## Group vanHeukelum

Group Description |
DNA electrophoresis model. Alexander van Heukelum, Utrect Univ, The Netherlands. Date: Wed, 5 Jun 2002 14:12:02 +0200 (MET DST) From: Alexander van Heukelum <A.vanHeukelum :at the domain: phys.uu.nl> To: davis :at the domain: cise.ufl.edu Subject: Sparse matrix library -- Alexander van Heukelum -- Institute for Theoretical Physics Room: Minnaert Building 307 Utrecht University Phone: (+31) (30) 253 4622 Leuvenlaan 4 Fax: (+31) (30) 253 5937 3584 CE Utrecht Email: heukelum :at the domain: phys.uu.nl The Netherlands ----------------------------------------------------------------------- The cage model of DNA electrophoresis The cage model of DNA electrophoresis describes the drift, induced by a constant electric field, of homogeneously charged polymers through a gel. The gel forms an effective "tube", from which the polymers can only escape by reptation, i.e., motion of stored length along the chain. The polymer chain is modeled as a random walk on a cubic lattice, and stored length is represented by two adjacent segments with opposite directions (a kink). The dynamics consists of single-monomer moves: only configurations which differ by the direction of a kink or the direction of an end segment have a finite transition probability. The direction of the field is chosen in the direction of the main body diagonal of the lattice, such that many polymer configurations become equivalent. The matrices presented here describe the transition probabilities between such equivalence-classes of the configurations, for an applied field of E = (0.1, 0.1, 0.1) for polymers of L = 3 to 15 monomers. name length rows columns nonzeros -------- -------- -------- -------- -------- cage3 3 5 5 19 cage4 4 9 9 49 cage5 5 37 37 233 cage6 6 93 93 785 cage7 7 340 340 3084 cage8 8 1015 1015 11003 cage9 9 3534 3534 41594 cage10 10 11397 11397 150645 cage11 11 39082 39082 559722 cage12 12 130228 130228 2032536 cage13 13 445315 445315 7479343 cage14 14 1505785 1505785 27130349 cage15 15 5154859 5154859 99199551 For more information on the matrices, see A. van Heukelum, G. T. Barkema, and R. H. Bisseling, "DNA electrophoresis studied with the cage model", J. Comp. Phys. 180, 313-326 (2002), or http://arxiv.org/format/cond-mat/0101467. |
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**all 13**matricesId | Name | Group | Rows | Cols | Nonzeros | Kind | Date | Download File |
---|---|---|---|---|---|---|---|---|

904 | cage3 | vanHeukelum | 5 | 5 | 19 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

905 | cage4 | vanHeukelum | 9 | 9 | 49 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

906 | cage5 | vanHeukelum | 37 | 37 | 233 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

907 | cage6 | vanHeukelum | 93 | 93 | 785 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

908 | cage7 | vanHeukelum | 340 | 340 | 3,084 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

909 | cage8 | vanHeukelum | 1,015 | 1,015 | 11,003 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

910 | cage9 | vanHeukelum | 3,534 | 3,534 | 41,594 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

911 | cage10 | vanHeukelum | 11,397 | 11,397 | 150,645 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

912 | cage11 | vanHeukelum | 39,082 | 39,082 | 559,722 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

913 | cage12 | vanHeukelum | 130,228 | 130,228 | 2,032,536 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

914 | cage13 | vanHeukelum | 445,315 | 445,315 | 7,479,343 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

915 | cage14 | vanHeukelum | 1,505,785 | 1,505,785 | 27,130,349 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |

916 | cage15 | vanHeukelum | 5,154,859 | 5,154,859 | 99,199,551 | Directed Weighted Graph | 2003 | MATLAB Rutherford Boeing Matrix Market |