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Ken A. Dill Distinguished Professor Physics and Astronomy College of Arts and Sciences

Contact Information

117 Laufer Center

Stony Brook, 11794

631/632-5401

Biography

Ken Dill is Director of the Laufer Center for Physical & Quantitative Biology. Currently, he studies the physics of proteins, biological cells, and water. He develops methods in statistical physics and computational biology to learn more about cells and their processes in biology and in diseases. His work has led to insights about how the laws of physics constrain and enable the biological properties and evolution of cells. He is best known for his role with solving the "protein-folding" problem, the question of how a protein’s amino acid sequence dictates its three-dimensional atomic structure. Protein folding rules are offering practical applications in the development of pharmaceuticals and medical diagnostics.

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Education

  • Postdoctoral Fellow, Stanford University
  • PhD, University of California
  • SB and SM, Massachusetts Institute of Technology

Research Grants

Award Start End Sponsor Type Amount Status
Bio-Molecular Recognition and Catalysis Project 2011-02-18T00:00:00 2012-02-03T00:00:00 Lawrence Berkeley National Laboratory Nonfederal 216103 Closed
Combinatorial Statistical Mechanics of Protein Folding 2010-11-01T00:00:00 2012-06-30T00:00:00 National Institute of General Medical Sciences Federal 264880.07 Closed
New Mathematical Methods for Protein Loop Modeling 2010-11-01T00:00:00 2014-07-31T00:00:00 University of New Mexico Nonfederal 518338.95 Closed
Modeling Aqueous Solvation in Biology 2011-01-01T00:00:00 2015-04-17T00:00:00 National Institute of General Medical Sciences Federal 1169511.13 Closed
Petascale Integrative Approaches to Protein Structure Prediction 2017-08-01T00:00:00 2019-07-31T00:00:00 National Science Foundation Federal 15566 Approved
Collaborative Research: Maximum Caliber: An Approach to Modeling Stochastic Dynamics in Biology 2012-09-15T00:00:00 2018-02-28T00:00:00 National Science Foundation Federal 961333 Approved
Funds from SBF Endowments for Laufer Center Payroll 2012-07-01T00:00:00 2018-06-30T00:00:00 Stony Brook Foundation Nonfederal 2808332.54 Approved
INSPIRE Track 1: Origins-of-Life and Self-Evolving Polymeric Materials 2013-09-15T00:00:00 2018-08-31T00:00:00 National Science Foundation Federal 1000000 Approved
Modeling Aqueous Solvation in Biology 2015-04-01T00:00:00 2018-03-31T00:00:00 National Institute of General Medical Sciences Federal 902110.01 Approved
Predicting Protein Structures with Physical Petascale Molecular Simulations 2015-08-01T00:00:00 2018-07-31T00:00:00 National Science Foundation Federal 30000 Approved
Computations on Peptide and Macrocyles 2015-09-28T00:00:00 2017-09-30T00:00:00 Merck Sharp and Dohme Corporation Nonfederal 79007 Approved

Publications

  1. Author Article Biophysical Journal Extracting Kinetic Models from Single Molecule Experiments by Direct Inference 2012 102 3
  2. Author Article Journal of the American Chemical Society Growth Rates of Protein Crystals 2012 120223124959000
  3. Author Article Biophysical Journal Using Delaunay Tessellation of Proteins to Improve Current ENM 2012 102 3
  4. Author Article Proceedings of the National Academy of Sciences of the United States of America Reply to Vazquez: Optimal density is robust to variations in calculation 2012 109 9
  5. Author Article Biophysical Journal Physics Based Protein Structure Refinement 2012 102 3
  6. Author Article Biophysical Journal A Simple Model of Protein Folding Kinetics Based on Native Topology 2012 102 3
  7. Author Article Biophysical Journal Accurate Solutions with the Semi-Explicit Assembly Water Model 2012 102 3
  8. Author Article The Journal of Chemical Physics Markov processes follow from the principle of maximum caliber 2012 136 6 64108
  9. Author Article Proteins: Structure, Function, and Bioinformatics Assessment of protein structure refinement in CASP9 2011 79 74 - 90
  10. Author Article Peptide Science Peptoid conformational free energy landscapes from implicit-solvent molecular simulations in AMBER 2011 96 5 639 - 650
  11. Author Article Journal of Physical Chemistry B Comparison of Charge Models for Fixed-Charge Force Fields: Small Molecule Hydration Free Energies in Explicit Solvent 2011 115 5 1329 - 1332
  12. Author Article Journal of Physical Chemistry B Modeling Stochastic Dynamics in Biochemical Systems with Feedback Using Maximum Caliber 2011 115 19 6202 - 6212
  13. Author Article The Journal of Chemical Physics Electrostatics and aggregation: How charge can turn a crystal into a gel 2011 135 8 85103
  14. Author Article Journal of Physical Chemistry B Correction to "Charge Asymmetries in Hydration of Polar Solutes" 2011 115 50 15145 - 15145
  15. Author Article Proceedings of the National Academy of Sciences of the United States of America Modeling aqueous solvation with semi-explicit assembly 2011 108 8 3234 - 3239
  16. Author Article Proceedings of the National Academy of Sciences of the United States of America Inaugural Article: Physical limits of cells and proteomes 2011 108 44 17876 - 17882
  17. Author Article Biophysical Journal What Drives Amyloid Molecules To Assemble into Oligomers and Fibrils? 2011 100 2 450 - 458
  18. Author Article Physical Review E Dynamical fluctuations in biochemical reactions and cycles 2010 82 3
  19. Author Article The Journal of Physical Chemistry B Receptacle Model of Salting-In by Tetramethylammonium Ions 2010 114 46 15085 - 15091
  20. Author Article Journal of the American Chemical Society Oil/Water Transfer Is Partly Driven by Molecular Shape, Not Just Size 2010 132 1 234 - 240
  21. Author Article The Journal of Physical Chemistry B The Stabilities of Protein Crystals 2010 114 11 4020 - 4027
  22. Author Article Biophysical Journal Solution Dynamics of Monoclonal Antibodies: Experimental and Computational Approach 2010 98 3
  23. Author Article Physical Chemistry Chemical Physics Aqueous alkali halide solutions: can osmotic coefficients be explained on the basis of the ionic sizes alone? 2010 12 23 6260
  24. Author Article Biophysical Journal Cellular Proteomes Have Broad Distributions of Protein Stability 2010 99 12 3996 - 4002
  25. Author Article Biophysical Journal Iterative Assembly of Protein Fragments 2010 98 3
  26. Author Article Biophysical Journal Improving Protein Structure Prediction by Smoothing Energy Functions 2010 98 3
  27. Author Article The Journal of Chemical Physics A statistical mechanical theory for a two-dimensional model of water 2010 132 22 224507
  28. Author Article Biophysical Journal Predicting the Toggle Switch Bistability from Maximum Uncertainty Principles 2010 98 3
  29. Author Article Proceedings of the National Academy of Sciences Nonuniversal power law scaling in the probability distribution of scientific citations 2010 107 37 16023 - 16027
  30. Author Article Biophysical Journal Theory of the Solubility of Protein Crystals 2010 98 3
  31. Author Article Biophysical Journal A New Semi-Explicit Solvation Model: Fast Physics for Better Results 2010 98 3
  32. Author Article Biophysical Journal Capturing the Roles of Attraction and Shape in Nonpolar Solvation 2010 98 3
  33. Author Article Proteins: Structure, Function, and Bioinformatics Assessment of the protein-structure refinement category in CASP8 2009 77 66 - 80
  34. Author Article Journal of Chemical Theory and Computation Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations 2009 5 2 350 - 358
  35. Author Article Journal of the American Chemical Society Theory for Protein Folding Cooperativity: Helix Bundles 2009 131 6 2306 - 2312
  36. Author Article Physical Review Letters Trajectory Approach to Two-State Kinetics of Single Particles on Sculpted Energy Landscapes 2009 103 5
  37. Author Article Journal of Molecular Biology Predicting Ligand Binding Affinity with Alchemical Free Energy Methods in a Polar Model Binding Site 2009 394 4 747 - 763
  38. Author Article The Journal of Physical Chemistry B Ion Pairing in Molecular Simulations of Aqueous Alkali Halide Solutions 2009 113 19 6782 - 6791
  39. Author Article The Journal of Physical Chemistry B Predictions of Hydration Free Energies from All-Atom Molecular Dynamics Simulations 2009 113 14 4533 - 4537
  40. Author Article The Journal of Physical Chemistry B Computer Simulations of Ionenes, Hydrophobic Ions with Unusual Solution Thermodynamic Properties. The Ion-Specific Effects 2009 113 43 14270 - 14276
  41. Author Article Structure Binding of Small-Molecule Ligands to Proteins: ?What You See? Is Not Always ?What You Get? 2009 17 4 489
  42. Author Article Proceedings of the National Academy of Sciences Computing protein stabilities from their chain lengths 2009 106 26 10649 - 10654
  43. Author Article The Journal of Chemical Physics Theory for the three-dimensional Mercedes-Benz model of water 2009 131 19 194504
  44. Author Article PLoS Computational Biology <title>Author Summary</title> <p>Proteins must fold to unique native structures in order to perform their functions. To do this, proteins must solve a complicated conformational search problem, the details of which remain difficult to study experimentally 2009 5 2 2009
  45. Author Article Bioorganic &amp; Medicinal Chemistry Development of an optimized activatable MMP-14 targeted SPECT imaging probe 2009 17 2 653 - 659
  46. Author Article International Journal of Peptide and Protein Research 13C n.m.r. study of the structure and the metal ion binding sites of neuropeptides composed of L-Asp and L-Glu 2009 28 1 67 - 78
  47. Author Article The Journal of Chemical Physics Explicit-water molecular dynamics study of a short-chain 3,3 ionene in solutions with sodium halides 2009 130 13 134903
  48. Author Article Biophysical Journal Blind Test of Physics-Based Prediction of Protein Structures 2009 96 3 917 - 924
  49. Author Article Protein Science Predicting the structures of 18 peptides using Geocore 2008 8 4 716 - 721
  50. Author Article The Journal of Physical Chemistry B Treating Entropy and Conformational Changes in Implicit Solvent Simulations of Small Molecules 2008 112 3 938 - 946
  51. Author Article Protein Science Folding proteins with a simple energy function and extensive conformational searching 2008 5 2 254 - 261
  52. Author Article Structure Iterative Assembly of Helical Proteins by Optimal Hydrophobic Packing 2008 16 8 1257
  53. Author Article Protein Science Modeling the effects of mutations on the denatured states of proteins 2008 1 2 201 - 215
  54. Author Article Annual Review of Biophysics The Protein Folding Problem 2008 37 1 289 - 316
  55. Author Article Protein Science Principles of protein folding - A perspective from simple exact models 2008 4 4 561 - 602
  56. Author Article Protein Science Ligand binding to proteins: The binding landscape model 2008 6 10 2166 - 2179
  57. Author Article The Journal of Physical Chemistry B A Test on Peptide Stability of AMBER Force Fields with Implicit Solvation 2008 112 22 6878 - 6886
  58. Author Article The Journal of Chemical Physics Maximum Caliber: A variational approach applied to two-state dynamics 2008 128 19 194102
  59. Author Article Journal of the American Chemical Society Biomimetic Nanostructures: Creating a High-Affinity Zinc-Binding Site in a Folded Nonbiological Polymer 2008 130 27 8847 - 8855
  60. Author Article The Journal of Physical Chemistry B Charge Asymmetries in Hydration of Polar Solutes 2008 112 8 2405 - 2414
  61. Author Article Journal of the American Chemical Society The Ultimate Speed Limit to Protein Folding Is Conformational Searching 2007 129 39 11920 - 11927
  62. Author Article Journal of Molecular Biology Predicting Absolute Ligand Binding Free Energies to a Simple Model Site 2007 371 4 1118 - 1134
  63. Author Article Current Opinion in Structural Biology The protein folding problem: when will it be solved? 2007 17 3 342 - 346
  64. Author Article The Journal of Physical Chemistry B Comparison of Charge Models for Fixed-Charge Force Fields:  Small-Molecule Hydration Free Energies in Explicit Solvent 2007 111 9 2242 - 2254
  65. Author Article The Journal of Chemical Physics Theory for the solvation of nonpolar solutes in water 2007 127 17 174505
  66. Author Article Journal of Chemical Theory and Computation Use of the Weighted Histogram Analysis Method for the Analysis of Simulated and Parallel Tempering Simulations 2007 3 1 26 - 41
  67. Author Article Proceedings of the National Academy of Sciences Protein folding by zipping and assembly 2007 104 29 11987 - 11992
  68. Author Article Polymer Computational linguistics: A new tool for exploring biopolymer structures and statistical mechanics 2007 48 15 4289 - 4300
  69. Author Article Journal of Molecular Biology Transition-States in Protein Folding Kinetics: The Structural Interpretation of F values 2007 365 5 1578 - 1586
  70. Author Article The Journal of Physical Chemistry B Measuring Flux Distributions for Diffusion in the Small-Numbers Limit 2007 111 9 2288 - 2292
  71. Author Article Journal of the American Chemical Society Statistical Mechanics of Helix Bundles Using a Dynamic Programming Approach 2007 129 14 4272 - 4281
  72. Author Article Journal of Chemical Theory and Computation Confine-and-Release Method:  Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change 2007 3 4 1231 - 1235
  73. Author Article The Journal of Chemical Physics An improved thermodynamic perturbation theory for Mercedes-Benz water 2007 127 17 174511
  74. Author Article The Journal of Chemical Physics Automatic discovery of metastable states for the construction of Markov models of macromolecular conformational dynamics 2007 126 15 155101
  75. Author Article Proceedings of the National Academy of Sciences Stochastic innovation as a mechanism by which catalysts might self-assemble into chemical reaction networks 2007 104 24 10098 - 10103
  76. Author Article Inter-Asia Cultural Studies Embodying gender: transgender body/subject formations in Taiwan 2006 7 2 228 - 242
  77. Author Article PLoS Computational Biology Correction: Folding Very Short Peptides Using Molecular Dynamics 2006 2 5
  78. Author Article PLoS Computational Biology Folding Very Short Peptides Using Molecular Dynamics 2006 2 4
  79. Author Article The Journal of Chemical Physics On the use of orientational restraints and symmetry corrections in alchemical free energy calculations 2006 125 8 84902
  80. Author Article The Journal of Physical Chemistry B Confined Water:  A Mercedes-Benz Model Study 2006 110 10 4963 - 4970
  81. Author Article International Journal of Quantum Chemistry Resultants and loop closure 2006 106 1 176 - 189
  82. Author Article Multiscale Modeling & Simulation Long-Time Protein Folding Dynamics from Short-Time Molecular Dynamics Simulations 2006 5 4 1214
  83. Author Article Proteins: Structure, Function, and Bioinformatics Exploring zipping and assembly as a protein folding principle 2006 66 4 877 - 888
  84. Author Article Proteins: Structure, Function, and Bioinformatics Routes are trees: The parsing perspective on protein folding 2006 66 1 1 - 15
  85. Author Article Journal of Computational Biology A Grammatical Theory for the Conformational Changes of Simple Helix Bundles 2006 13 1 21 - 42
  86. Author Article American Journal of Physics Teaching the principles of statistical dynamics 2006 74 2 123
  87. Author Article The Journal of Physical Chemistry B Water's Hydrogen Bonds in the Hydrophobic Effect:  A Simple Model 2005 109 49 23611 - 23617
  88. Author Article Annual Review of Biophysics and Biomolecular Structure MODELING WATER, THE HYDROPHOBIC EFFECT, AND ION SOLVATION 2005 34 1 173 - 199
  89. Author Article Journal of Molecular Biology Comprehensive Analysis of Protein Folding Activation Thermodynamics Reveals a Universal Behavior Violated by Kinetically Stable Proteases 2005 347 2 355 - 366
  90. Author Article Journal of Computational Chemistry Rotational superposition and least squares: The SVD and quaternions approaches yield identical results. Reply to the preceding comment by G. Kneller 2005 26 15 1663 - 1665
  91. Author Article Proceedings of the National Academy of Sciences   values in protein-folding kinetics have energetic and structural components 2005 102 29 10171 - 10175
  92. Author Article The Journal of Physical Chemistry B Surfaces Affect Ion Pairing 2005 109 50 24056 - 24060
  93. Author Article Journal of the American Chemical Society Folding a Nonbiological Polymer into a Compact Multihelical Structure 2005 127 31 10999 - 11009
  94. Author Article Protein Science The flexibility in the proline ring couples to the protein backbone 2005 14 4 1011 - 1018
  95. Author Article Bioconjugate Chemistry Incorporation of Chemoselective Functionalities into Peptoids via Solid-Phase Submonomer Synthesis 2004 15 2 428 - 435
  96. Author Article Protein Science Cooperativity in two-state protein folding kinetics 2004 13 3 822 - 829
  97. Author Article Current Opinion in Colloid & Interface Science Short-range interactions: from simple ions to polyelectrolyte solutions 2004 9 1 128 - 132
  98. Author Article Journal of Molecular Liquids Water-like fluid in the presence of Lennard-Jones obstacles: predictions of an associative replica Ornstein-Zernike theory 2004 112 1 71 - 80
  99. Author Article Journal of Computational Chemistry A kinematic view of loop closure 2004 25 4 510 - 528
  100. Author Article Journal of Computational Biology Using Motion Planning to Map Protein Folding Landscapes and Analyze Folding Kinetics of Known Native Structures 2004 10 3
  101. Author Article Journal of Computational Chemistry Using quaternions to calculate RMSD 2004 25 15 1849 - 1857

Courses

Term Role Course ID Description
Spring 2017 Primary Instructor AMS 599 Research
Spring 2017 Primary Instructor CHE 599 Research
Spring 2017 Primary Instructor PHY 580 Special Research Projects
Spring 2017 Primary Instructor PHY 585 Special Study
Fall 2017 Primary Instructor AMS 599 Research
Fall 2017 Primary Instructor CHE 599 Research
Fall 2017 Primary Instructor CHE 699 Dissertation Resrch on Campus
Fall 2017 Primary Instructor PHY 580 Special Research Projects
Fall 2017 Primary Instructor PHY 699 Dissertation Resrch on Campus
Spring 2016 Primary Instructor CHE 599 Research
Spring 2016 Primary Instructor PHY 585 Special Study
Spring 2016 Primary Instructor PHY 699 Dissertation Resrch on Campus
Fall 2016 Primary Instructor CHE 599 Research
Fall 2016 Primary Instructor PHY 585 Special Study
Fall 2016 Primary Instructor PHY 699 Dissertation Resrch on Campus
Spring 2015 Primary Instructor BME 599 Biomedical Engineering Rsrch
Spring 2015 Primary Instructor CHE 599 Research
Spring 2015 Primary Instructor PHY 699 Dissertation Resrch on Campus
Fall 2015 Primary Instructor CHE 599 Research
Fall 2015 Primary Instructor PHY 584 Rotation in Physical Biology
Fall 2015 Primary Instructor PHY 699 Dissertation Resrch on Campus
Spring 2014 Primary Instructor BME 599 Biomedical Engineering Rsrch
Spring 2014 Primary Instructor PHY 595 Master's Degree Thesis Rsrch
Spring 2014 Primary Instructor PHY 699 Dissertation Resrch on Campus
Spring 2014 Primary Instructor PHY 699 Dissertation Resrch on Campus
Fall 2014 Primary Instructor CHE 558 Physical Biology
Fall 2014 Primary Instructor CHE 589 Directed Study
Fall 2014 Primary Instructor PHY 558 Physical Biology
Fall 2014 Primary Instructor PHY 699 Dissertation Resrch on Campus
Fall 2013 Primary Instructor BME 599 Biomedical Engineering Rsrch
Fall 2013 Primary Instructor PHY 699 Dissertation Resrch on Campus
Fall 2013 Primary Instructor PHY 699 Dissertation Resrch on Campus

Honors

Type Description Year
Academy Membership National Academy of Sciences
Academy Membership National Academy of Sciences, elected Member
Advanced Degree Ph.D. Biology Department, (Bruno H. Zimm), UC San Diego, La Jolla
Advanced Degree Ph.D., UCSD, La Jolla, CA Biology
Advanced Degree S.B. and S.M., Mechanical Engineering Department, M.I.T.
Advanced Degree S.M., MIT, Cambridge, MA Mechanical Engineering
Award AAAS, elected Fellow
Award American Physical Society, elected Fello
Award Biophysical Society Emily Gray Award
Award Biophysical Society, Distinguished Service Award
Award Biophysical Society, elected Fellow
Award Fellow, AAAS
Award Fellow, American Physical Society
Award Fellow, Biophysical Society
Award Fellow, Institute of Physics
Award Hans Neurath Award, Protein Society
Award Institute of Physics, elected Fellow
Award Pew Scholar
Award Protein Society Hans Neurath Award
Award UCSF 53rd Faculty Research Lecturer
Award UCSF Academic Senate, Distinguished Teaching Award, UCSF Joseph M. Long Foundation Prize for Excellence in Teaching
Other Postdoc, Stanford, Palo Alto, CA Chemistry
Other Postdoctoral Fellow (Paul J. Flory), Chemistry, Stanford University

Scholarly Activities

Activity Title Date
Lecture About 20-25 per year.

Professional Service

Service Title Date
Service on Editorial Boards Annual Reviews of Biophysics (Associate Editor), Ed board: Protein Engineering, Physical Biology, Multiscale Modeling & Simulation, Structure, Biopolymers, Biophysical Chemistry, J. Molecular Recognition 2011 - 2012
Outside Consulting Outside reviewer of the Department of Biochem and Molecular Biophysics, Wash U, St Louis 2010 - 2011
Service on Editorial Boards Annual Reviews of Biophysics (Associate Editor), Ed board: Protein Engineering, Physical Biology, Multiscale Modeling & Simulation, Structure, Biopolymers, Biophysical Chemistry, J. Molecular Recognition 2010 - 2011

University Service

Service Title Date
Administrative Work Assignment Setting up and directing the Laufer Center Assembled a community of 12 faculty from about 6 Stony Brook University departments and from Cold Spring Harbor and Brookhaven National Labs. Designed and guided space renovations of 10,000 ASF Created 3 Junior Fellow positions Co-recruited two faculty jointly with the Stony Brook University Applied Math & Statistics Department Currently recruiting 2 endowed Laufer Center professors Developed the Laufer Center website & logo Working with the Stony Brook University Physics Department to create a new graduate track in Physical Biology Creating 3 new graduate courses: Biology for Physical Scientists, Introduction to Physical Biology, and Biological Dynamics and Networks Started a communal computational resource of 400 CPUs and 100 CPUs, to grow in the future Contributing to planning the campus-wide LC opening event Hosting a Protein Folding meeting at Stony Brook University (about 100 people, Jun 2012) Member of the Advisory Board of the Institute of Chemical Biology & Drug Discovery Member of the Institute for Cell & Developmental Biology in the Department of Biochemistry & Cell Biology. 2011 - 2012
Administrative Work Assignment Setting up and directing the Laufer Center 2010 - 2011
Other I was at UCSF until 2010 2010 - 2011

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