From conformational spread to allosteric and cooperative models of <i>E. coli</i> flagellar motor

The recent experimental progresses in handling microscopic systems have allowed to probe them at levels where fluctuations are prominent, calling for stochastic modeling in a large number of physical, chemical and biological phenomena. This has provided fruitful applications for established stochastic methods and motivated further developments. These systems often involve processes taking place on widely separated time scales. For an efficient modeling one usually focuses on the slower degrees of freedom and it is of great importance to accurately eliminate the fast variables in a controlled fashion, carefully accounting for their net effect on the slower dynamics. This procedure in general requires to perform two different operations: decimation and coarse-graining. We introduce the asymptotic methods that form the basis of this procedure and discuss their application to a series of physical, biological and chemical examples. We then turn our attention to functionals of the stochastic trajectories such as residence times, counting statistics, fluxes, entropy production, etc. which have been increasingly studied in recent years. For such functionals, the elimination of the fast degrees of freedom can present additional difficulties and naive procedures can lead to blatantly inconsistent results. Homogenization techniques for functionals are less covered in the literature and we will pedagogically present them here, as natural extensions of the ones employed for the trajectories. We will also discuss recent applications of these techniques to the thermodynamics of small systems and their interpretation in terms of information-theoretic concepts.

show abstract

“…The resulting effective cooperative binding model reproduces well the experimental observations, see [50].…”

Section: Decimation: From the Conformational Spread Model To Mwcsupporting

confidence: 77%

“…Following Ref. [50] we show below how the strong coupling limit amounts to reducing the conformational spread model to an effective Monod-Wyman-Changeux model [55] and the slow-binding limit further reduces it to an effective cooperative binding model.…”

Section: Fli Moleculesmentioning

confidence: 85%

Multiple-scale stochastic processes: Decimation, averaging and beyond

Bò

Celani

2017

Physics Reports

View full text Add to dashboard Cite

show abstract

From conformational spread to allosteric and cooperative models of E. coli flagellar motor

Cited by 1 publication

References 24 publications

Multiple-scale stochastic processes: Decimation, averaging and beyond

Multiple-scale stochastic processes: Decimation, averaging and beyond

Contact Info

Product

Resources

About