dorsal/arxiv
View SchemaUtilizing the information content in two-state trajectories
| Authors | Ophir Flomenbom, Robert J. Silbey |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0703013 |
| URL | https://arxiv.org/abs/q-bio/0703013 |
| DOI | 10.1073/pnas.0604546103 |
| Journal | Proc. Natl. Acad. Sci. USA 103, 10907-10910 (2006) |
Abstract
The signal from many single molecule experiments monitoring molecular processes, such as enzyme turnover via fluorescence and opening and closing of ion channel via the flux of ions, consists of a time series of stochastic on and off (or open and closed) periods, termed a two-state trajectory. This signal reflects the dynamics in the underlying multi-substate on-off kinetic scheme (KS) of the process. The determination of the underlying KS is difficult and sometimes even impossible due to the loss of information in the mapping of the mutli dimensional KS onto two dimensions. Here we introduce a new procedure that efficiently and optimally relates the signal to all equivalent underlying KSs. This procedure partitions the space of KSs into canonical (unique) forms that can handle any KS, and obtains the topology and other details of the canonical form from the data without the need for fitting. Also established are relationships between the data and the topology of the canonical form to the on-off connectivity of a KS. The suggested canonical forms constitute a powerful tool in discriminating between KSs. Based on our approach, the upper bound on the information content in two state trajectories is determined.
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"abstract": "The signal from many single molecule experiments monitoring molecular\nprocesses, such as enzyme turnover via fluorescence and opening and closing of\nion channel via the flux of ions, consists of a time series of stochastic on\nand off (or open and closed) periods, termed a two-state trajectory. This\nsignal reflects the dynamics in the underlying multi-substate on-off kinetic\nscheme (KS) of the process. The determination of the underlying KS is difficult\nand sometimes even impossible due to the loss of information in the mapping of\nthe mutli dimensional KS onto two dimensions. Here we introduce a new procedure\nthat efficiently and optimally relates the signal to all equivalent underlying\nKSs. This procedure partitions the space of KSs into canonical (unique) forms\nthat can handle any KS, and obtains the topology and other details of the\ncanonical form from the data without the need for fitting. Also established are\nrelationships between the data and the topology of the canonical form to the\non-off connectivity of a KS. The suggested canonical forms constitute a\npowerful tool in discriminating between KSs. Based on our approach, the upper\nbound on the information content in two state trajectories is determined.",
"arxiv_id": "q-bio/0703013",
"authors": [
"Ophir Flomenbom",
"Robert J. Silbey"
],
"categories": [
"q-bio.QM"
],
"doi": "10.1073/pnas.0604546103",
"journal_ref": "Proc. Natl. Acad. Sci. USA 103, 10907-10910 (2006)",
"title": "Utilizing the information content in two-state trajectories",
"url": "https://arxiv.org/abs/q-bio/0703013"
},
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