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Stochastic bistability

Farzaneh Maleki, Attila Becskei
Bistability permits the co-existence of two distinct cell fates in a population of genetically identical cells. Noise induced transitions between two fates of a bistable system are difficult to calculate due to the intricate interplay between nonlinear dynamics and noise in bistable positive feedback loops. Here we opened multivariable feedback loops at the slowest variable to obtain the open-loop function and the fluctuations in the open-loop output. By the subsequent reclosing of the loop, we calculated the mean first passage time (MFPT) using the Fokker-Planck equation in good agreement with the exact stochastic simulation...
December 18, 2016: Journal of Theoretical Biology
Tiejun Xiao
In this paper, stochastic thermodynamics of delayed bistable Langevin systems near coherence resonance is discussed. We calculate the heat dissipation rate and the information flow of a delayed bistable Langevin system under various noise intensities. Both the heat dissipation rate and the information flow are found to be bell-shaped functions of the noise intensity, which implies that coherence resonance manifests itself in the thermodynamic properties.
November 2016: Physical Review. E
David A Sivak, Gavin E Crooks
We explore the thermodynamic geometry of a simple system that models the bistable dynamics of nucleic acid hairpins in single molecule force-extension experiments. Near equilibrium, optimal (minimum-dissipation) driving protocols are governed by a generalized linear response friction coefficient. Our analysis demonstrates that the friction coefficient of the driving protocols is sharply peaked at the interface between metastable regions, which leads to minimum-dissipation protocols that drive rapidly within a metastable basin, but then linger longest at the interface, giving thermal fluctuations maximal time to kick the system over the barrier...
November 2016: Physical Review. E
Miriam Leon, Mae L Woods, Alex J H Fedorec, Chris P Barnes
BACKGROUND: Genetic switches exhibit multistability, form the basis of epigenetic memory, and are found in natural decision making systems, such as cell fate determination in developmental pathways. Synthetic genetic switches can be used for recording the presence of different environmental signals, for changing phenotype using synthetic inputs and as building blocks for higher-level sequential logic circuits. Understanding how multistable switches can be constructed and how they function within larger biological systems is therefore key to synthetic biology...
December 7, 2016: BMC Systems Biology
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
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
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
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...
January 2017: Vision Research
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
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