Implementation and performance of the needle chain-algorithm for Brownian dynamics simulation |
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| Institution: | Norwegian University of Science and Technology (NTNU), Norwegian Biopolymer Laboratory (NOBIPOL), Department of Physics, Sem Saelandsvei 9, N-7465 Trondheim, Norway;School of Energy and Power Engineering, Northeast Electric Power University, Jilin City 132012, China;Hassan II University, Faculty of Sciences Aïn Chock, Laboratory of Mechanics, B.P. 5366 Mâarif, Casablanca, Morocco;Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, 110 8th St., Troy, NY 12180, USA;Department of Physics, The Ohio State University, 191 W Woodruff Ave., Columbus, Ohio 43210, USA;Institute of Chemistry, State University of Campinas – UNICAMP, 13083-970, Campinas, Brazil |
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| Abstract: | The first algorithm for Brownian dynamics (BD) simulation of needle chains (the NC-algorithm) was developed recently by Nyland et al. (J. Chem. Phys. 1996;105:1198). Here we report on an implementation of the NC-algorithm using Nn rigid segments composed of Nbn spherical beads, and its efficiency relative to the Ermak–McCammon BD algorithm (J. Chem. Phys. 1978;69:1352) used to simulate bead-spring polymer chains consisting of Nb beads arranged into Nn stiff segments each composed of Nbn beads. For segmented chains the NC-algorithm can use a dimensionless time-step that is about four orders of magnitude larger than that of the bead-spring BD algorithm. In addition, the computer time required to perform a single dimensionless time-step scales as Nb2 and Nb3 for the NC-algorithm and the bead-spring algorithms, respectively. This demonstrates that, for polymer chains consisting of needles or rigid segments with aspect ratios larger than three, the NC-algorithm is vastly more efficient than the Ermak–McCammon BD algorithm. |
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