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An improvement of the sequential algorithm for modeling the chain-like-bodies motion

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Języki publikacji
EN
Abstrakty
EN
Numerous simulation studies in statistical physics make use of various algorithms that are designed for modeling of the chain-like-body (CLB) motion. In recent years within this group a new sequential algorithm was proposed. The main idea of this new approach to the algorithmization of the CLB motion is based on the incorporation of the tension propagation mechanism into each simulated move. In this paper, improvement of this algorithm by implementation of the direction-preference-mechanism is proposed. This modification enables one to better mimic the real behavior of the CLB. The impact of the new procedure on the simulation process is studied with the help of metamodels that relate to some important characteristics of the CLB motion with the algorithm’s new parameters.
Rocznik
Strony
5--16
Opis fizyczny
Bibliogr. 21 poz., rys., tab.
Twórcy
  • Institute of Mathematics, Czestochowa University of Technology Częstochowa, Poland
Bibliografia
  • [1] Dubbeldam, J.L.A., Rostiashvili, V.G., Milchev, A., & Vilgis, T.A. (2012). Forced translocation of polymer: Dynamical scaling versus molecular dynamics simulation. Physical Review E, 85, 041801.
  • [2] Huopaniemi, I., & Luo, K. (2006). Langevin dynamics simulations of polymer translocation through nanopores. The Journal of Chemical Physics, 125, 124901.
  • [3] Liang, L., Shen, J-W., Zhang, Z., & Wang Q. (2017). DNA sequencing by two-dimensional materials: As theoretical modeling meets experiments. Biosensors and Bioelectronics, 89, 280-292.
  • [4] Panja, D., Barkema, G.T., & van Leeuwen, J.M.J. (2016). Dynamics of a double-stranded DNA segment in a shear flow, arXiv: 1603.05227v1 [cond-mat.soft].
  • [5] Gundersen-Rindal D. (2012). Integration of Polydnavirus DNA into Host Cellular Genomic DNA, In: Parasitoid Viruses. Symbionts and Pathogens, 99-113.
  • [6] Wickner, W., & Schekman, R. (2005). Protein translocation across biological membranes. Science, 310, 1452-6.
  • [7] Miller T.V. (1998). Bacterial Gene Swapping in Nature. Scientific American.
  • [8] Luo, K., Ala-Nissila, T., & Ying, S.C. (2006). Polymer translocation through a nanopore: A two-dimensional Monte Carlo Study. The Journal of Chemical Physics, 124(3), 034714.
  • [9] Lubensky, D.K., & Nelson, D.R. (1999). Driven polymer translocation through a narrow pore. Biophysical Journal, 77, 1824-1838.
  • [10] Abdolvahab, R.H. (2006). Investigating binding particles distribution effects on polymer translocation through nanopore. Physics Letters A, 380, 1023-1030.
  • [11] Sarabadani, J., Ghosh, B., Chaudhury, S., & Ala-Nissila, T. (2017). Dynamics of end-pulled polymer translocation through a nanopore, arXiv:1708.09184 [cond-mat.soft].
  • [12] Żurek, S., Kośmider, M., Drzewiński, A., & van Leeuwen, J.M.J. (2012). Translocation of polymers in a lattice model. The European Phys. J. E: Soft Matter and Biological Physics, 35, 47.
  • [13] Chatelain, C., Kantor, Y., & Kardar, M. (2008). Probability distributions for polymer translocation. Physical Review E, 78, 021129.
  • [14] D’Adamo, G., Pelissetto, A., & Pierleoni, C. (2012). Polymers as compressible soft spheres. arXiv: 1205.5654v1, cond-mat.soft.
  • [15] Kolli, H.B., & Murthy, K.P.N. (2012). Phase transition in a bond fluctuating lattice polymer, arXiv: 1204.2691v2 [cond-mat.soft].
  • [16] Gauthier, M.G., & Slater, G.W. (2008). A Monte Carlo algorithm to study polymer translocation through nanopores. I. Theory and numerical approach. The Journal of Chemical Physics, 128, 065103.
  • [17] Gauthier, M.G. & Slater, G.W. (2008). A Monte Carlo algorithm to study polymer translocation through nanopores. II. Scaling laws. The Journal of Chemical Physics, 128, 205103.
  • [18] Grzybowski, A.Z., & Domanski, Z. (2011). A sequential algorithm for modeling random movements of chain-like structures. Scientific Research of the Institute of Mathematics and Computer Science, 10(1), 5-10.
  • [19] Grzybowski, A.Z., Domański, Z., & Bartłomiejczyk, K. (2013). Algorithmization and simulation of the chain-like structures’ dynamics-interrelations between movement characteristics. Acta Eletrotechnica et Informatica, 13(4).
  • [20] Grzybowski, A.Z., & Domański, Z. (2013). A sequential algorithm with built in tensionpropagation mechanism for modeling the chain-like bodies dynamics, http://arxiv.org/pdf/1312.4206v1.pdf.
  • [21] Yu, W., Ma, Y., & Luo, K. (2012). Translocation of stiff polymers through a nanopore driven by binding particles. The Journal of Chemical Physics, 137, 244905.
Uwagi
Opracowanie rekordu w ramach umowy 509/P-DUN/2018 ze środków MNiSW przeznaczonych na działalność upowszechniającą naukę (2018).
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-e083d70c-61a4-475d-8b1e-7e6bf9e53e8a
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