dorsal/arxiv
View SchemaSampling rare switching events in biochemical networks
| Authors | Rosalind J. Allen, Patrick B. Warren, Pieter Rein ten Wolde |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0406006 |
| URL | https://arxiv.org/abs/q-bio/0406006 |
| DOI | 10.1103/PhysRevLett.94.018104 |
Abstract
Bistable biochemical switches are ubiquitous in gene regulatory networks and signal transduction pathways. Their switching dynamics, however, are difficult to study directly in experiments or conventional computer simulations, because switching events are rapid, yet infrequent. We present a simulation technique that makes it possible to predict the rate and mechanism of flipping of biochemical switches. The method uses a series of interfaces in phase space between the two stable steady states of the switch to generate transition trajectories in a ratchet-like manner. We demonstrate its use by calculating the spontaneous flipping rate of a symmetric model of a genetic switch consisting of two mutually repressing genes. The rate constant can be obtained orders of magnitude more efficiently than using brute-force simulations. For this model switch, we show that the switching mechanism, and consequently the switching rate, depends crucially on whether the binding of one regulatory protein to the DNA excludes the binding of the other one. Our technique could also be used to study rare events and non-equilibrium processes in soft condensed matter systems.
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"abstract": "Bistable biochemical switches are ubiquitous in gene regulatory networks and\nsignal transduction pathways. Their switching dynamics, however, are difficult\nto study directly in experiments or conventional computer simulations, because\nswitching events are rapid, yet infrequent. We present a simulation technique\nthat makes it possible to predict the rate and mechanism of flipping of\nbiochemical switches. The method uses a series of interfaces in phase space\nbetween the two stable steady states of the switch to generate transition\ntrajectories in a ratchet-like manner. We demonstrate its use by calculating\nthe spontaneous flipping rate of a symmetric model of a genetic switch\nconsisting of two mutually repressing genes. The rate constant can be obtained\norders of magnitude more efficiently than using brute-force simulations. For\nthis model switch, we show that the switching mechanism, and consequently the\nswitching rate, depends crucially on whether the binding of one regulatory\nprotein to the DNA excludes the binding of the other one. Our technique could\nalso be used to study rare events and non-equilibrium processes in soft\ncondensed matter systems.",
"arxiv_id": "q-bio/0406006",
"authors": [
"Rosalind J. Allen",
"Patrick B. Warren",
"Pieter Rein ten Wolde"
],
"categories": [
"q-bio.MN"
],
"doi": "10.1103/PhysRevLett.94.018104",
"title": "Sampling rare switching events in biochemical networks",
"url": "https://arxiv.org/abs/q-bio/0406006"
},
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