[Interesting open problem for NKS-ish bio] - A New Kind of Science: The NKS Forum

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Interesting open problem for NKS-ish bio

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Posted by: Jason Cawley

Connectivity, clusters, and transport:

use of percolation concepts and atomistic simulation
to track intracellular ion migration

Ann Marie Sastry and Christian M. Lastoskie


Philosophical Transactions of the Royal Society of London Series A-Mathematical Physical and Engineering Sciences

Abstract -

The cytoskeleton is an intracellular highway system, teeming with signalling ions that zip from site to site along filaments. These tiny particles alternately embrace and slip free of protein receptors with wide-ranging affinities, as they propagate in a blur of motion along, cytoskeletal corridors at transport rates far exceeding ordinary diffusive motion. Recent experimental breakthroughs have enabled optical tracking of these sin-le ion-binding events in the physiological and diseased states. However, traditional continuum modelling methods have proven ineffective for modelling migration of biometals such as copper and zinc, whose cytosolic concentrations are putatively vanishingly, small or very tightly controlled. Rather, the key modelling problem that must be solved for biometals is determination of the optimal placement of biosensors that bind and detect the metal ions within the heterogeneous environment of the cell. We discuss herein how, percolation concepts, in combination with atomistic simulation and sensor delivery, models. have been used to gain insights on this problem and a roadmap for future breakthroughs.


Posted by: Jason Cawley

A reduced version of this would be to look at transport rates from site to site along some chain or surface, with preferential binding to specific locations along the surface, diffusion between them, and various sorts of periodic shake ups and/or gradient effects "shaking loose" bound items and biasing diffusion directions. Not simply diffusion because the transported objects can be "caught", ratchet style, by their binding sites. One would look at various parameters like occupation or openness of sites, their distribution, shake up frequency, gradient strength, concentration, etc. Ought to be model-able. One might dispense with some of these features to simplify the set up, while still aiming for results formally distinct from ordinary diffusion.




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