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International Journal for Multiscale Computational Engineering

年間 6 号発行

ISSN 印刷: 1543-1649

ISSN オンライン: 1940-4352

The Impact Factor measures the average number of citations received in a particular year by papers published in the journal during the two preceding years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) IF: 1.4 To calculate the five year Impact Factor, citations are counted in 2017 to the previous five years and divided by the source items published in the previous five years. 2017 Journal Citation Reports (Clarivate Analytics, 2018) 5-Year IF: 1.3 The Immediacy Index is the average number of times an article is cited in the year it is published. The journal Immediacy Index indicates how quickly articles in a journal are cited. Immediacy Index: 2.2 The Eigenfactor score, developed by Jevin West and Carl Bergstrom at the University of Washington, is a rating of the total importance of a scientific journal. Journals are rated according to the number of incoming citations, with citations from highly ranked journals weighted to make a larger contribution to the eigenfactor than those from poorly ranked journals. Eigenfactor: 0.00034 The Journal Citation Indicator (JCI) is a single measurement of the field-normalized citation impact of journals in the Web of Science Core Collection across disciplines. The key words here are that the metric is normalized and cross-disciplinary. JCI: 0.46 SJR: 0.333 SNIP: 0.606 CiteScore™:: 3.1 H-Index: 31

Indexed in

Parallel Multiscale Modeling of Biopolymer Dynamics with Hydrodynamic Correlations

巻 6, 発行 1, 2008, pp. 25-37
DOI: 10.1615/IntJMultCompEng.v6.i1.30
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要約

We employ a multiscale approach to model the translocation of biopolymers through nanometer size pores. Our computational scheme combines microscopic molecular dynamics with a mesoscopic lattice Boltzmann method for the solvent dynamics, explicitly taking into account the interactions of the molecule with the surrounding fluid. We describe an efficient parallel implementation of the method that exhibits excellent scalability on the Blue Gene platform. We investigate both dynamical and statistical aspects of the translocation process by simulating polymers of various initial configurations and lengths. For a representative molecule size, we explore the effects of important parameters that enter in the simulation, paying particular attention to the strength of the molecule-solvent coupling and of the external electric field which drives the translocation process. Finally, we explore the connection between the generic polymers modeled in the simulation and DNA, for which interesting recent experimental results are available.

によって引用された
  1. Bernaschi Massimo, Fatica Massimiliano, Melchionna Simone, Succi Sauro, Kaxiras Efthimios, A flexible high-performance Lattice Boltzmann GPU code for the simulations of fluid flows in complex geometries, Concurrency and Computation: Practice and Experience, 22, 1, 2010. Crossref

  2. Bernaschi M., Melchionna S., Succi S., Fyta M., Kaxiras E., Sircar J.K., MUPHY: A parallel MUlti PHYsics/scale code for high performance bio-fluidic simulations, Computer Physics Communications, 180, 9, 2009. Crossref

  3. Ilg Patrick, Mavrantzas Vlasis, öttinger Hans Christian, Multiscale Modeling and Coarse Graining of Polymer Dynamics: Simulations Guided by Statistical Beyond-Equilibrium Thermodynamics, in Modeling and Simulation in Polymers, 2010. Crossref

  4. Bernaschi Massimo, Succi Sauro, Fyta Maria, Kaxiras Efthimios, Melchionna Simone, Sircar Jayanta K., MUPHY: A parallel high performance MUlti PHYsics/Scale code, 2008 IEEE International Symposium on Parallel and Distributed Processing, 2008. Crossref

  5. Peng Zhangli, Chen Yeng-Long, Lu Huijie, Pan Zehao, Chang Hsueh-Chia, Mesoscale simulations of two model systems in biophysics: from red blood cells to DNAs, Computational Particle Mechanics, 2, 4, 2015. Crossref

  6. Alapati Suresh, Che Woo, Suh Yong, Effect of Nanopore Length on the Translocation Process of a Biopolymer: Numerical Study, Materials, 6, 9, 2013. Crossref

  7. Afrasiabian Navid, Denniston Colin, The journey of a single polymer chain to a nanopore, Soft Matter, 16, 39, 2020. Crossref

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