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Stochastic bistability

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https://www.readbyqxmd.com/read/27920766/a-degu-p-and-degq-dependent-regulatory-pathway-for-the-k-state-in-bacillus-subtilis
#1
Mathieu Miras, David Dubnau
The K-state in the model bacterium Bacillus subtilis is associated with transformability (competence) as well as with growth arrest and tolerance for antibiotics. Entry into the K-state is determined by the stochastic activation of the transcription factor ComK and occurs in about ∼15% of the population in domesticated strains. Although the upstream mechanisms that regulate the K-state have been intensively studied and are well understood, it has remained unexplained why undomesticated isolates of B. subtilis are poorly transformable compared to their domesticated counterparts...
2016: Frontiers in Microbiology
https://www.readbyqxmd.com/read/27911933/driving-cells-to-the-desired-state-in-a-bimodal-distribution-through-manipulation-of-internal-noise-with-biologically-practicable-approaches
#2
Che-Chi Shu, Chen-Chao Yeh, Wun-Sin Jhang, Shih-Chiang Lo
The stochastic nature of gene regulatory networks described by Chemical Master Equation (CME) leads to the distribution of proteins. A deterministic bistability is usually reflected as a bimodal distribution in stochastic simulations. Within a certain range of the parameter space, a bistable system exhibits two stable steady states, one at the low end and the other at the high end. Consequently, it appears to have a bimodal distribution with one sub-population (mode) around the low end and the other around the high end...
2016: PloS One
https://www.readbyqxmd.com/read/27902489/effects-of-cell-cycle-noise-on-excitable-gene-circuits
#3
Alan Veliz-Cuba, Chinmaya Gupta, Matthew R Bennett, Krešimir Josić, William Ott
We assess the impact of cell cycle noise on gene circuit dynamics. For bistable genetic switches and excitable circuits, we find that transitions between metastable states most likely occur just after cell division and that this concentration effect intensifies in the presence of transcriptional delay. We explain this concentration effect with a three-states stochastic model. For genetic oscillators, we quantify the temporal correlations between daughter cells induced by cell division. Temporal correlations must be captured properly in order to accurately quantify noise sources within gene networks...
November 30, 2016: Physical Biology
https://www.readbyqxmd.com/read/27871885/vestibular-signals-of-self-motion-modulate-global-motion-perception
#4
Hinze Hogendoorn, Frans A J Verstraten, Hamish MacDougall, David Alais
Certain visual stimuli can have two possible interpretations. These perceptual interpretations may alternate stochastically, a phenomenon known as bistability. Some classes of bistable stimuli, including binocular rivalry, are sensitive to bias from input through other modalities, such as sound and touch. Here, we address the question whether bistable visual motion stimuli, known as plaids, are affected by vestibular input that is caused by self-motion. In Experiment 1, we show that a vestibular self-motion signal biases the interpretation of the bistable plaid, increasing or decreasing the likelihood of the plaid being perceived as globally coherent or transparently sliding depending on the relationship between self-motion and global visual motion directions...
November 25, 2016: Vision Research
https://www.readbyqxmd.com/read/27768683/intrinsic-noise-profoundly-alters-the-dynamics-and-steady-state-of-morphogen-controlled-bistable-genetic-switches
#5
Ruben Perez-Carrasco, Pilar Guerrero, James Briscoe, Karen M Page
During tissue development, patterns of gene expression determine the spatial arrangement of cell types. In many cases, gradients of secreted signalling molecules-morphogens-guide this process by controlling downstream transcriptional networks. A mechanism commonly used in these networks to convert the continuous information provided by the gradient into discrete transitions between adjacent cell types is the genetic toggle switch, composed of cross-repressing transcriptional determinants. Previous analyses have emphasised the steady state output of these mechanisms...
October 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27763522/effectiveness-testing-of-a-piezoelectric-energy-harvester-for-an-automobile-wheel-using-stochastic-resonance
#6
Yunshun Zhang, Rencheng Zheng, Keisuke Shimono, Tsutomu Kaizuka, Kimihiko Nakano
The collection of clean power from ambient vibrations is considered a promising method for energy harvesting. For the case of wheel rotation, the present study investigates the effectiveness of a piezoelectric energy harvester, with the application of stochastic resonance to optimize the efficiency of energy harvesting. It is hypothesized that when the wheel rotates at variable speeds, the energy harvester is subjected to on-road noise as ambient excitations and a tangentially acting gravity force as a periodic modulation force, which can stimulate stochastic resonance...
October 17, 2016: Sensors
https://www.readbyqxmd.com/read/27641730/random-sex-determination-when-developmental-noise-tips-the-sex-balance
#7
Nicolas Perrin
Sex-determining factors are usually assumed to be either genetic or environmental. The present paper aims at drawing attention to the potential contribution of developmental noise, an important but often-neglected component of phenotypic variance. Mutual inhibitions between male and female pathways make sex a bistable equilibrium, such that random fluctuations in the expression of genes at the top of the cascade are sufficient to drive individual development toward one or the other stable state. Evolutionary modeling shows that stochastic sex determinants should resist elimination by genetic or environmental sex determinants under ecologically meaningful settings...
September 19, 2016: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27630669/a-comparison-of-deterministic-and-stochastic-modeling-approaches-for-biochemical-reaction-systems-on-fixed-points-means-and-modes
#8
Sayuri K Hahl, Andreas Kremling
In the mathematical modeling of biochemical reactions, a convenient standard approach is to use ordinary differential equations (ODEs) that follow the law of mass action. However, this deterministic ansatz is based on simplifications; in particular, it neglects noise, which is inherent to biological processes. In contrast, the stochasticity of reactions is captured in detail by the discrete chemical master equation (CME). Therefore, the CME is frequently applied to mesoscopic systems, where copy numbers of involved components are small and random fluctuations are thus significant...
2016: Frontiers in Genetics
https://www.readbyqxmd.com/read/27627294/stochastic-bifurcations-in-a-prototypical-thermoacoustic-system
#9
E A Gopalakrishnan, J Tony, E Sreelekha, R I Sujith
We study the influence of noise in a prototypical thermoacoustic system, which represents a nonlinear self-excited bistable oscillator. We analyze the time series of unsteady pressure obtained from a horizontal Rijke tube and a mathematical model to identify the effect of noise. We report the occurrence of stochastic bifurcations in a thermoacoustic system by tracking the changes in the stationary amplitude distribution. We observe a complete suppression of a bistable zone in the presence of high intensity noise...
August 2016: Physical Review. E
https://www.readbyqxmd.com/read/27627287/particle-dynamics-in-a-symmetrically-driven-underdamped-inhomogeneous-periodic-potential-system
#10
D Kharkongor, W L Reenbohn, Mangal C Mahato
We numerically solve the underdamped Langevin equation to obtain the trajectories of a particle in a sinusoidal potential driven by a temporally sinusoidal force in a medium with coefficient of friction periodic in space as the potential but with a phase difference. With the appropriate choice of system parameters, like the mean friction coefficient and the period of the applied field, only two kinds of periodic trajectories are obtained for all possible initial conditions at low noise strengths: one with a large amplitude and a large phase lag with respect to the applied field and the other with a small amplitude and a small phase lag...
August 2016: Physical Review. E
https://www.readbyqxmd.com/read/27627256/fluctuating-systems-under-cyclic-perturbations-relation-between-energy-dissipation-and-intrinsic-relaxation-processes
#11
Fabrizio Camerin, Diego Frezzato
This study focuses on fluctuating classical systems in contact with a thermal bath, and whose configurational energetics undergoes cyclic transformations due to interaction with external perturbing agents. Under the assumptions that the configurational dynamics is a stochastic Markov process in the overdamped regime and that the nonequilibrium configurational distribution remains close to the underlying equilibrium one, we derived an analytic approximation of the average dissipated energy per cycle in the asymptotic limit (i...
August 2016: Physical Review. E
https://www.readbyqxmd.com/read/27541958/inverse-stochastic-resonance-in-cerebellar-purkinje-cells
#12
Anatoly Buchin, Sarah Rieubland, Michael Häusser, Boris S Gutkin, Arnd Roth
Purkinje neurons play an important role in cerebellar computation since their axons are the only projection from the cerebellar cortex to deeper cerebellar structures. They have complex internal dynamics, which allow them to fire spontaneously, display bistability, and also to be involved in network phenomena such as high frequency oscillations and travelling waves. Purkinje cells exhibit type II excitability, which can be revealed by a discontinuity in their f-I curves. We show that this excitability mechanism allows Purkinje cells to be efficiently inhibited by noise of a particular variance, a phenomenon known as inverse stochastic resonance (ISR)...
August 2016: PLoS Computational Biology
https://www.readbyqxmd.com/read/27485552/stochastic-induction-of-long-term-potentiation-and-long-term-depression
#13
G Antunes, A C Roque, F M Simoes-de-Souza
Long-term depression (LTD) and long-term potentiation (LTP) of granule-Purkinje cell synapses are persistent synaptic alterations induced by high and low rises of the intracellular calcium ion concentration ([Ca(2+)]), respectively. The occurrence of LTD involves the activation of a positive feedback loop formed by protein kinase C, phospholipase A2, and the extracellular signal-regulated protein kinase pathway, and its expression comprises the reduction of the population of synaptic AMPA receptors. Recently, a stochastic computational model of these signalling processes demonstrated that, in single synapses, LTD is probabilistic and bistable...
2016: Scientific Reports
https://www.readbyqxmd.com/read/27475397/noise-induced-multistability-in-the-regulation-of-cancer-by-genes-and-pseudogenes
#14
K G Petrosyan, Chin-Kun Hu
We extend a previously introduced model of stochastic gene regulation of cancer to a nonlinear case having both gene and pseudogene messenger RNAs (mRNAs) self-regulated. The model consists of stochastic Boolean genetic elements and possesses noise-induced multistability (multimodality). We obtain analytical expressions for probabilities for the case of constant but finite number of microRNA molecules which act as a noise source for the competing gene and pseudogene mRNAs. The probability distribution functions display both the global bistability regime as well as even-odd number oscillations for a certain range of model parameters...
July 28, 2016: Journal of Chemical Physics
https://www.readbyqxmd.com/read/27442281/high-resolution-mapping-of-bifurcations-in-nonlinear-biochemical-circuits
#15
A J Genot, A Baccouche, R Sieskind, N Aubert-Kato, N Bredeche, J F Bartolo, V Taly, T Fujii, Y Rondelez
Analog molecular circuits can exploit the nonlinear nature of biochemical reaction networks to compute low-precision outputs with fewer resources than digital circuits. This analog computation is similar to that employed by gene-regulation networks. Although digital systems have a tractable link between structure and function, the nonlinear and continuous nature of analog circuits yields an intricate functional landscape, which makes their design counter-intuitive, their characterization laborious and their analysis delicate...
August 2016: Nature Chemistry
https://www.readbyqxmd.com/read/27425413/creating-single-copy-genetic-circuits
#16
Jeong Wook Lee, Andras Gyorgy, D Ewen Cameron, Nora Pyenson, Kyeong Rok Choi, Jeffrey C Way, Pamela A Silver, Domitilla Del Vecchio, James J Collins
Synthetic biology is increasingly used to develop sophisticated living devices for basic and applied research. Many of these genetic devices are engineered using multi-copy plasmids, but as the field progresses from proof-of-principle demonstrations to practical applications, it is important to develop single-copy synthetic modules that minimize consumption of cellular resources and can be stably maintained as genomic integrants. Here we use empirical design, mathematical modeling, and iterative construction and testing to build single-copy, bistable toggle switches with improved performance and reduced metabolic load that can be stably integrated into the host genome...
July 21, 2016: Molecular Cell
https://www.readbyqxmd.com/read/27358454/collective-activity-of-many-bistable-assemblies-reproduces-characteristic-dynamics-of-multistable-perception
#17
Robin Cao, Alexander Pastukhov, Maurizio Mattia, Jochen Braun
UNLABELLED: The timing of perceptual decisions depends on both deterministic and stochastic factors, as the gradual accumulation of sensory evidence (deterministic) is contaminated by sensory and/or internal noise (stochastic). When human observers view multistable visual displays, successive episodes of stochastic accumulation culminate in repeated reversals of visual appearance. Treating reversal timing as a "first-passage time" problem, we ask how the observed timing densities constrain the underlying stochastic accumulation...
June 29, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27300883/noise-induced-transitions-in-a-double-well-oscillator-with-nonlinear-dissipation
#18
Vladimir V Semenov, Alexander B Neiman, Tatyana E Vadivasova, Vadim S Anishchenko
We develop a model of bistable oscillator with nonlinear dissipation. Using a numerical simulation and an electronic circuit realization of this system we study its response to additive noise excitations. We show that depending on noise intensity the system undergoes multiple qualitative changes in the structure of its steady-state probability density function (PDF). In particular, the PDF exhibits two pitchfork bifurcations versus noise intensity, which we describe using an effective potential and corresponding normal form of the bifurcation...
May 2016: Physical Review. E
https://www.readbyqxmd.com/read/27300849/analytic-descriptions-of-stochastic-bistable-systems-under-force-ramp
#19
Raymond W Friddle
Solving the two-state master equation with time-dependent rates, the ubiquitous driven bistable system, is a long-standing problem that does not permit a complete solution for all driving rates. Here we show an accurate approximation to this problem by considering the system in the control parameter regime. The results are immediately applicable to a diverse range of bistable systems including single-molecule mechanics.
May 2016: Physical Review. E
https://www.readbyqxmd.com/read/27266276/hypothetical-biomolecular-probe-based-on-a-genetic-switch-with-tunable-symmetry-and-stability
#20
Nikolay Martyushenko, Sigurd Hagen Johansen, Cheol-Min Ghim, Eivind Almaas
BACKGROUND: Genetic switches are ubiquitous in nature, frequently associated with the control of cellular functions and developmental programs. In the realm of synthetic biology, it is of great interest to engineer genetic circuits that can change their mode of operation from monostable to bistable, or even to multistable, based on the experimental fine-tuning of readily accessible parameters. In order to successfully design robust, bistable synthetic circuits to be used as biomolecular probes, or understand modes of operation of such naturally occurring circuits, we must identify parameters that are key in determining their characteristics...
2016: BMC Systems Biology
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