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Stochastic bistability

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https://www.readbyqxmd.com/read/29227103/a-robust-molecular-network-motif-for-period-doubling-devices
#1
Christian Cuba Samaniego, Elisa Franco
Life is sustained by a variety of cyclic processes such as cell division, muscle contraction, and neuron firing. The periodic signals powering these processes often direct a variety of other downstream systems, which operate at different time scales and must have the capacity to divide or multiply the period of the master clock. Period modulation is also an important challenge in synthetic molecular systems, where slow and fast components may have to be coordinated simultaneously by a single oscillator whose frequency is often difficult to tune...
December 11, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29219465/emergent-bistability-and-switching-in-a-nonequilibrium-crystal
#2
Guram Gogia, Justin C Burton
Multistability is an inseparable feature of many physical, chemical, and biological systems which are driven far from equilibrium. In these nonequilibrium systems, stochastic dynamics often induces switching between distinct states on emergent time scales; for example, bistable switching is a natural feature of noisy, spatially extended systems that consist of bistable elements. Nevertheless, here we present experimental evidence that bistable elements are not required for the global bistability of a system...
October 27, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29209016/direct-measurement-of-kramers-turnover-with-a-levitated-nanoparticle
#3
Loïc Rondin, Jan Gieseler, Francesco Ricci, Romain Quidant, Christoph Dellago, Lukas Novotny
Understanding the thermally activated escape from a metastable state is at the heart of important phenomena such as the folding dynamics of proteins, the kinetics of chemical reactions or the stability of mechanical systems. In 1940, Kramers calculated escape rates both in the high damping and low damping regimes, and suggested that the rate must have a maximum for intermediate damping. This phenomenon, today known as the Kramers turnover, has triggered important theoretical and numerical studies. However, as yet, there is no direct and quantitative experimental verification of this turnover...
December 2017: Nature Nanotechnology
https://www.readbyqxmd.com/read/29197392/genetic-toggle-switch-controlled-by-bacterial-growth-rate
#4
Joanna Jaruszewicz-Błońska, Tomasz Lipniacki
BACKGROUND: In favorable conditions bacterial doubling time is less than 20 min, shorter than DNA replication time. In E. coli a single round of genome replication lasts about 40 min and it must be accomplished about 20 min before cell division. To achieve such fast growth rates bacteria perform multiple replication rounds simultaneously. As a result, when the division time is as short as 20 min E. coli has about 8 copies of origin of replication (ori) and the average copy number of the genes situated close to ori can be 4 times larger than those near the terminus of replication (ter)...
December 2, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/29186174/parallel-arrangements-of-positive-feedback-loops-limit-cell-to-cell-variability-in-differentiation
#5
Anupam Dey, Debashis Barik
Cellular differentiations are often regulated by bistable switches resulting from specific arrangements of multiple positive feedback loops (PFL) fused to one another. Although bistability generates digital responses at the cellular level, stochasticity in chemical reactions causes population heterogeneity in terms of its differentiated states. We hypothesized that the specific arrangements of PFLs may have evolved to minimize the cellular heterogeneity in differentiation. In order to test this we investigated variability in cellular differentiation controlled either by parallel or serial arrangements of multiple PFLs having similar average properties under extrinsic and intrinsic noises...
2017: PloS One
https://www.readbyqxmd.com/read/29155808/a-hierarchical-stochastic-model-for-bistable-perception
#6
Stefan Albert, Katharina Schmack, Philipp Sterzer, Gaby Schneider
Viewing of ambiguous stimuli can lead to bistable perception alternating between the possible percepts. During continuous presentation of ambiguous stimuli, percept changes occur as single events, whereas during intermittent presentation of ambiguous stimuli, percept changes occur at more or less regular intervals either as single events or bursts. Response patterns can be highly variable and have been reported to show systematic differences between patients with schizophrenia and healthy controls. Existing models of bistable perception often use detailed assumptions and large parameter sets which make parameter estimation challenging...
November 20, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/29092418/an-alternate-protocol-to-achieve-stochastic-and-deterministic-resonances
#7
Ishant Tiwari, Darshil Dave, Richa Phogat, Neev Khera, P Parmananda
Periodic and Aperiodic Stochastic Resonance (SR) and Deterministic Resonance (DR) are studied in this paper. To check for the ubiquitousness of the phenomena, two unrelated systems, namely, FitzHugh-Nagumo and a particle in a bistable potential well, are studied. Instead of the conventional scenario of noise amplitude (in the case of SR) or chaotic signal amplitude (in the case of DR) variation, a tunable system parameter ("a" in the case of FitzHugh-Nagumo model and the damping coefficient "j" in the bistable model) is regulated...
October 2017: Chaos
https://www.readbyqxmd.com/read/29089531/entropy-production-selects-nonequilibrium-states-in-multistable-systems
#8
Robert G Endres
Far-from-equilibrium thermodynamics underpins the emergence of life, but how has been a long-outstanding puzzle. Best candidate theories based on the maximum entropy production principle could not be unequivocally proven, in part due to complicated physics, unintuitive stochastic thermodynamics, and the existence of alternative theories such as the minimum entropy production principle. Here, we use a simple, analytically solvable, one-dimensional bistable chemical system to demonstrate the validity of the maximum entropy production principle...
October 31, 2017: Scientific Reports
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
#9
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
#10
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...
December 2017: Neural Computation
https://www.readbyqxmd.com/read/28950646/regime-shifts-driven-by-dynamic-correlations-in-gene-expression-noise
#11
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
#12
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
#13
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
#14
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
#15
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
#16
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
#17
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
#18
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
#19
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
#20
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
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