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Stochastic bistability

Ye Guan, Zhengda Li, Shiyuan Wang, Patrick M Barnes, Xuwen Liu, Haotian Xu, Minjun Jin, Allen P Liu, Qiong Yang
Single-cell analysis is pivotal to deciphering complex phenomena like heterogeneity, bistability, and asynchronous oscillations, where a population ensemble cannot represent individual behaviors. Bulk cell-free systems, despite having unique advantages of manipulation and characterization of biochemical networks, lack the essential single-cell information to understand a class of out-of-steady-state dynamics including cell cycles. Here, by encapsulating Xenopus egg extracts in water-in-oil microemulsions, we developed artificial cells that are adjustable in sizes and periods, sustain mitotic oscillations for over 30 cycles, and function in forms from the simplest cytoplasmic-only to the more complicated ones involving nuclear dynamics, mimicking real cells...
April 5, 2018: ELife
Bo Wang, Qianqian Qi
In the reality, the lake system will be disturbed by stochastic factors including the external and internal factors. By adding the additive noise and the multiplicative noise to the right-hand sides of the model equation, the additive stochastic model and the multiplicative stochastic model are established respectively in order to reduce model errors induced by the absence of some physical processes. For both the two kinds of stochastic ecosystems, the authors studied the bifurcation characteristics with the FPK equation and the Lyapunov exponent method based on the Stratonovich-Khasminiskii stochastic average principle...
March 20, 2018: Mathematical Biosciences
Hao Ge, Pingping Wu, Hong Qian, Sunney Xiaoliang Xie
Within an isogenic population, even in the same extracellular environment, individual cells can exhibit various phenotypic states. The exact role of stochastic gene-state switching regulating the transition among these phenotypic states in a single cell is not fully understood, especially in the presence of positive feedback. Recent high-precision single-cell measurements showed that, at least in bacteria, switching in gene states is slow relative to the typical rates of active transcription and translation...
March 12, 2018: PLoS Computational Biology
Dola Sengupta, Sandip Kar
Neural stem cells (NSCs) often give rise to a mixed population of cells during differentiation. However, the dynamical origin of these mixed states is poorly understood. In this article, our mathematical modeling study demonstrates that the bone morphogenetic protein 2 (BMP2) mediated disparate differentiation dynamics of NSCs in central and peripheral nervous systems essentially function through two distinct bistable switches that are mutually interconnected via a mushroom-like bifurcation. Stochastic simulations of the model reveal that the mixed population originates due to the existence of these bistable switching regulations and that the maintenance of such mixed states depends on the level of stochastic fluctuations of the system...
February 27, 2018: Biophysical Journal
Anjan Roy, Stefan Klumpp
We computationally study genetic circuits in bacterial populations with heterogeneities in the growth rate. To that end, we present a stochastic simulation method for gene circuits in populations of cells and propose an efficient implementation that we call the "Next Family Method". Within this approach, we implement different population setups, specifically Chemostat-type growth and growth in an ideal Mother Machine and show that the population structure and its statistics are different for the different setups whenever there is growth heterogeneity...
January 23, 2018: Biophysical Journal
Josep Sardanyés, Tomás Alarcón
Tumor cell populations are highly heterogeneous. Such heterogeneity, both at genotypic and phenotypic levels, is a key feature during tumorigenesis. How to investigate the impact of this heterogeneity in the dynamics of tumors cells becomes an important issue. Here we explore a stochastic model describing the competition dynamics between a pool of heterogeneous cancer cells with distinct phenotypes and healthy cells. This model is used to explore the role of demographic fluctuations on the transitions involving tumor clearance...
January 18, 2018: Scientific Reports
Lei Zhang, Wenbin Zheng, Fei Xie, Aiguo Song
Some noisy nonlinear systems could be exploited to operate reliable logic operation in an optimal window of noise intensity, which is termed as logical stochastic resonance (LSR). We investigated the LSR phenomenon in bistable systems when internal noise and external noise are correlated. The LSR effect is evaluated by the success probability of the obtained desired output with various combinations of logic inputs. It is shown that the or-nor, and-nand, and Latch operations still can operate reliably with the correlated internal noise and external noise...
November 2017: Physical Review. E
Sarah A M Loos, Sabine H L Klapp
This paper is concerned with the Fokker-Planck (FP) description of classical stochastic systems with discrete time delay. The non-Markovian character of the corresponding Langevin dynamics naturally leads to a coupled infinite hierarchy of FP equations for the various n-time joint distribution functions. Here, we present an approach to close the hierarchy at the one-time level based on a linearization of the deterministic forces in all members of the hierarchy starting from the second one. This leads to a closed equation for the one-time probability density in the steady state...
July 2017: Physical Review. E
Avishek Chowdhury, Sylvain Barbay, Marcel G Clerc, Isabelle Robert-Philip, Rémy Braive
Stochastic resonance is a general phenomenon usually observed in one-dimensional, amplitude modulated, bistable systems. We show experimentally the emergence of phase stochastic resonance in the bidimensional response of a forced nanoelectromechanical membrane by evidencing the enhancement of a weak phase modulated signal thanks to the addition of phase noise. Based on a general forced Duffing oscillator model, we demonstrate experimentally and theoretically that phase noise acts multiplicatively, inducing important physical consequences...
December 8, 2017: Physical Review Letters
Ting Wang, Petr Plecháč
Stochastic reaction networks that exhibit bistable behavior are common in systems biology, materials science, and catalysis. Sampling of stationary distributions is crucial for understanding and characterizing the long-time dynamics of bistable stochastic dynamical systems. However, simulations are often hindered by the insufficient sampling of rare transitions between the two metastable regions. In this paper, we apply the parallel replica method for a continuous time Markov chain in order to improve sampling of the stationary distribution in bistable stochastic reaction networks...
December 21, 2017: Journal of Chemical Physics
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...
January 19, 2018: ACS Synthetic Biology
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
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
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
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
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 2017: PLoS Computational Biology
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
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
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
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
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