Allen, Michael P., Quigley, David and Růžička, Štěpán. (2012) Folding kinetics of a polymer. Physical Chemistry Chemical Physics . ISSN 1463-9076 (In Press)

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Abstract

We simulate the first-order globule-crystal transition of a flexible homopolymer chain, both by collision dynamics, and Wang-Landau Monte Carlo with unphysical (connectivity-altering) moves. We observe that the top eigenvalue in the spectrum of the nonbonded contact matrix provides insight into the ensembles of folding and unfolding trajectories, and may be a suitable additional reaction coordinate for the folding transition of chain molecules. In particular, it seems to identify a large fraction of configurations on the folding pathway at the free energy maximum that have a very low probability of reaching the crystallized state. We also discuss the difference between the effective kinetic and thermodynamic transition temperatures, in the light of possible kinetic hindering effects.

Item Type:	Journal Article
Subjects:	Q Science > QC Physics Q Science > QD Chemistry
Divisions:	Faculty of Science > Physics
Library of Congress Subject Headings (LCSH):	Solid-liquid interfaces -- Computer simulation, Chemical kinetics -- Computer simulation
Journal or Publication Title:	Physical Chemistry Chemical Physics
Publisher:	Royal Society of Chemistry
ISSN:	1463-9076
Date:	2012
Identification Number:	10.1039/c2cp00051b
Status:	Peer Reviewed
Publication Status:	In Press
Access rights to Published version:	Restricted or Subscription Access
References:	1 Y. Q. Zhou, C. K. Hall and M. Karplus, Phys. Rev. Lett., 1996, 77, 2822– 2825. 2 Y. Q. Zhou, M. Karplus, J. M. Wichert and C. K. Hall, J. Chem. Phys., 1997, 107, 10691–10708. 3 J. E. Magee, V. R. Vasquez and L. Lue, Phys. Rev. Lett., 2006, 96, 207802. 4 W. Paul, T. Strauch, F. Rampf and K. Binder, Phys. Rev. E, 2007, 75, 060801. 5 M. P. Taylor, W. Paul and K. Binder, Phys. Rev. E, 2009, 79, 050801. 6 M. P. Taylor, W. Paul and K. Binder, J. Chem. Phys., 2009, 131, 114907. 7 D. T. Seaton, T. W¨ust and D. P. Landau, Phys. Rev. E, 2010, 81, 011802. 8 M. P. Taylor, W. Paul and K. Binder, Phys. Procedia, 2010, 4, 151. 9 D. L. Pagan and J. D. Gunton, J. Chem. Phys., 2005, 122, 184515/1–6. 10 H. Liu, S. Garde and S. Kumar, J. Chem. Phys., 2005, 123, 174505/1–4. 11 F. G. Wang and D. P. Landau, Phys. Rev. Lett., 2001, 86, 2050–2053. 12 M. Cheon, I. Chang and C. K. Hall, Proteins: Structure, Function, and Bioinformatics, 2010, 78, 2950–2960. 13 N. Kikuchi, J. F. Ryder, C. M. Pooley and J. M. Yeomans, Phys. Rev. E, 2005, 71, 061804/1–8. 14 T. T. Pham, M. Bajaj and J. R. Prakash, Soft Matter, 2008, 4, 1196–1207. 15 R. S. Hoy and C. S. O’Hern, Soft Matter, 2012, 8, 1215–1225. 16 P. R. ten Wolde and D. Chandler, Proc. Nat. Acad. Sci., 2002, 99, 6539– 6543. 17 T. F. Miller, E. Vanden-Eijnden and D. Chandler, Proc. Nat. Acad. Sci., 2007, 104, 14559–14564. 18 R. J. Allen, P. B. Warren and P. R. ten Wolde, Phys. Rev. Lett., 2005, 94, 018104. 19 R. J. Allen, C. Valeriani and P. R. ten Wolde, J. Phys. Condens. Matter, 2009, 21, 463102. 20 F. A. Escobedo, E. E. Borrero and J. C. Araque, J. Phys. Condens. Matter, 2009, 21, 333101. 21 M. Vendruscolo, B. Subramanian, I. Kanter, E. Domany and J. Lebowitz, Phys. Rev. E, 1999, 59, 977. 22 J. L. England and E. I. Shakhnovich, Phys. Rev. Lett., 2003, 90, 218101. 23 L. Mirny and E. Shakhnovich, Annual Review of Biophysics and Biomolecular Structure, 2001, 30, 361–396. 24 G. Lois, J. Blawzdziewicz and C. S. O’Hern, Phys. Rev. E, 2010, 81, 051907. 25 R. S. Hoy and C. S. O’Hern, Phys. Rev. Lett., 2010, 105, 068001. 26 J. M. Polson and M. J. Zuckermann, J. Chem. Phys., 2002, 116, 7244– 7254. 27 M. Dijkstra, D. Frenkel and J. P. Hansen, J. Chem. Phys., 1994, 101, 3179–3189. 28 G. Luna-Barcenas, G. E. Bennett, I. C. Sanchez and K. P. Johnston, J. Chem. Phys., 1996, 104, 9971–9973. 29 J. K. C. Suen, F. A. Escobedo and J. J. de Pablo, J. Chem. Phys., 1997, 106, 1288–1290. 30 A. Montesi, M. Pasquali and F. C. MacKintosh, Phys. Rev. E, 2004, 69, 021916. 31 R. Chang and A. Yethiraj, J. Chem. Phys., 2001, 114, 7688–7699. 32 S. B. Opps, J. M. Polson and N. A. Risk, J. Chem. Phys., 2006, 125, 194904. 33 D. Frenkel and B. Smit, Understanding molecular simulation: from algorithms to applications, Academic Pr, 2002. 34 D. P. Landau and K. Binder, Guide To Monte Carlo Simulations In Statistical Physics, Cambridge Univ Pr, 2009. 35 M. P. Allen and D. J. Tildesley, Computer simulation of liquids, Oxford University Press, 1987. 36 D. C. Rapaport, The art of molecular dynamics simulation, Cambridge Univ Pr, 2004. 37 P. G. Bolhuis, J. Chem. Phys., 2008, 129, 114108. 38 F. Pietrucci and W. Andreoni, Phys. Rev. Lett., 2011, 107, 085504. 39 I. Bahar, A. R. Atilgan, M. C. Demirel and B. Erman, Phys. Rev. Lett., 1998, 80, 2733. 40 J. F. Sadoc, Eur. Phys. J. E, 2005, 18, 321. 41 K. Chen, W. G. Ellenbroek, Z. Zhang, D. T. N. Chen, P. J. Yunker, S. Henkes, C. Brito, O. Dauchot, W. van Saarloos, A. J. Liu and A. G. Yodh, Phys. Rev. Lett., 2010, 105, 025501. 42 C. Valeriani, R. J. Allen, M. J. Morelli, D. Frenkel and P. R. ten Wolde, J. Chem. Phys., 2007, 127, 114109. 43 R. Zwanzig, Proc. Nat. Acad. Sci., 1997, 94, 148–150. 44 P. Geiger and C. Dellago, Phys. Rev. E, 2010, 81, 021127. 45 J. T. Berryman and T. Schilling, Journal of Chemical Physics, 2010, 133, 244101. 46 T. van Erp, Advances in Chemical Physics, in press, http://arxiv.org/abs/1101.0927v2. 47 D. Wales, Energy Landscapes, Cambridge University Press, 2004. 48 A. Bar, Y. Kafri and D. Mukamel, Phys. Rev. Lett., 2007, 98, 038103. 49 A. Olivetti, J. Barre, B. Marcos, F. Bouchet and R. Kaiser, Phys. Rev. Lett., 2009, 103, 224301. 50 P. J. Steinhardt, D. R. Nelson and M. Ronchetti, Phys. Rev. B, 1983, 28, 784–805. 51 P.-R. ten Wolde, M. J. Ruiz-Montero and D. Frenkel, J. Chem. Phys., 1996, 104, 9932–9947. 52 B. E. Eichinger, Macromolecules, 1980, 13, 1–11. 53 K.-h. Nitta, Entropy, 2009, 11, 907–916. 54 T. Haliloglu, I. Bahar and B. Erman, Phys. Rev. Lett., 1997, 79, 3090– 3093. 55 M. Dolgushev, G. Berezovska and A. Blumen, J. Chem. Phys., 2010, 133, 154905.
URI:	http://wrap.warwick.ac.uk/id/eprint/43230

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