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Stochastic bistability

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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
B Pfeuty, K Kaneko
The proper functioning of multicellular organisms requires the robust establishment of precise proportions between distinct cell types. This developmental differentiation process typically involves intracellular regulatory and stochastic mechanisms to generate cell-fate diversity as well as intercellular signaling mechanisms to coordinate cell-fate decisions at tissue level. We thus surmise that key insights about the developmental regulation of cell-type proportion can be captured by the modeling study of clustering dynamics in population of inhibitory-coupled noisy bistable systems...
April 2016: Physical Biology
Rati Sharma, Elijah Roberts
Many vital eukaryotic cellular functions require the cell to respond to a directional gradient of a signaling molecule. The first two steps in any eukaryotic chemotactic/chemotropic pathway are gradient detection and cell polarization. Like many processes, such chemotactic and chemotropic decisions are made using a relatively small number of molecules and are thus susceptible to internal and external fluctuations during signal transduction. Large cell-to-cell variations in the magnitude and direction of a response are therefore possible and do, in fact, occur in natural systems...
2016: Physical Biology
Hang Chen, Peter Thill, Jianshu Cao
In biochemical systems, intrinsic noise may drive the system switch from one stable state to another. We investigate how kinetic switching between stable states in a bistable network is influenced by dynamic disorder, i.e., fluctuations in the rate coefficients. Using the geometric minimum action method, we first investigate the optimal transition paths and the corresponding minimum actions based on a genetic toggle switch model in which reaction coefficients draw from a discrete probability distribution. For the continuous probability distribution of the rate coefficient, we then consider two models of dynamic disorder in which reaction coefficients undergo different stochastic processes with the same stationary distribution...
May 7, 2016: Journal of Chemical Physics
Robert Gnügge, Lekshmi Dharmarajan, Moritz Lang, Jörg Stelling
Feedback loops in biological networks, among others, enable differentiation and cell cycle progression, and increase robustness in signal transduction. In natural networks, feedback loops are often complex and intertwined, making it challenging to identify which loops are mainly responsible for an observed behavior. However, minimal synthetic replicas could allow for such identification. Here, we engineered a synthetic permease-inducer-repressor system in Saccharomyces cerevisiae to analyze if a transport-mediated positive feedback loop could be a core mechanism for the switch-like behavior in the regulation of metabolic gene networks such as the S...
October 21, 2016: ACS Synthetic Biology
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