Graph-based analysis of kinetics on multidimensional potential-energy surfaces Export

@article{citeulike:5891582, abstract = {The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters.}, author = {Okushima, T. and Niiyama, T. and Ikeda, K. S. and Shimizu, Y.}, citeulike-article-id = {5891582}, citeulike-linkout-0 = {http://scitation.aip.org/getabs/servlet/GetabsServlet?prog=normal&id=PLEEE8000080000003036112000001&idtype=cvips&gifs=yes}, citeulike-linkout-1 = {http://link.aps.org/abstract/PRE/v80/e036112}, citeulike-linkout-2 = {http://dx.doi.org/10.1103/PhysRevE.80.036112}, doi = {10.1103/PhysRevE.80.036112}, journal = {Physical Review E (Statistical, Nonlinear, and Soft Matter Physics)}, keywords = {cmn, first\_passage, free-energy, kinetic\_models, qha, transition\_path}, number = {3}, pages = {036112+}, posted-at = {2009-10-05 17:07:19}, priority = {2}, publisher = {APS}, title = {Graph-based analysis of kinetics on multidimensional potential-energy surfaces}, url = {http://dx.doi.org/10.1103/PhysRevE.80.036112}, volume = {80}, year = {2009} }

TY - JOUR ID - citeulike:5891582 L3 - citeulike-article-id:5891582 N2 - The aim of this paper is twofold: one is to give a detailed description of an alternative graph-based analysis method, which we call saddle connectivity graph, for analyzing the global topography and the dynamical properties of many-dimensional potential-energy landscapes and the other is to give examples of applications of this method in the analysis of the kinetics of realistic systems. A Dijkstra-type shortest path algorithm is proposed to extract dynamically dominant transition pathways by kinetically defining transition costs. The applicability of this approach is first confirmed by an illustrative example of a low-dimensional random potential. We then show that a coarse-graining procedure tailored for saddle connectivity graphs can be used to obtain the kinetic properties of 13- and 38-atom Lennard-Jones clusters. The coarse-graining method not only reduces the complexity of the graphs, but also, with iterative use, reveals a self-similar hierarchical structure in these clusters. We also propose that the self-similarity is common to many-atom Lennard-Jones clusters. IS - 3 JF - Physical Review E (Statistical, Nonlinear, and Soft Matter Physics) TI - Graph-based analysis of kinetics on multidimensional potential-energy surfaces PB - APS VL - 80 SP - 036112 KW - cmn KW - first_passage KW - free-energy KW - kinetic_models KW - qha KW - transition_path AU - Okushima, T AU - Niiyama, T AU - Ikeda, KS AU - Shimizu, Y PY - 2009/// UR - http://dx.doi.org/10.1103/PhysRevE.80.036112 ER -