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The Comparison of Monte Carlo Algorithms Applied for Off-Lattice Models of Polymer Chains

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EN
Abstrakty
EN
We designed two simplified models of macromolecular systems. Model chains were built of united atoms (statistical segments): the first one was a bead-spring model while in the second one beads were connected by bonds of constant length. The only potential introduced was the excluded volume and thus the system was athermal. Monte Carlo simulations of these models were carried out using Metropolis-like algorithms appropriate for each model: the one-bead displacement and the backrub algorithm. The scaling analysis of the chain’s static and dynamic properties was carried out. The universal behavior of the chain’s properties under consideration was found and discussed. The efficiency of both algorithms was compared and discussed.
Twórcy
autor
  • Department of Chemistry, University of Warsaw Pasteura 1, 02-093 Warszawa, Poland
autor
  • Department of Chemistry, University of Warsaw Pasteura 1, 02-093 Warszawa, Poland
autor
  • Department of Chemistry, University of Warsaw Pasteura 1, 02-093 Warszawa, Poland
Bibliografia
  • [1] J. Baschnagel, J.P. Wittmer, H. Meyer, Monte Carlo Simulation of Polymers: Coarse-Grained Models, in: Computational Soft Matter: From Synthetic Polymers to Proteins, Lecture Notes, N. Attig, K. Binder, H. Grubmüller, K. Kremer (eds.), John von Neumann Institute for Computing, Jülich, Vol. 23, p. 83-140, 2004.
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  • [5] P. Gniewek, A. Kolinski, Coarse-Grained Monte Carlo Simulations of Mucus: Structure, Dynamics, and Thermodynamics, Biophys. J. 99, 3507-3516 (2010).
  • [6] K. Binder, A. Milchev, Off-lattice Monte Carlo methods for coarse-grained models of polymeric materials and selected applications, J. Comput.-Aided Mater. 9, 33-74 (2002).
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  • [9] C.A. Smith, T. Kortemme, Backrub-like backbone simulation recapitulates natural protein conformational variability and improves mutant side-chain prediction, J. Mol. Biol. 380, 742-756 (2008).
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  • [11] I.W. Davis, W.B. Arendall III, D.C. Richardson, J.S. Richardson, The backrub motion: how protein backbone shrugs when a sidechain dances, Structure 14, 265-274 (2006).
  • [12] I. Teraoka, Polymer Solutions. An Introduction to Physical Properties, Wiley-Interscience, New York 2002.
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  • [16] C.F. Abrams, K. Kremer, Effects of excluded volume and bond length on the dynamics of dense bead-spring polymer melts, J. Chem. Phys. 116, 3162-3165 (2002).
  • [17] D.P. Landau, K. Binder, A Guide to Monte Carlo Simulations in Statistical Physics, 3rd edition, Cambridge University Press, Cambridge, chapter 6.6, 2009.
  • [18] P. Romiszowski, A. Sikorski, Dynamics of polymer chains in confined space. A computer simulation study, Physica A 357, 356-363 (2005).
  • [19] P. Polanowski, J.K. Jeszka, A. Sikorski, Dynamic properties of linear and cyclic chains in two dimensions. Computer simulation atudies, Macromolecules 47, 4830-4839 (2014).
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Uwagi
PL
Opracowanie ze środków MNiSW w ramach umowy 812/P-DUN/2016 na działalność upowszechniającą naukę.
Typ dokumentu
Bibliografia
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