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Arrar, M.; Boubeta, F.M.; Szretter, M.E.; Sued, M.; Boechi, L.; Rodriguez, D. "On the accurate estimation of free energies using the jarzynski equality" (2019) Journal of Computational Chemistry. 40(4):688-696
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Abstract:

The Jarzynski equality is one of the most widely celebrated and scrutinized nonequilibrium work theorems, relating free energy to the external work performed in nonequilibrium transitions. In practice, the required ensemble average of the Boltzmann weights of infinite nonequilibrium transitions is estimated as a finite sample average, resulting in the so-called Jarzynski estimator, (Formula presented.). Alternatively, the second-order approximation of the Jarzynski equality, though seldom invoked, is exact for Gaussian distributions and gives rise to the Fluctuation-Dissipation estimator (Formula presented.). Here we derive the parametric maximum-likelihood estimator (MLE) of the free energy (Formula presented.) considering unidirectional work distributions belonging to Gaussian or Gamma families, and compare this estimator to (Formula presented.). We further consider bidirectional work distributions belonging to the same families, and compare the corresponding bidirectional (Formula presented.) to the Bennett acceptance ratio ((Formula presented.)) estimator. We show that, for Gaussian unidirectional work distributions, (Formula presented.) is in fact the parametric MLE of the free energy, and as such, the most efficient estimator for this statistical family. We observe that (Formula presented.) and (Formula presented.) perform better than (Formula presented.) and (Formula presented.), for unidirectional and bidirectional distributions, respectively. These results illustrate that the characterization of the underlying work distribution permits an optimal use of the Jarzynski equality. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Registro:

Documento: Artículo
Título:On the accurate estimation of free energies using the jarzynski equality
Autor:Arrar, M.; Boubeta, F.M.; Szretter, M.E.; Sued, M.; Boechi, L.; Rodriguez, D.
Filiación:Instituto de Química-Física de los Materiales, Medio Ambiente y Energía, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina, Departamento de Química Inorgánica, Analítica y Química Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Departamento de Matemática, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina, Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
Instituto de Cálculo, CONICET-Facultad de Ciencias Exactas y Naturales, Universidad de Buenos AiresBuenos Aires, Argentina
Palabras clave:free energy; Jarzynski; maximum-likelihood; steered molecular dynamics; Free energy; Gaussian distribution; Maximum likelihood; Maximum likelihood estimation; Molecular dynamics; Sampling; Accurate estimation; Bennett acceptance ratio; Fluctuation dissipation; Jarzynski; Maximum likelihood estimators (MLE); Nonequilibrium transition; Second-order approximation; Steered molecular dynamics; Parameter estimation
Año:2019
Volumen:40
Número:4
Página de inicio:688
Página de fin:696
DOI: http://dx.doi.org/10.1002/jcc.25754
Título revista:Journal of Computational Chemistry
Título revista abreviado:J. Comput. Chem.
ISSN:01928651
CODEN:JCCHD
Registro:https://bibliotecadigital.exactas.uba.ar/collection/paper/document/paper_01928651_v40_n4_p688_Arrar

Referencias:

  • Jarzynski, C., (1997) Phys. Rev. Lett., 78, p. 2690
  • Zwanzig, R.W., (1955) J. Chem. Phys., 23, p. 1915
  • Bizzarri, A.R., Cannistraro, S., (2011) Phys. Chem. Chem. Phys., 13, p. 2738. , https://doi.org/10.1039/C0CP01474E
  • Orzechowski, M., Cieplak, P., (2005) J. Phys. Condens. Matter, 17, p. S1627. , http://stacks.iop.org/0953-8984/17/i=18/a=018
  • Oberhofer, H., Dellago, C., Boresch, S., (2007) Phys. Rev. E, 75, p. 061106. , http://link.aps.org/doi/10.1103/PhysRevE.75.061106
  • Liu, W., Montana, V., Parpura, V., Mohideen, U., (2008) Biophys. J., 95, p. 419. , http://www.sciencedirect.com/science/article/pii/S000634950870314X
  • Hyeon, C., Thirumalai, D., (2005) Proc. Natl. Acad. Sci. U. S. A., 102, p. 6789. , http://www.pnas.org/content/102/19/6789.full.pdf, http://www.pnas.org/content/102/19/6789.abstract
  • Ozer, G., Valeev, E.F., Quirk, S., Hernandez, R., (2010) J. Chem. Theory Comput., 6, p. 3026. , https://doi.org/10.1021/ct100320g, https://doi.org/10.1021/ct100320g
  • Nicoletti, F.P., Comandini, A., Bonamore, A., Boechi, L., Boubeta, F.M., Feis, A., Smulevich, G., Boffi, A., (2010) Biochemistry, 49, p. 2269
  • Boechi, L., Arrar, M., Martí, M.A., Olson, J.S., Roitberg, A.E., Estrin, D.A., (2013) J. Biol. Chem., 288, p. 6754
  • Arroyo Manez, P., Bikiel, D.E., Boechi, L., Capece, L., Di Lella, S., Estrin, D.A., Marti, M.A., Petruk, A.A., (2011) Biochim. Biophys. Acta, 1814, p. 1054
  • Park, S., Schulten, K., (2004) J. Chem. Phys., 120, p. 5946
  • Procacci, P., Marsili, S., (2010) Chem. Phys., 375, p. 8. , http://www.sciencedirect.com/science/article/pii/S0301010410003216
  • Jarzynski, C., (2011) Annu. Rev. Condens. Matter Phys., 2, p. 329
  • Gore, J., Ritort, F., Bustamante, C., (2003) Proc. Natl. Acad. Sci., 100, p. 12564
  • Hermans, J., (1991) J. Phys. Chem., 95, p. 9029
  • Wood, R.H., Muhlbauer, W.C., Thompson, P.T., (1991) J. Phys. Chem., 95, p. 6670
  • Callen, H.B., Welton, T., (1951) Phys. Rev., 83, p. 34
  • Jarzynski, C., (2006) Phys. Rev. E, 73, p. 046105
  • Yunger Halpern, N., Jarzynski, C., (2016) Phys. Rev. E, 93, p. 052144
  • Pohorille, A., Jarzynski, C., Chipot, C., (2010) J. Phys. Chem. B, 114, p. 10235
  • Hummer, G., (2007) Free Energy Calculations, p. 171. , Springer, New York, p
  • Hummer, G., (2001) J. Chem. Phys., 114, p. 7330
  • Ramírez, C.L., Zeida, A., Jara, G.E., Roitberg, A.E., Marti, M.A., (2014) J. Chem. Theory Comput., 10, p. 4609
  • Vaikuntanathan, S., Jarzynski, C., (2008) Phys. Rev. Lett., 100, p. 190601
  • Schmiedl, T., Seifert, U., (2007) Phys. Rev. Lett., 98, p. 108301
  • Chelli, R., (2012) J. Chem. Theory Comput., 8, p. 4040
  • Nicolini, P., Frezzato, D., Chelli, R., (2011) J. Chem. Theory Comput., 7, p. 582
  • Zerbetto, M., Piserchia, A., Frezzato, D., (2014) J. Comput. Chem., 35, p. 1865
  • Zuckerman, D.M., Woolf, T.B., (2001), Phys. Ther./0107066 (,), related9VAObcuyCwwJ; Ytreberg, F.M., Zuckerman, D.M., (2004) J. Comput. Chem., 25, p. 1749
  • Zuckerman, D.M., Woolf, T.B., (2002) Chem. Phys. Lett., 351, p. 445
  • Bucher, D., Walker, R.C., McCammon, J.A., (2014) J. Chem. Theory Comput., 10, p. 2677
  • Echeverria, I., Amzel, L.M., (2012) J. Phys. Chem. B, 116, p. 10986
  • Crooks, G.E., (2000) Phys. Rev. E, 61, p. 2361
  • Shirts, M.R., Bair, E., Hooker, G., Pande, V.S., (2003) Phys. Rev. Lett., 91, p. 140601
  • Bennett, C.H., (1976) J. Comput. Phys., 22, p. 245
  • Hummer, G., Szabo, A., (2001) Proc. Natl. Acad. Sci., 98, p. 3658
  • Minh, D.D.L., Adib, A.B., (2008) Phys. Rev. Lett., 100, p. 180602. , http://link.aps.org/doi/10.1103/PhysRevLett.100.180602
  • Minh, D.D.L., Chodera, J.D., (2009) J. Chem. Phys., 131, p. 134110
  • Nicolini, P., Procacci, P., Chelli, R., (2010) J. Phys. Chem. B, 114, p. 9546
  • Shirts, M.R., Pande, V.S., (2005) J. Chem. Phys., 122, p. 144107
  • Minh, D.D., McCammon, J.A., (2008) J. Phys. Chem. B, 112, p. 5892
  • Ferguson, D.M., (1993) J. Chem. Phys., 99, p. 10086
  • Mazonka, O., Jarzynski, C., (1999); Liphardt, J., Dumont, S., Smith, S.B., Tinoco, I.J., Bustamante, C., (2002) Science, 296, p. 1832
  • Giorgino, T., De Fabritiis, G., (2011) J. Chem. Theory Comput., 7, p. 1943
  • Boubeta, F.M., Bari, S.E., Estrin, D.A., Boechi, L., (2016) J. Phys. Chem. B, 120, p. 9642
  • Chipot, C., Hénin, J., (2005) J. Chem. Phys., 123, p. 244906
  • Xiong, H., Crespo, A., Marti, M., Estrin, D., Roitberg, A.E., (2006) Theor. Chem. Accounts, 116, p. 338
  • Boresch, S., Woodcock, H.L., (2017) Mol. Phys., 115, p. 1200
  • Nategholeslam, M., Gray, C.G., Tomberli, B., (2017) J. Phys. Chem. B, 121, p. 391. , https://doi.org/10.1021/acs.jpcb.6b08701, https://doi.org/10.1021/acs.jpcb.6b08701
  • Lu, N., Kofke, D.A., (2001) J. Chem. Phys., 114, p. 7303
  • Lu, N., Kofke, D.A., (2001) J. Chem. Phys., 115, p. 6866
  • Wu, D., Kofke, D.A., (2005) J. Chem. Phys., 123, p. 054103
  • Wu, D., Kofke, D.A., (2004) Phys. Rev. E, 70, p. 066702
  • Crooks, G.E., Jarzynski, C., (2007) Phys. Rev. E, 75, p. 021116. , http://link.aps.org/doi/10.1103/PhysRevE.75.021116
  • Wasserman, L., (2013) All of statistics: a concise course in statistical inference, , Springer Science & Business Media, New York
  • Scott, D.W., (2015) Multivariate density estimation: theory, practice, and visualization, , John Wiley & Sons, New Jersey
  • Eric Jones, P.P., (2001), http://www.scipy.org/, Travis Oliphant,, SciPy Open source scientific tools for Python; Shirts, M.R., Chodera, J.D., (2008) J. Chem. Phys., 129, p. 124105
  • Lehmann, E.L., Casella, G., (2006) Theory of point estimation, , Springer Science & Business Media, New York
  • Casella, G., Berger, R.L., (2002) Statistical inference, 2. , Duxbury Pacific Grove, CA
  • Zhang, D., Gullingsrud, J., McCammon, J.A., (2006) J. Am. Chem. Soc., 128, p. 3019
  • Hayashi, K., Ueno, H., Iino, R., Noji, H., (2010) Phys. Rev. Lett., 104, p. 218103
  • Jensen, J.L.W.V., (1906) Acta Math., 30, p. 175
  • Jarzynski, C., (1997) Phys. Rev. E, 56, p. 5018
  • Douarche, F., Ciliberto, S., Petrosyan, A., Rabbiosi, I., (2005) Europhy. Lett., 70, p. 593
  • Harris, N.C., Song, Y., Kiang, C.-H., (2007) Phys. Rev. Lett., 99, p. 068101. , http://link.aps.org/doi/10.1103/PhysRevLett.99.068101
  • Forti, F., Boechi, L., Estrin, D.A., Marti, M.A., (2011) J. Comput. Chem., 32, pp. 2219-2231. , https://doi.org/10.1002/jcc.21805
  • Palassini, M., Ritort, F., (2011) Phys. Rev. Lett., 107, p. 060601. , http://link.aps.org/doi/10.1103/PhysRevLett.107.060601
  • Wu, D., Kofke, D.A., (2004) J. Chem. Phys., 121, p. 8742
  • Shirts, M.R., Pande, V.S., (2005) J. Chem. Phys., 122, p. 144107
  • Zuckerman, D.M., Woolf, T.B., (2002) Phys. Rev. Lett., 89, p. 180602
  • Wu, D., Kofke, D.A., (2005) J. Chem. Phys., 123, p. 084109

Citas:

---------- APA ----------
Arrar, M., Boubeta, F.M., Szretter, M.E., Sued, M., Boechi, L. & Rodriguez, D. (2019) . On the accurate estimation of free energies using the jarzynski equality. Journal of Computational Chemistry, 40(4), 688-696.
http://dx.doi.org/10.1002/jcc.25754
---------- CHICAGO ----------
Arrar, M., Boubeta, F.M., Szretter, M.E., Sued, M., Boechi, L., Rodriguez, D. "On the accurate estimation of free energies using the jarzynski equality" . Journal of Computational Chemistry 40, no. 4 (2019) : 688-696.
http://dx.doi.org/10.1002/jcc.25754
---------- MLA ----------
Arrar, M., Boubeta, F.M., Szretter, M.E., Sued, M., Boechi, L., Rodriguez, D. "On the accurate estimation of free energies using the jarzynski equality" . Journal of Computational Chemistry, vol. 40, no. 4, 2019, pp. 688-696.
http://dx.doi.org/10.1002/jcc.25754
---------- VANCOUVER ----------
Arrar, M., Boubeta, F.M., Szretter, M.E., Sued, M., Boechi, L., Rodriguez, D. On the accurate estimation of free energies using the jarzynski equality. J. Comput. Chem. 2019;40(4):688-696.
http://dx.doi.org/10.1002/jcc.25754