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Stochastic bistability

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https://www.readbyqxmd.com/read/28968438/microrna-16-feedback-loop-with-p53-and-wip1-can-regulate-cell-fate-determination-between-apoptosis-and-senescence-in-dna-damage-response
#1
Maria Vitória C Issler, José Carlos M Mombach
Cell fate regulation is an open problem whose comprehension impacts several areas of the biosciences. DNA damage induces cell cycle checkpoints that activate the p53 pathway to regulate cell fate mechanisms such as apoptosis or senescence. Experiments with different cell types show that the p53 pathway regulates cell fate through a switch behavior in its dynamics. For low DNA damage the pathway presents an oscillatory pattern associated with intense DNA damage repair while for high damage there are no oscillations and either p53 concentration increases inducing apoptosis or the cell enters a senescence state...
2017: PloS One
https://www.readbyqxmd.com/read/28957020/capturing-the-dynamical-repertoire-of-single-neurons-with-generalized-linear-models
#2
Alison I Weber, Jonathan W Pillow
A key problem in computational neuroscience is to find simple, tractable models that are nevertheless flexible enough to capture the response properties of real neurons. Here we examine the capabilities of recurrent point process models known as Poisson generalized linear models (GLMs). These models are defined by a set of linear filters and a point nonlinearity and are conditionally Poisson spiking. They have desirable statistical properties for fitting and have been widely used to analyze spike trains from electrophysiological recordings...
September 28, 2017: Neural Computation
https://www.readbyqxmd.com/read/28950646/regime-shifts-driven-by-dynamic-correlations-in-gene-expression-noise
#3
Yogita Sharma, Partha Sharathi Dutta
Gene expression is a noisy process that leads to regime shifts between alternative steady states among individual living cells, inducing phenotypic variability. The effects of white noise on the regime shift in bistable systems have been well characterized, however little is known about such effects of colored noise (noise with nonzero correlation time). Here, we show that noise correlation time, by considering a genetic circuit of autoactivation, can have a significant effect on the regime shift between distinct phenotypic states in gene expression...
August 2017: Physical Review. E
https://www.readbyqxmd.com/read/28831039/exit-from-quiescence-displays-a-memory-of-cell-growth-and-division
#4
Xia Wang, Kotaro Fujimaki, Geoffrey C Mitchell, Jungeun Sarah Kwon, Kimiko Della Croce, Chris Langsdorf, Hao Helen Zhang, Guang Yao
Reactivating quiescent cells to proliferate is critical to tissue repair and homoeostasis. Quiescence exit is highly noisy even for genetically identical cells under the same environmental conditions. Deregulation of quiescence exit is associated with many diseases, but cellular mechanisms underlying the noisy process of exiting quiescence are poorly understood. Here we show that the heterogeneity of quiescence exit reflects a memory of preceding cell growth at quiescence induction and immediate division history before quiescence entry, and that such a memory is reflected in cell size at a coarse scale...
August 22, 2017: Nature Communications
https://www.readbyqxmd.com/read/28764404/l%C3%A3-vy-noise-induced-phenomena-in-co-oxidation-on-ir-111-surfaces
#5
Jing Feng, Wei Xu, Yong Xu, Xiaolong Wang, Jürgen Kurths
The influences of external Lévy noise in CO oxidation on the Ir(111) surfaces are numerically examined. Depending on the control parameters, such as the temperature T  and the CO fraction Y  in the total reactant input gas flux, the reaction exhibits one or two stable stationary states in the absence of noise. Lévy noise is introduced in the reaction by randomly varying the quality of the influx mixture. We then observe a large variety of different types of behaviors depending on the initial CO fraction Y, in particular, the phenomenon of noise-induced shifts of the steady state in the monostable regime is regarded...
July 2017: Chaos
https://www.readbyqxmd.com/read/28741470/ecological-feedback-in-quorum-sensing-microbial-populations-can-induce-heterogeneous-production-of-autoinducers
#6
Matthias Bauer, Johannes Knebel, Matthias Lechner, Peter Pickl, Erwin Frey
Autoinducers are small signaling molecules that mediate intercellular communication in microbial populations and trigger coordinated gene expression via 'quorum sensing'. Elucidating the mechanisms that control autoinducer production is, thus, pertinent to understanding collective microbial behavior, such as virulence and bioluminescence. Recent experiments have shown a heterogeneous promoter activity of autoinducer synthase genes, suggesting that some of the isogenic cells in a population might produce autoinducers, whereas others might not...
July 25, 2017: ELife
https://www.readbyqxmd.com/read/28709324/geometric-structure-and-information-change-in-phase-transitions
#7
Eun-Jin Kim, Rainer Hollerbach
We propose a toy model for a cyclic order-disorder transition and introduce a geometric methodology to understand stochastic processes involved in transitions. Specifically, our model consists of a pair of forward and backward processes (FPs and BPs) for the emergence and disappearance of a structure in a stochastic environment. We calculate time-dependent probability density functions (PDFs) and the information length L, which is the total number of different states that a system undergoes during the transition...
June 2017: Physical Review. E
https://www.readbyqxmd.com/read/28667253/inhibitors-alter-the-stochasticity-of-regulatory-proteins-to-force-cells-to-switch-to-the-other-state-in-the-bistable-system
#8
Wun-Sin Jhang, Shih-Chiang Lo, Chen-Chao Yeh, Che-Chi Shu
The cellular behaviors under the control of genetic circuits are subject to stochastic fluctuations, or noise. The stochasticity in gene regulation, far from a nuisance, has been gradually appreciated for its unusual function in cellular activities. In this work, with Chemical Master Equation (CME), we discovered that the addition of inhibitors altered the stochasticity of regulatory proteins. For a bistable system of a mutually inhibitory network, such a change of noise led to the migration of cells in the bimodal distribution...
June 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28485372/optically-levitated-nanoparticle-as-a-model-system-for-stochastic-bistable-dynamics
#9
F Ricci, R A Rica, M Spasenović, J Gieseler, L Rondin, L Novotny, R Quidant
Nano-mechanical resonators have gained an increasing importance in nanotechnology owing to their contributions to both fundamental and applied science. Yet, their small dimensions and mass raises some challenges as their dynamics gets dominated by nonlinearities that degrade their performance, for instance in sensing applications. Here, we report on the precise control of the nonlinear and stochastic bistable dynamics of a levitated nanoparticle in high vacuum. We demonstrate how it can lead to efficient signal amplification schemes, including stochastic resonance...
May 9, 2017: Nature Communications
https://www.readbyqxmd.com/read/28415354/stochastic-resonance-across-bifurcation-cascades
#10
C Nicolis, G Nicolis
The classical setting of stochastic resonance is extended to account for parameter variations leading to transitions between a unique stable state, bistability, and multistability regimes, across singularities of various kinds. Analytic expressions for the amplitude and the phase of the response in terms of key parameters are obtained. The conditions for optimal responses are derived in terms of the bifurcation parameter, the driving frequency, and the noise strength.
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415353/noise-induced-symmetry-breaking-far-from-equilibrium-and-the-emergence-of-biological-homochirality
#11
Farshid Jafarpour, Tommaso Biancalani, Nigel Goldenfeld
The origin of homochirality, the observed single-handedness of biological amino acids and sugars, has long been attributed to autocatalysis, a frequently assumed precursor for early life self-replication. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross-inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here we present a theory for a stochastic individual-level model of autocatalytic prebiotic self-replicators that are maintained out of thermal equilibrium...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28415301/nonlinear-signaling-on-biological-networks-the-role-of-stochasticity-and-spectral-clustering
#12
Gonzalo Hernandez-Hernandez, Jesse Myers, Enrique Alvarez-Lacalle, Yohannes Shiferaw
Signal transduction within biological cells is governed by networks of interacting proteins. Communication between these proteins is mediated by signaling molecules which bind to receptors and induce stochastic transitions between different conformational states. Signaling is typically a cooperative process which requires the occurrence of multiple binding events so that reaction rates have a nonlinear dependence on the amount of signaling molecule. It is this nonlinearity that endows biological signaling networks with robust switchlike properties which are critical to their biological function...
March 2017: Physical Review. E
https://www.readbyqxmd.com/read/28246663/steady-state-statistical-correlations-predict-bistability-in-reaction-motifs
#13
Suchana Chakravarty, Debashis Barik
Various cellular decision making processes are regulated by bistable switches that take graded input signals and convert them to binary all-or-none responses. Traditionally, a bistable switch generated by a positive feedback loop is characterized either by a hysteretic signal response curve with two distinct signaling thresholds or by characterizing the bimodality of the response distribution in the bistable region. To identify the intrinsic bistability of a feedback regulated network, here we propose that bistability can be determined by correlating higher order moments and cumulants (≥2) of the joint steady state distributions of two components connected in a positive feedback loop...
March 28, 2017: Molecular BioSystems
https://www.readbyqxmd.com/read/28219776/deactivation-in-the-posterior-mid-cingulate-cortex-reflects-perceptual-transitions-during-binocular-rivalry-evidence-from-simultaneous-eeg-fmri
#14
Abhrajeet V Roy, Keith W Jamison, Sheng He, Stephen A Engel, Bin He
Binocular rivalry is a phenomenon in which perception spontaneously shifts between two different images that are dichoptically presented to the viewer. By elucidating the cortical networks responsible for these stochastic fluctuations in perception, we can potentially learn much about the neural correlates of visual awareness. We obtained concurrent EEG-fMRI data for a group of 20 healthy human subjects during the continuous presentation of dichoptic visual stimuli. The two eyes' images were tagged with different temporal frequencies so that eye specific steady-state visual evoked potential (SSVEP) signals could be extracted from the EEG data for direct comparison with changes in fMRI BOLD activity associated with binocular rivalry...
May 15, 2017: NeuroImage
https://www.readbyqxmd.com/read/28169220/stochastic-resonance-in-bistable-atomic-switches
#15
Kenji Yoshida, Kazuhiko Hirakawa
We have investigated the conductance of bistable gold atomic switches as a function of periodic input voltages mixed with a random noise. With increasing noise amplitude, the atomic switches biased below the threshold voltage for conductance switching start exhibiting switching in conductance between two stable states. Clear synchronization between the input and output signals is observed when an optimized noise amplitude is mixed with the periodic input voltage, even when the atomic switches are driven by an input voltage as low as approximately 10% of the threshold voltage...
March 24, 2017: Nanotechnology
https://www.readbyqxmd.com/read/28139764/deliberate-switching-of-single-photochromic-triads
#16
Johannes Maier, Martti Pärs, Tina Weller, Mukundan Thelakkat, Jürgen Köhler
Photochromic molecules can be reversibly converted between two bistable conformations by light, and are considered as promising building blocks in novel macromolecular structures for sensing and imaging techniques. We have studied individual molecular triads consisting of two strong fluorophores (perylene bisimide) that are covalently linked via a photochromic unit (dithienylcyclopentene) and distinguished between deliberate switching and spontaneous blinking. It was verified that the probability for observing deliberate light-induced switching of a single triad (rather than stochastic blinking) amounts to 0...
January 31, 2017: Scientific Reports
https://www.readbyqxmd.com/read/27993627/an-open-loop-approach-to-calculate-noise-induced-transitions
#17
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...
February 21, 2017: Journal of Theoretical Biology
https://www.readbyqxmd.com/read/27967182/heat-dissipation-and-information-flow-for-delayed-bistable-langevin-systems-near-coherence-resonance
#18
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
https://www.readbyqxmd.com/read/27967045/thermodynamic-geometry-of-minimum-dissipation-driven-barrier-crossing
#19
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
https://www.readbyqxmd.com/read/27927198/a-computational-method-for-the-investigation-of-multistable-systems-and-its-application-to-genetic-switches
#20
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
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