dorsal/arxiv
View SchemaA Central Partition of Molecular Conformational Space.III. Combinatorial Determination of the Volume Spanned by a Molecular System
| Authors | Jacques Gabarro-Arpa |
|---|---|
| Categories | |
| ArXiv ID | physics/0509126 |
| URL | https://arxiv.org/abs/physics/0509126 |
| DOI | 10.1007/s10910-006-9079-8 |
| Journal | J. Math. Chem. 42, 691-706 (2006) |
Abstract
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into a hierarchical set of cells that can be encoded by the face lattice poset of the arrangement. The model however, lacked explicit rotational symmetry which made impossible to distinguish rotated structures in conformational space. This problem was solved in a second work [physics/0404052] by sorting the elementary 3D components of the molecular system into a set of morphological classes that can be properly oriented in a standard 3D reference frame. This also made possible to find a solution to the problem that is being adressed in the present work: for a molecular system immersed in a heat bath we want to enumerate the subset of cells in conformational space that are visited by the molecule in its thermal wandering. If each visited cell is a vertex on a graph with edges to the adjacent cells, here it is explained how such graph can be built.
{
"annotation_id": "94ce869e-883a-4db8-a90c-6ba3addc4d30",
"date_created": "2026-03-02T18:01:00.919000Z",
"date_modified": "2026-03-02T18:01:00.919000Z",
"file_hash": "c68ab82846e97d13dace454c6cf90b8f0523cf5cfd3525715300daa46cbc2cdb",
"private": false,
"record": {
"abstract": "In the first work of this series [physics/0204035] it was shown that the\nconformational space of a molecule could be described to a fair degree of\naccuracy by means of a central hyperplane arrangement. The hyperplanes divide\nthe espace into a hierarchical set of cells that can be encoded by the face\nlattice poset of the arrangement. The model however, lacked explicit rotational\nsymmetry which made impossible to distinguish rotated structures in\nconformational space. This problem was solved in a second work\n[physics/0404052] by sorting the elementary 3D components of the molecular\nsystem into a set of morphological classes that can be properly oriented in a\nstandard 3D reference frame. This also made possible to find a solution to the\nproblem that is being adressed in the present work: for a molecular system\nimmersed in a heat bath we want to enumerate the subset of cells in\nconformational space that are visited by the molecule in its thermal wandering.\nIf each visited cell is a vertex on a graph with edges to the adjacent cells,\nhere it is explained how such graph can be built.",
"arxiv_id": "physics/0509126",
"authors": [
"Jacques Gabarro-Arpa"
],
"categories": [
"physics.comp-ph",
"physics.chem-ph"
],
"doi": "10.1007/s10910-006-9079-8",
"journal_ref": "J. Math. Chem. 42, 691-706 (2006)",
"title": "A Central Partition of Molecular Conformational Space.III. Combinatorial Determination of the Volume Spanned by a Molecular System",
"url": "https://arxiv.org/abs/physics/0509126"
},
"schema_id": "dorsal/arxiv",
"source": {
"execution_id": "aeca9db3-054d-413f-872d-a6e4fcd6a15b",
"id": "arXiv Dataset IDs",
"type": "Model",
"variant": "snapshot-2026-03-01",
"version": "0.1.0"
},
"user_id": 1000002
}