Gavin E. Crooks, Ph.D. - Publications

Affiliations: 
Lawrence Berkeley National Laboratory, Berkeley, CA, USA 
Area:
Thermodynamics
Website:
http://threeplusone.com

46 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2018 Fass J, Sivak DA, Crooks GE, Beauchamp KA, Leimkuhler B, Chodera JD. Quantifying Configuration-Sampling Error in Langevin Simulations of Complex Molecular Systems. Entropy (Basel, Switzerland). 20. PMID 30393452 DOI: 10.3390/e20050318  1
2017 Rotskoff GM, Crooks GE, Vanden-Eijnden E. Geometric approach to optimal nonequilibrium control: Minimizing dissipation in nanomagnetic spin systems. Physical Review. E. 95: 012148. PMID 28208424 DOI: 10.1103/PhysRevE.95.012148  0.84
2016 Sivak DA, Crooks GE. Thermodynamic geometry of minimum-dissipation driven barrier crossing. Physical Review. E. 94: 052106. PMID 27967045 DOI: 10.1103/PhysRevE.94.052106  1
2016 Gingrich TR, Rotskoff GM, Crooks GE, Geissler PL. Near-optimal protocols in complex nonequilibrium transformations. Proceedings of the National Academy of Sciences of the United States of America. PMID 27573816 DOI: 10.1073/pnas.1606273113  0.84
2015 Rotskoff GM, Crooks GE. Optimal control in nonequilibrium systems: Dynamic Riemannian geometry of the Ising model. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 92: 060102. PMID 26764609 DOI: 10.1103/PhysRevE.92.060102  1
2014 Iyer-Biswas S, Wright CS, Henry JT, Lo K, Burov S, Lin Y, Crooks GE, Crosson S, Dinner AR, Scherer NF. Scaling laws governing stochastic growth and division of single bacterial cells. Proceedings of the National Academy of Sciences of the United States of America. 111: 15912-7. PMID 25349411 DOI: 10.1073/pnas.1403232111  1
2014 Iyer-Biswas S, Crooks GE, Scherer NF, Dinner AR. Universality in stochastic exponential growth. Physical Review Letters. 113: 028101. PMID 25062238 DOI: 10.1103/PhysRevLett.113.028101  1
2014 Sivak DA, Chodera JD, Crooks GE. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems. The Journal of Physical Chemistry. B. 118: 6466-74. PMID 24555448 DOI: 10.1021/jp411770f  1
2014 Sivak DA, Chodera JD, Crooks GE. Time step rescaling recovers continuous-time dynamical properties for discrete-time Langevin integration of nonequilibrium systems Journal of Physical Chemistry B. 118: 6466-6474. DOI: 10.1021/jp411770f  1
2013 Sivak DA, Chodera JD, Crooks GE. Using nonequilibrium fluctuation theorems to understand and correct errors in equilibrium and nonequilibrium simulations of discrete Langevin dynamics Physical Review X. 3. DOI: 10.1103/PhysRevX.3.011007  1
2012 Zulkowski PR, Sivak DA, Crooks GE, DeWeese MR. Geometry of thermodynamic control. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 86: 041148. PMID 23214570 DOI: 10.1103/PhysRevE.86.041148  1
2012 Still S, Sivak DA, Bell AJ, Crooks GE. Thermodynamics of prediction. Physical Review Letters. 109: 120604. PMID 23005932  1
2012 Sivak DA, Crooks GE. Thermodynamic metrics and optimal paths. Physical Review Letters. 108: 190602. PMID 23003019 DOI: 10.1103/PhysRevLett.108.190602  1
2012 Sivak DA, Crooks GE. Near-equilibrium measurements of nonequilibrium free energy. Physical Review Letters. 108: 150601. PMID 22587237 DOI: 10.1103/PhysRevLett.108.150601  1
2012 Still S, Sivak DA, Bell AJ, Crooks GE. Thermodynamics of prediction Physical Review Letters. 109. DOI: 10.1103/PhysRevLett.109.120604  1
2012 Sivak DA, Crooks GE. Thermodynamic metrics and optimal paths Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.190602  1
2012 Sivak DA, Crooks GE. Near-equilibrium measurements of nonequilibrium free energy Physical Review Letters. 108. DOI: 10.1103/PhysRevLett.108.150601  1
2012 Nilmeier JP, Crooks GE, Minh DDL, Chodera JD. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation (Proceedings of the National Academy of Sciences of the United States of America (2011) 108, 45 (E1009-E1018) 10.1073/pnas.1106094108) Proceedings of the National Academy of Sciences of the United States of America. 109: 9665. DOI: 10.1073/pnas.1207617109  1
2011 Nilmeier JP, Crooks GE, Minh DD, Chodera JD. Nonequilibrium candidate Monte Carlo is an efficient tool for equilibrium simulation. Proceedings of the National Academy of Sciences of the United States of America. 108: E1009-18. PMID 22025687 DOI: 10.1073/pnas.1106094108  1
2011 Crooks GE. On thermodynamic and microscopic reversibility Journal of Statistical Mechanics: Theory and Experiment. 2011. DOI: 10.1088/1742-5468/2011/07/P07008  1
2011 Crooks GE, Sivak DA. Measures of trajectory ensemble disparity in nonequilibrium statistical dynamics Journal of Statistical Mechanics: Theory and Experiment. 2011. DOI: 10.1088/1742-5468/2011/06/P06003  1
2009 Greenfield D, McEvoy AL, Shroff H, Crooks GE, Wingreen NS, Betzig E, Liphardt J. Self-organization of the Escherichia coli chemotaxis network imaged with super-resolution light microscopy. Plos Biology. 7: e1000137. PMID 19547746 DOI: 10.1371/journal.pbio.1000137  1
2009 Feng EH, Crooks GE. Far-from-equilibrium measurements of thermodynamic length Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 79. DOI: 10.1103/PhysRevE.79.012104  1
2009 Crooks GE. 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)] Journal of Chemical Physics. 130. DOI: 10.1063/1.3080751  1
2008 Maragakis P, Ritort F, Bustamante C, Karplus M, Crooks GE. Bayesian estimates of free energies from nonequilibrium work data in the presence of instrument noise. The Journal of Chemical Physics. 129: 024102. PMID 18624511 DOI: 10.1063/1.2937892  1
2008 Feng EH, Crooks GE. Length of time's arrow Physical Review Letters. 101. DOI: 10.1103/PhysRevLett.101.090602  1
2008 Crooks GE. On the Jarzynski relation for dissipative quantum dynamics Journal of Statistical Mechanics: Theory and Experiment. 2008. DOI: 10.1088/1742-5468/2008/10/P10023  1
2007 Crooks GE. Measuring thermodynamic length Physical Review Letters. 99. DOI: 10.1103/PhysRevLett.99.100602  1
2007 Crooks GE. Beyond Boltzmann-Gibbs statistics: Maximum entropy hyperensembles out of equilibrium Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 75. DOI: 10.1103/PhysRevE.75.041119  1
2007 Crooks GE, Jarzynski C. Work distribution for the adiabatic compression of a dilute and interacting classical gas Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 75. DOI: 10.1103/PhysRevE.75.021116  1
2006 Casbon JA, Crooks GE, Saqi MAS. A high level interface to SCOP and ASTRAL implemented in Python Bmc Bioinformatics. 7. PMID 16403221 DOI: 10.1186/1471-2105-7-10  1
2005 Crooks GE, Green RE, Brenner SE. Pairwise alignment incorporating dipeptide covariation Bioinformatics. 21: 3704-3710. PMID 16123116 DOI: 10.1093/bioinformatics/bti616  1
2005 Price GA, Crooks GE, Green RE, Brenner SE. Statistical evaluation of pairwise protein sequence comparison with the Bayesian bootstrap Bioinformatics. 21: 3824-3831. PMID 16105900 DOI: 10.1093/bioinformatics/bti627  1
2005 Zachariah MA, Crooks GE, Holbrook SR, Brenner SE. A generalized affine gap model significantly improves protein sequence alignment accuracy Proteins: Structure, Function and Genetics. 58: 329-338. PMID 15562515 DOI: 10.1002/prot.20299  1
2005 Crooks GE, Brenner SE. An alternative model of amino acid replacement Bioinformatics. 21: 975-980. PMID 15531614 DOI: 10.1093/bioinformatics/bti109  1
2004 Crooks GE, Wolfe J, Brenner SE. Measurements of protein sequence-structure correlations Proteins: Structure, Function and Genetics. 57: 804-810. PMID 15476257 DOI: 10.1002/prot.20262  1
2004 Trepagnier EH, Jarzynski C, Ritort F, Crooks GE, Bustamante CJ, Liphardt J. Experimental test of Hatano and Sasa's nonequilibrium steady-state equality. Proceedings of the National Academy of Sciences of the United States of America. 101: 15038-41. PMID 15469914 DOI: 10.1073/pnas.0406405101  1
2004 Crooks GE, Hon G, Chandonia JM, Brenner SE. WebLogo: A sequence logo generator Genome Research. 14: 1188-1190. PMID 15173120 DOI: 10.1101/gr.849004  1
2004 Crooks GE, Brenner SE. Protein secondary structure: Entropy, correlations and prediction Bioinformatics. 20: 1603-1611. PMID 14988117 DOI: 10.1093/bioinformatics/bth132  1
2001 Crooks GE, Chandler D. Efficient transition path sampling for nonequilibrium stochastic dynamics. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 64: 026109. PMID 11497653  0.96
2001 Crooks GE, Chandler D. Efficient transition path sampling for nonequilibrium stochastic dynamics Physical Review E - Statistical, Nonlinear, and Soft Matter Physics. 64: 261091-261094.  1
2000 Crooks GE. Path-ensemble averages in systems driven far from equilibrium Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 61: 2361-2366.  1
1999 Crooks GE, Ostrovsky B, Bar-Yam Y. Mesostructure of polymer collapse and fractal smoothing Physical Review. E, Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 4559-4563. PMID 11970313  1
1999 Crooks GE. Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 60: 2721-2726. PMID 11970075  1
1998 Crooks GE. Nonequilibrium measurements of free energy differences for microscopically reversible Markovian systems Journal of Statistical Physics. 90: 1481-1487.  1
1997 Crooks GE, Chandler D. Gaussian statistics of the hard-sphere fluid Physical Review E - Statistical Physics, Plasmas, Fluids, and Related Interdisciplinary Topics. 56: 4217-4221.  1
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