dorsal/arxiv
View SchemaA Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells
| Authors | Jacques Gabarro-Arpa |
|---|---|
| Categories | |
| ArXiv ID | physics/0611108 |
| URL | https://arxiv.org/abs/physics/0611108 |
| DOI | 10.1007/s10910-008-9384-5 |
| Journal | J. Math. Chem. 44, 872-883 (2008) |
Abstract
In previous works [physics/0204035, physics/0404052, physics/0509126] a procedure was described for dividing the $3 \times N$-dimensional conformational space of a molecular system into a number of discrete cells, this partition allowed the building of a combinatorial structure from data sampled in molecular dynamics trajectories: the graph of cells, that encodes the set of cells in conformational space that are visited by the system in its thermal wandering. Here we outline a set of procedures for extracting useful information from this structure: 1st) interesting regions in the volume occupied by the system in conformational space can be bounded by a polyhedral cone whose faces are determined empirically from a set of relations between the coordinates of the molecule, 2nd) it is also shown that this cone can be decomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a cone can be encoded by a simple combinatorial sequence.
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"abstract": "In previous works [physics/0204035, physics/0404052, physics/0509126] a\nprocedure was described for dividing the $3 \\times N$-dimensional\nconformational space of a molecular system into a number of discrete cells,\nthis partition allowed the building of a combinatorial structure from data\nsampled in molecular dynamics trajectories: the graph of cells, that encodes\nthe set of cells in conformational space that are visited by the system in its\nthermal wandering. Here we outline a set of procedures for extracting useful\ninformation from this structure: 1st) interesting regions in the volume\noccupied by the system in conformational space can be bounded by a polyhedral\ncone whose faces are determined empirically from a set of relations between the\ncoordinates of the molecule, 2nd) it is also shown that this cone can be\ndecomposed into a hierarchical set of smaller cones, 3rd) the set of cells in a\ncone can be encoded by a simple combinatorial sequence.",
"arxiv_id": "physics/0611108",
"authors": [
"Jacques Gabarro-Arpa"
],
"categories": [
"physics.comp-ph",
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],
"doi": "10.1007/s10910-008-9384-5",
"journal_ref": "J. Math. Chem. 44, 872-883 (2008)",
"title": "A Central Partition of Molecular Conformational Space. IV. Extracting information from the graph of cells",
"url": "https://arxiv.org/abs/physics/0611108"
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