Gavin E. Crooks

Gavin E. Crooks

Bespoke research on non-equilibrium thermodynamics, quantum computing, and the physics of information.

Berkeley Institute for the Theoretical Sciences

Normal Computing

Publications

Favorites: Favorites

Academic Articles

  1. 50. Thermodynamic linear algebra, Maxwell Aifer, Kaelan Donatella, Max Hunter Gordon, Samuel Duffield, Thomas Ahle, Daniel Simpson, Gavin E. Crooks, and Patrick J. Coles , npj Unconventional Computing, 1, 1(2024) [PDF | Journal]

  2. 49. Protein–ligand binding free-energy calculations with ARROW – A purely first-principles parameterized polarizable force field, Grzegorz Nawrocki, Igor Leontyev, Serzhan Sakipov, Mikhail Darkhovskiy, Igor Kurnikov, Leonid Pereyaslavets, Ganesh Kamath, Ekaterina Voronina, Oleg Butin, Alexey Illarionov, Michael Olevanov, Alexander Kostikov, Ilya Ivahnenko, Dhilon S. Patel, Subramanian K. R. S. Sankaranarayanan, Maria G. Kurnikova, Christopher Lock, Gavin E. Crooks, Michael Levitt, Roger D. Kornberg, and Boris Fain, J. Chem. Theory Comput (2022) [PDF | Journal]

  3. 48. Measuring Analytic Gradients of General Quantum Evolution with the Stochastic Parameter Shift Rule., Leonardo Banchi and Gavin E. Crooks, Quantum, 5, 386 (2021) [PDF | Journal]

  4. 47. Two-Qubit Circuit Depth and the Monodromy Polytope., Eric C. Peterson, Gavin E. Crooks, and Robert S. Smith, Quantum, 4, 247, arXiv:1904.10541 (2020) [ PDF] Favorites

  5. 46. Marginal and conditional second laws of thermodynamics, Gavin E. Crooks and Susanne Still, EPL 125:40005 (2019). [ PDF | Journal] Favorites

  6. 45. Quantifying configuration-sampling error in Langevin simulations of complex molecular systems, Josh Fass, David A. Sivak, Gavin E. Crooks, Kyle A. Beauchamp, Benedict Leimkuhler, and John D. Chodera, Entropy, 20(5):318 (2018). [ PDF | Journal]

  7. 44. Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems, Grant M. Rotskoff, Gavin E. Crooks, Eric Vanden-Eijnden, Phys. Rev. E, 95:012148 (2017). [ PDF | Journal ]

  8. 43. Thermodynamic geometry of minimum-dissipation driven barrier crossing, David A. Sivak, Gavin E. Crooks, Phys. Rev. E,94(5):052106 (2016) [ PDF | Journal ]

  9. 42. Near-optimal protocols in complex nonequilibrium transformations, Todd R. Gingrich, Grant M. Rotskoff, Gavin E. Crooks, Phillip L. Geissler Proc. Natl. Acad. Sci. U.S.A. 113 10263-10268 (2016) [ PDF | Journal]

  10. 41. Optimal control in nonequilibrium systems: Dynamic Riemannian geometry of the Ising model, [Grant M. Rotskoff, Gavin E. Crooks, Phys. Rev. E, 92, 060102 (2015) [ PDF | Journal| arXiv | More ] Favorites

  11. 40. Scaling laws governing stochastic growth and division of single bacterial cells, Srividya Iyer-Biswas, Charles S. Wright, Jonathan T. Henry, Klevin Lo, Stanislav Burov, Yihan Lin, Gavin E. Crooks, Sean Crosson, Aaron R. Dinner, Norbert F. Scherer, Proc. Natl. Acad. Sci. U.S.A. (2014) [ PDF | Journal | arXiv | More ]

  12. 39. Universality in Stochastic Exponential Growth, Srividya Iyer-Biswas, Gavin E. Crooks, Norbert F. Scherer, and Aaron R. Dinner, Phys. Rev. Lett., 113, 028101 (2014) [ PDF | Journal | More ]

  13. 38. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems, David A. Sivak, John D. Chodera, Gavin E. Crooks, J. Phys. Chem. B, 2013 [PDF | Journal | ArXiv | More ]

  14. 37. Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium discrete Langevin dynamics, David A. Sivak, John D. Chodera, Gavin E. Crooks, Phys. Rev. X 3, 011007 (2013) [PDF | Journal | More ]

  15. 36. The geometry of thermodynamic control, Patrick R. Zulkowski, David A. Sivak, Gavin E. Crooks and Michael R. DeWeese, Phys. Rev. E, 86, 041148 (2012) [ PDF | Journal | More]

  16. 35. Thermodynamics of prediction, Susanne Still, David A. Sivak, Anthony J. Bell and Gavin E. Crooks, Phys. Rev. Lett., 109, 120604 (2012) [ PDF | Journal | Press | arXiv | More ] Favorites

  17. 34. Thermodynamic metrics and optimal paths, David A. Sivak, Gavin E. Crooks, Phys. Rev. Lett., 108, 190602 (2012) [ PDF | Journal | More ] ] Favorites

  18. 33. Near-equilibrium measurements of nonequilibrium free energy, David A. Sivak, Gavin E. Crooks, Phys. Rev. Lett. 108, 150601 (2012) [ PDF | Journal | More ] Favorites

  19. 32. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation, Jerome P. Nilmeier, Gavin E. Crooks, David L. D. Minh, and John D. Chodera, Proc. Natl. Acad. Sci. U.S.A. (2011) 108(45) E1009-E1018 [ PDF | Journal | Author summary | Errata | More ]

  20. 31. On thermodynamic and microscopic reversibility, Gavin E. Crooks, J. Stat. Mech. (2011) P07008 [ PDF | More ]

  21. 30. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics, G.E. Crooks and D. A. Sivak, J. Stat. Mech.: Theor. Exp. P06003 (2011) [ PDF | Errata | More]

  22. 29. Self-organization of the chemotaxis network imaged with super-resolution light microscopy, Derek Greenfield, Ann L. McEvoy, Hari Shroff, Gavin E. Crooks, Ned S. Wingreen, Eric Betzig, Jan Liphardt, Plos Biol. 7:e1000137 (2009) [ PDF | Journal ]

  23. 28. Comment regarding “On the Crooks fluctuation theorem and the Jarzynski equality” [J. Chem. Phys. 129, 091101 (2008)] and “Nonequilibrium fluctuation-dissipation theorem of Brownian dynamics” [J. Chem. Phys. 129, 144113 (2008)], G.E. Crooks, J. Chem. Phys. 130:107101 (2009) [ PDF | Journal ]

  24. 27. Far-from-equilibrium measurements of thermodynamic length, E. H. Feng, G.E. Crooks, Phys. Rev. E 79, 012104 (2009) [ PDF | Journal ]

  25. 26. On the Jarzynski relation for dissipative quantum dynamics, G.E. Crooks J. Stat. Mech.: Theor. Exp. P10023 (9pp) (2008) [ PDF]

  26. 25. The length of time’s arrow, E. H. Feng, G.E. Crooks, Phys. Rev. Lett. 101 090602 (2008) [ PDF | Journal | Press ] Favorites

  27. 24. Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise, Paul Maragakis, Felix Ritort, Carlos Bustamante, Martin Karplus, Gavin E. Crooks, J. Chem. Phys. 129 024102 (2008) [ PDF | Journal | Errata ]

  28. 23. Quantum operation time reversal, G.E. Crooks, Phys. Rev. A 77 034101(4) (2008) [ PDF | Journal | Preprint ] Favorites

  29. 22. Measuring thermodynamic length, G.E. Crooks Phys. Rev. Lett. 99 100602 (2007) [PDF | Journal | Highlight | Errata ] Favorites

  30. 21. Beyond Boltzmann-Gibbs statistics: Maximum entropy hyperensembles out-of-equilibrium, G.E. Crooks, Phys. Rev. E 75 041119 (2007) [ PDF | Journal | Errata ]

  31. 20. Work distribution for the adiabatic compression of a dilute and interacting classical gas, G.E. Crooks, C. Jarzynski. Phys. Rev. E 75 021116 (2007) [ PDF | Journal | Errata ]

  32. 19. A high level interface to SCOP and ASTRAL implemented in Python, J.A. Casbon, G.E. Crooks, M.A.S. Saqi, BMC Bioinformatics 7:10 (2006) [ PDF | Journal ]

  33. 18. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap, G.A. Price G.E. Crooks, R.E. Green, S.E. Brenner, Bioinformatics 20:3824-3831 (2005) Erratum: Bioinformatics 21:4138 (2005) [ PDF | Journal | Errata ]

  34. 17. Pairwise alignment incorporating dipeptide covariation, G. E. Crooks, R. E. Green, S. E. Brenner, Bioinformatics 21:3704-3710, (2005) [ PDF | Appendix |
    Source Code and Data (103 MB) ]

  35. 16. A generalized affine gap model significantly improves protein sequence alignment accuracy Marcus A. Zachariah, Gavin E. Crooks, Stephen R. Holbrook, and Steven E. Brenner, Proteins 58(2):329-338 (2005) [ PDF]

  36. 15. An alternative model of amino acid replacement, G. E. Crooks, S. E. Brenner, Bioinformatics 21:975-980, (2005) [ PDF] Favorites

  37. 14. Experimental test of Hatano and Sasas nonequilibrium steady-state equality E. H. Trepagnier, C. Jarzynski, F. Ritort, G. E. Crooks, C. J. Bustamante, and J. Liphardt, PNAS 101: 15038-15041 (2004) [ PDF | Journal ]

  38. 13. Measurements of protein sequence-structure correlations G. E. Crooks, J. Wolfe, S. E. Brenner, Proteins 57(4):804-810 (2004) [ PDF | Journal | Source Code and Data (10 Mb) ] Favorites

  39. 12. Protein secondary structure: Entropy, correlations and prediction Gavin E. Crooks and Steven E. Brenner, Bioinformatics 20:1603-1611 (2004) [ PDF | Journal | Preprint | Source code and data] Favorites

  40. 11. WebLogo: A sequence logo generator, G. E. Crooks, G. Hon, J.-M. Chandonia and S. E. Brenner, Genome Research, 14:1188-1190 (2004) [ PDF | Journal | Web Site ]

  41. 10. Efficient transition path sampling for nonequilibrium stochastic dynamics Gavin E. Crooks and David Chandler, Phys. Rev. E, 64, 026109 (2001) [ PDF ]

  42. 9. Cellular automata for polymer simulation with application to polymer melts and polymer collapse, including implications for protein folding B. Ostrovsky, Gavin Crooks, M.A. Smith and Y. Bar-Yam, Parallel Computing 27, 613-641 (2001) [ PDF ]

  43. 8. Path ensemble averages in systems driven far from equilibrium, Gavin E. Crooks, Phys. Rev. E 61, 2361 (2000) [ PDF ] Favorites

  44. 7. The mesostructure of polymer collapse and fractal smoothing G. E. Crooks, B. Ostrovsky, Y. Bar-Yam, 60, 4559 (1999), [ PDF ]

  45. 6. The entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences G. E. Crooks, 60, 2721 (1999), [ PDF ] Favorites

  46. 5. Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems G. E. Crooks, 90, 1481 (1998) [ PDF ] Favorites

  47. 4. Gaussian statistics of the hard-sphere fluid G. E. Crooks and D. Chandler, Phys. Rev. E., 56(4):4217-21 (1997) [ PDF ] Favorites

  48. 3. Lipases in Water-in-Oil Microemulsions, Organogels and Windor II Systems: Aspects of Reactivity and Separation Science, G. D. Rees, K. Carlile, G. E. Crooks, T. R-J. Jenta, L. A. Price, and R. H. Robinson. In F.X. Malcata, editor, Engineering of/with Lipases., pages 577-595. Kluwer Academic Press, 1996.

  49. 2. Comparison of hydrolysis and esterification behavior of and lipases in AOT-stabilized water-in-oil microemulsions: II. Effect of temperature on reaction kinetics and general considerations of stability and productivity, G. E. Crooks, G. D. Rees, B. H. Robinson, M. Svensson, and G. R. Stephenson, Biotechnol. Bioen., 48(3):190-196, 1995. [ PDF ]

  50. 1. Comparison of hydrolysis and esterification behavior of and lipases in AOT-stabilized water-in-oil microemulsions: I. Effect of pH and water content on reaction kinetics, G. E. Crooks, G. D. Rees, B. H. Robinson, M. Svensson, and G. R. Stephenson, Biotechnol. Bioen., 48(1):78-88, 1995 [ PDF]

Books

  1. [gud] Field guide to continuous probability distributions Gavin E. Crooks, 2019 [ PDF | More ] Favorites

Dissertations

  1. [phd] Excursions in statistical dynamics Gavin E. Crooks, Ph.D. thesis, University of California, Berkeley, 1999 [ PDF | Errata | More ] Favorites

  2. [msc] Characterization of lipases in water-in-oil microemulsions Gavin E. Crooks, Master’s thesis, University of East Anglia, 1993

Errata

  1. Cumulative Errata: A memorandum of minor miscellaneous mistakes. Gavin E. Crooks (1997-2019) PDF