions Among PC and PE Headgroups in Phospholipid Monolayers and Bilayers. Biochemistry, 27 (9): 3446−3453 (1988). 34. D. Stigter, K.A. Dill, Lateral Interactions Among Phospholipid Headgroups at the Heptane/Water Interface. Langmuir, 4 (1): 200−209 (1988). 33. K.A. Dill, Protein Surgery. Protein Eng., 1 (5): 369−372 (1987). 32. K.A. Dill, The Mechanism of Solute Retention in Reversed Phase Liquid Chromatography. J. Phys. Chem., 91 (7): 1980−1988 (1987). 31. K.A. Dill, The Stabilities of Globular Proteins. In Protein Engineering, D.L. Oxender, C.F. Fox (Eds.), Alan R. Liss, Inc., New York, pp 187−192 (1987). 30. D. Stigter, K.A. Dill, Interactions in Dilute Monolayers of Long Chain Ions at the Interface Between n-Heptane and Aqueous Salt Solutions. Langmuir, 2 (6): 791−796 (1986). 29. J.A. Marqusee, K.A. Dill, Chain Configurations in Lamellar Semicrystalline Polymer Interphases. Macromolecules, 19 (9): 2420−2426 (1986). 28. J.A. Marqusee, K.A. Dill, Solute Partitioning into Chain Molecule Interphases: Monolayers, Bilayer Membranes and Micelles. J. Chem. Phys., 85 (1): 434−444 (1986). 27. R.S. Cantor, K.A. Dill, Theory for the Equation of State of Phospholipid Monolayers. Langmuir, 2 (3): 331−337 (1986).

67. J. Mingins, D. Stigter, K.A. Dill, Phospholipid Interactions in Model Membrane Systems. I. Experiments on Monolayers. Biophys. J., 61 (6): 1603−1615 (1992). 66. L.A. Cole, J.G. Dorsey, K.A. Dill, Temperature Dependence of Retention in Reversed-Phase Liquid Chromatography: II. Mobile Phase Considerations. Anal. Chem., 64 (13): 1324−1327 (1992). 65. K. Yue, K.A. Dill, Inverse Protein Folding Problem: Designing Polymer Sequences. Proc. Natl. Acad. Sci. U.S.A., 89 (9): 4163−4167 (1992). 64. D. Shortle, H.S. Chan, K.A. Dill, Modeling the Effects of Mutations on the Denatured States of Proteins. Protein Sci., 1 (2): 201−215 (1992). 63. R. Miller, C.A. Danko, M.J. Fasolka, A.C. Balazs, H.S. Chan, K.A. Dill, Folding Kinetics of Proteins and Copolymers. J. Chem. Phys., 96 (1): 768−780 (1992). 62. D.O.V. Alonso, K.A. Dill, D. Stigter, The Three States of Globular Proteins: Acid Denaturation. Biopolymers, 31 (13): 1631−1649 (1991). 61. P.A. Kollman, K.A. Dill, Decisions in Force Field Development: An Alternative to Those Described by Roterman et al. (J. Biomol. Struct. Dyn. 7, 421 (1989)). J. Biomol. Struct. Dyn., 8 (6): 1103−1107 (1991). 60. H.S. Chan, M.R. Wattenbarger, D.F. Evans, V.A. Bloomfield, K.A. Dill, Enhanced Structure in Polymers at Interfaces. J. Chem. Phys., 94 (12): 8542−8557 (1991). 59. J. Naghizadeh, K.A. Dill, Statistical Mechanics of Chain Molecules at Interfaces. Macromolecules, 24 (8): 1768− 1778 (1991). 58. D.O.V. Alonso, K.A. Dill, Solvent Denaturation and Stabilization of Globular Proteins. Biochemistry, 30 (24): 5974−5985 (1991). 57. D. Stigter, D.O.V. Alonso, K.A. Dill, Protein Stability: Electrostatics and Compact Denatured States. Proc. Natl. Acad. Sci. U.S.A., 88 (10): 4176−4180 (1991). 56. H.S. Chan, K.A. Dill, “Sequence Space Soup” of Proteins and Copolymers. J. Chem. Phys., 95 (5): 3775−3787 (1991). 55. K.A. Dill, D. Shortle, Denatured States of Proteins. Annu. Rev. Biochem., 60 (1): 795−825 (1991). 54. H.S. Chan, K.A. Dill, Polymer Principles in Protein Structure and Stability. Annu. Rev. Biophys. Biophys. Chem., 20 (1): 447−490 (1991). 53. M.R. Wattenbarger, H.S. Chan, D.F. Evans, V.A. Bloomfield, K.A. Dill, Surface-Induced Enhancement of Internal Structure in Polymers and Proteins. J. Chem. Phys., 93 (11): 8343−8351 (1990). 52. K.A. Dill, The Meaning of Hydrophobicity. Science, 250 (4978): 297−298 (1990). 51. H.S. Chan, K.A. Dill, Origins of Structure in Globular Proteins. Proc. Natl. Acad. Sci. U.S.A., 87 (16): 6388− 6392 (1990). 50. K.A. Dill, Dominant Forces in Protein Folding. Biochemistry, 29 (31): 7133−7155 (1990). 49. H.S. Chan, K.A. Dill, The Effects of Internal Constraints on the Configurations of Chain Molecules. J. Chem. Phys., 92 (5): 3118−3135 (1990). 48. K.F. Lau, K.A. Dill, Theory for Protein Mutability and Biogenesis. Proc. Natl. Acad. Sci. U.S.A., 87 (2): 638−642 (1990). 47. D. Stigter, K.A. Dill, Charge Effects on Folded and Unfolded Proteins. Biochemistry, 29 (5): 1262−1271 (1990). 5276




7. K.A. Dill, B.H. Zimm, Dynamics of Polymer Solutions: II. The Determination of Molecular Weight Distribution by Viscoelasticity. Macromolecules, 13 (2): 432−436 (1980). 6. K.A. Dill, B.H. Zimm, Dynamics of Polymer Solutions I. Theory for an Instrument. Macromolecules, 13 (2): 426− 432 (1980). 5. Dill, K.A, Chain Folding in Semicrystalline Polymers. Faraday Discuss. Chem. Soc., 68: 104−140 (1979). 4. K.A. Dill, B.H. Zimm, A Rheological Separator for Very Large DNA Molecules. Nucleic Acids Res., 7 (3): 735− 749 (1979). 3. K.A. Dill, Theory for the Separation of Very Large DNA Molecules by Radial Migration. Biophys. Chem., 10 (3− 4): 327−334 (1979). 2. K.A. Dill, R.H. Shafer, Radial Migration of DNA Molecules in Cylindrical Flow. III. Circles and the Effect of Non-Gaussian Polymer Statistics. Biophys. Chem., 4 (1): 51−54 (1976). 1. K.A. Dill, M. Troll, FET Programs Op Amp for Invertible Gain. Electronics, 48: 113 (1975).

26. K.A. Dill, The Chain Conformations in Membranes and Micelles. Adv. Colloid. Interface Sci., 26: 99−110 (1986). 25. K.A. Dill, R.S. Cantor, The Statistical Thermodynamics of Surfactant Aggregates. In Physics of Amphiphiles: Micelles, Vesicles, and Microemulsions, V. Degiorgio, M. Corti (Eds.), North-Holland, Amsterdam, pp 376−393 (1986). 24. R.S. Cantor, K.A. Dill, Statistical Thermodynamic Theory for the Melting of n-Alkanes from Their Rotator Phases. Macromolecules, 18 (10): 1875−1882 (1985). 23. K.A. Dill, Molecular Conformations in Surfactant Micelles (reply). Nature, 313: 603−604 (1985). 22. K.A. Dill, Theory for the Folding and Stability of Globular Proteins. Biochemistry, 24 (6): 1501−1509 (1985). 21. S.H. Chen, K.A. Dill, Water in the Hydrocarbon Core of Micelles (reply). Nature, 314: 385−386 (1985). 20. J.A. Marqusee, M. Warner, K.A. Dill, Frequency Dependence of NMR Relaxation Rates in Bilayer Membranes. J. Chem. Phys., 8 (12): 6404−6405 (1984). 19. K.A. Dill, D.E. Koppel, R.S. Cantor, J.D. Dill, D. Bendedouch, S.H. Chen, The Molecular Conformations in Surfactant Micelles. Nature, 309 (5963): 42−45 (1984). 18. R.S. Cantor, K.A. Dill, Statistical Thermodynamics of Short Chain Molecule Interphases II. Configurational Properties of Amphiphilic Aggregates. Macromolecules, 17: 384−388 (1984). 17. K.A. Dill, R.S. Cantor, Statistical Thermodynamics of Short Chain Molecule Interphases I. Theory. Macromolecules, 17 (3): 380−384 (1984). 16. P.J. Flory, D.Y. Yoon, K.A. Dill, The Interphase in Lamellar Semicrystalline Polymers. Macromolecules, 17 (4): 862−868 (1984). 15. K.A. Dill, Molecular Organization in Amphiphilic Aggregates. In Surfactants in Solution, K.L. Mittal, B. Lindman (Eds.), Springer, Boston, MA, pp 307−320 (1983). 14. K.A. Dill, Configurations of Amphiphilic Molecules in Micelles. J. Phys. Chem., 86 (9): 1498−1500 (1982). 13. R.H. Tullis, K.A. Dill, P.A. Price, Fluorescence and Kinetic Studies on the Divalent Metal Ion Induced Conformational Changes in DNaseA. J. Biol. Chem., 256 (11): 5656−5661 (1981). 12. K.A. Dill, P.J. Flory, Molecular Organization in Micelles and Vesicles. Proc. Natl. Acad. Sci. U.S.A., 78 (2): 676− 680 (1981). 11. K.A. Dill, P.J. Flory, Interphases of Chain Molecules: Monolayers and Lipid Bilayer Membranes. Proc. Natl. Acad. Sci. U.S.A., 77 (6): 3115−3119 (1980). 10. K.A. Dill, Concentration Dependence of the Viscosity and Viscoelasticity of Polymer Solutions: Application of the Theory of Muthukumar and Freed. Macromolecules, 13 (3): 620−622 (1980). 9. K.A. Dill, Dynamics of Polymer Solutions: IV. ShearStress Relaxation Experiments on Solutions of DNA from Bacteriophage T2. Macromolecules, 13 (2): 438− 444 (1980). 8. M. Troll, K.A. Dill, B.H. Zimm, Dynamics of Polymer Solutions: III. An Instrument for Stress Relaxations on Dilute Solutions of Large Polymer Molecules. Macromolecules, 13 (2): 436−438 (1980). 5277


Selected Publications of Ken A. Dill - The Journal of Physical

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