378 research outputs found
Some Results on Brownian Motion Perturbed by Alternating Jumps in Biological Modeling
We consider the model of random evolution on the real line consisting in a Brownian motion perturbed by alternating jumps. We give the probability density of the process and pinpoint a connection with the limit density of a telegraph process subject to alternating jumps. We study the first-crossing-time probability in two special cases, in the presence of a constant upper boundary
A survey of random processes with reinforcement
The models surveyed include generalized P\'{o}lya urns, reinforced random
walks, interacting urn models, and continuous reinforced processes. Emphasis is
on methods and results, with sketches provided of some proofs. Applications are
discussed in statistics, biology, economics and a number of other areas.Comment: Published at http://dx.doi.org/10.1214/07-PS094 in the Probability
Surveys (http://www.i-journals.org/ps/) by the Institute of Mathematical
Statistics (http://www.imstat.org
Shaping bursting by electrical coupling and noise
Gap-junctional coupling is an important way of communication between neurons
and other excitable cells. Strong electrical coupling synchronizes activity
across cell ensembles. Surprisingly, in the presence of noise synchronous
oscillations generated by an electrically coupled network may differ
qualitatively from the oscillations produced by uncoupled individual cells
forming the network. A prominent example of such behavior is the synchronized
bursting in islets of Langerhans formed by pancreatic \beta-cells, which in
isolation are known to exhibit irregular spiking. At the heart of this
intriguing phenomenon lies denoising, a remarkable ability of electrical
coupling to diminish the effects of noise acting on individual cells.
In this paper, we derive quantitative estimates characterizing denoising in
electrically coupled networks of conductance-based models of square wave
bursting cells. Our analysis reveals the interplay of the intrinsic properties
of the individual cells and network topology and their respective contributions
to this important effect. In particular, we show that networks on graphs with
large algebraic connectivity or small total effective resistance are better
equipped for implementing denoising. As a by-product of the analysis of
denoising, we analytically estimate the rate with which trajectories converge
to the synchronization subspace and the stability of the latter to random
perturbations. These estimates reveal the role of the network topology in
synchronization. The analysis is complemented by numerical simulations of
electrically coupled conductance-based networks. Taken together, these results
explain the mechanisms underlying synchronization and denoising in an important
class of biological models
Single particle trajectories reveal active endoplasmic reticulum luminal flow
The endoplasmic reticulum (ER), a network of membranous sheets and pipes, supports functions encompassing biogenesis of secretory proteins and delivery of functional solutes throughout the cell[1, 2]. Molecular mobility through the ER network enables these functionalities, but diffusion alone is not sufficient to explain luminal transport across supramicrometre distances. Understanding the ER structure–function relationship is critical in light of mutations in ER morphology-regulating proteins that give rise to neurodegenerative disorders[3, 4]. Here, super-resolution microscopy and analysis of single particle trajectories of ER luminal proteins revealed that the topological organization of the ER correlates with distinct trafficking modes of its luminal content: with a dominant diffusive component in tubular junctions and a fast flow component in tubules. Particle trajectory orientations resolved over time revealed an alternating current of the ER contents, while fast ER super-resolution identified energy-dependent tubule contraction events at specific points as a plausible mechanism for generating active ER luminal flow. The discovery of active flow in the ER has implications for timely ER content distribution throughout the cell, particularly important for cells with extensive ER-containing projections such as neurons.Wellcome Trust - 3-3249/Z/16/Z and 089703/Z/09/Z [Kaminski]
UK Demential Research Institute [Avezov]
Wellcome Trust - 200848/Z/16/Z, WT: UNS18966 [Ron]
FRM Team Research Grant [Holcman]
Engineering and Physical Sciences Research Council (EPSRC) - EP/L015889/1 and EP/H018301/1 [Kaminski]
Medical Research Council (MRC) - MR/K015850/1 and MR/K02292X/1 [Kaminski
A Stochastic Compartmental Model for Fast Axonal Transport
In this paper we develop a probabilistic micro-scale compartmental model and
use it to study macro-scale properties of axonal transport, the process by
which intracellular cargo is moved in the axons of neurons. By directly
modeling the smallest scale interactions, we can use recent microscopic
experimental observations to infer all the parameters of the model. Then, using
techniques from probability theory, we compute asymptotic limits of the
stochastic behavior of individual motor-cargo complexes, while also
characterizing both equilibrium and non-equilibrium ensemble behavior. We use
these results in order to investigate three important biological questions: (1)
How homogeneous are axons at stochastic equilibrium? (2) How quickly can axons
return to stochastic equilibrium after large local perturbations? (3) How is
our understanding of delivery time to a depleted target region changed by
taking the whole cell point-of-view
On the Nature and Shape of Tubulin Trails: Implications on Microtubule Self-Organization
Microtubules, major elements of the cell skeleton are, most of the time, well
organized in vivo, but they can also show self-organizing behaviors in time
and/or space in purified solutions in vitro. Theoretical studies and models
based on the concepts of collective dynamics in complex systems,
reaction-diffusion processes and emergent phenomena were proposed to explain
some of these behaviors. In the particular case of microtubule spatial
self-organization, it has been advanced that microtubules could behave like
ants, self-organizing by 'talking to each other' by way of hypothetic (because
never observed) concentrated chemical trails of tubulin that are expected to be
released by their disassembling ends. Deterministic models based on this idea
yielded indeed like-looking spatio-temporal self-organizing behaviors.
Nevertheless the question remains of whether microscopic tubulin trails
produced by individual or bundles of several microtubules are intense enough to
allow microtubule self-organization at a macroscopic level. In the present
work, by simulating the diffusion of tubulin in microtubule solutions at the
microscopic scale, we measure the shape and intensity of tubulin trails and
discuss about the assumption of microtubule self-organization due to the
production of chemical trails by disassembling microtubules. We show that the
tubulin trails produced by individual microtubules or small microtubule arrays
are very weak and not elongated even at very high reactive rates. Although the
variations of concentration due to such trails are not significant compared to
natural fluctuations of the concentration of tubuline in the chemical
environment, the study shows that heterogeneities of biochemical composition
can form due to microtubule disassembly. They could become significant when
produced by numerous microtubule ends located in the same place. Their possible
formation could play a role in certain conditions of reaction. In particular,
it gives a mesoscopic basis to explain the collective dynamics observed in
excitable microtubule solutions showing the propagation of concentration waves
of microtubules at the millimeter scale, although we doubt that individual
microtubules or bundles can behave like molecular ants
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Large Scale Stochastic Dynamics
In focus are interacting stochastic systems with many components, ranging from stochastic partial differential equations to discrete systems as interacting particles on a lattice moving through random jumps. More specifically one wants to understand the large scale behavior, large in spatial extent but also over long time spans, as entailed by the characterization of stationary measures, effective macroscopic evolution laws, transport of conserved fields, homogenization, self-similar structure and scaling, critical dynamics, dynamical phase transitions, metastability, large deviations, to mention only a few key items
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