Publications




Academic Articles

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2014

38 Universality in Stochastic Exponential Growth, Srividya Iyer-Biswas, Gavin E. Crooks, Norbert F. Scherer, and Aaron R. Dinner, Phys. Rev. Lett., 113, 028101 (2014)
[ Full text | Journal | More ]
37 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
[ Full text | Journal | ArXiv | More ]

2013

36 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)
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2012

35 The geometry of thermodynamic control,
Patrick R. Zulkowski, David A. Sivak, Gavin E. Crooks and Michael R. DeWeese, Phys. Rev. E, 86, 041148 (2012)
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34 Thermodynamics of prediction,
Susanne Still, David A. Sivak, Anthony J. Bell and Gavin E. Crooks, Phys. Rev. Lett., 109, 120604 (2012)
[ Full Text | Journal | Press | arXiv | More ]

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33. Thermodynamic metrics and optimal paths,
David A. Sivak, Gavin E. Crooks, Phys. Rev. Lett., 108, 190602 (2012)
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32. Near-equilibrium measurements of nonequilibrium free energy,
David A. Sivak, Gavin E. Crooks, Phys. Rev. Lett. 108, 150601 (2012)
[ Full Text | Journal | More ]

2011

31. 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
[ Full text | Journal | Author summary | Errata | More ]
30. On thermodynamic and microscopic reversibility,
Gavin E. Crooks, J. Stat. Mech. (2011) P07008
[ Full text | Journal | More ]
29. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics,
G.E. Crooks and D. A. Sivak, J. Stat. Mech.: Theor. Exp. P06003 (2011)
[ Full text | Journal | Errata | More ]

2009


28. Self-organization of the Escherichia coli 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)
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27. 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)
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26. Far-from-equilibrium measurements of thermodynamic length,
E. H. Feng, G.E. Crooks, Phys. Rev. E 79, 012104 (2009)
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2008


25. On the Jarzynski relation for dissipative quantum dynamics,
G.E. Crooks J. Stat. Mech.: Theor. Exp. P10023 (9pp) (2008)
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*24. The length of time's arrow,
E. H. Feng, G.E. Crooks, Phys. Rev. Lett. 101 090602 (2008)
[ Full text | Journal | Press ]

*23. 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)
[ Full text | Journal | Errata ]

22. Quantum operation time reversal,
G.E. Crooks, Phys. Rev. A 77 034101(4) (2008)
[ Full text | Journal |Preprint ]

2007


*21. Measuring thermodynamic length,
G.E. Crooks Phys. Rev. Lett. 99 100602 (2007)
[ Full text | Journal | Highlight | Errata ]

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

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

2006


18. 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)
[ Full text | Journal ]

2005


17. 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)
[ Full text | Journal | Errata ]

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

15. 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)
[ Full text | Journal ]

*14. An alternative model of amino acid replacement,
G. E. Crooks, S. E. Brenner, Bioinformatics 21:975-980, (2005)
[ Full text | Journal ]

2004


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

*11. Protein secondary structure: Entropy, correlations and prediction
Gavin E. Crooks and Steven E. Brenner, Bioinformatics 20:1603-1611 (2004)
[ Full text | Journal | Preprint | Source code and data ]

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

2001

9. Efficient transition path sampling for nonequilibrium stochastic dynamics
Gavin E. Crooks and David Chandler, Phys. Rev. E, 64, 026109 (2001)
[ Full text ]
8. 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)
[ Full text ]

2000

* 7. Path ensemble averages in systems driven far from equilibrium,
Gavin E. Crooks, Phys. Rev. E 61, 2361 (2000)
[ Full text ]

1999

6. The mesostructure of polymer collapse and fractal smoothing
G. E. Crooks, B. Ostrovsky, Y. Bar-Yam, Phys. Rev. E 60, 4559 (1999),
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*5. The entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences
G. E. Crooks, Phys. Rev. E 60, 2721 (1999),
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1998

*4. Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems
G. E. Crooks, J. Stat. Phys. 90, 1481 (1998)
[ Full text ]

1997

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

1995


2. Comparison of hydrolysis and esterification behavior of humicola lanuginosa and rhizomucor miehei 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.
[ Full text ]

1. Comparison of hydrolysis and esterification behavior of humicola lanuginosa and rhizomucor miehei 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
[ Full text ]

Dissertations

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phdExcursions in statistical dynamics
Gavin E. Crooks, Ph.D. thesis, University of California, Berkeley, 1999
[ Full text | Errata | More ]
mscCharacterization of lipases in water-in-oil microemulsions
Gavin E. Crooks, Master's thesis, University of East Anglia, 1993

Conference Proceedings

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1996

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.

1993

Enzymes in water-in-oil microemulsions, organogels and Winsor II systems: Aspects of reactivity and separation science,
G. E. Crooks T. R-J. Jenta, L. A. Price, G. D. Rees, and B. H. Robinson, In Proceedings of the International Symposium on Industrial Applications of Microemulsion Technology, 9th-11th Dec. 1993, New Delhi, India., 1993.