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## Stable Stochastic Dynamics in Yeast Cell Cycle

Fonte: The Biophysical Society
Publicador: The Biophysical Society

Tipo: Artigo de Revista Científica

Português

Relevância na Pesquisa

37.878696%

Chemical reactions in cells are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of the cell is kept stable against those noisy perturbations. In this study, a stochastic model of the cell cycle of budding yeast was constructed to analyze the effects of noise on the cell-cycle oscillation. The model predicts intense noise in levels of mRNAs and proteins, and the simulated protein levels explain the observed statistical tendency of noise in populations of synchronous and asynchronous cells. Despite intense noise in levels of proteins and mRNAs, the cell cycle is stable enough to bring the largely perturbed cells back to the physiological cyclic oscillation. The model shows that consecutively appearing fixed points are the origin of this stability of the cell cycle.

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## Stochastic steady state gain in a gene expression process with mRNA degradation control

Fonte: The Royal Society
Publicador: The Royal Society

Tipo: Artigo de Revista Científica

Português

Relevância na Pesquisa

28.608271%

Recent analyses with high-resolution single-molecule experimental methods have shown highly irregular and variable bursting of mRNA in a wide range of organisms. Noise in gene expression is thought to be beneficial in cell fate specifications, as it can lay a foundation for phenotypic diversification of isogenetic cells in the homogeneous environment. However, because the stability of proteins is, in many cases, higher than that of mRNAs, noise from transcriptional bursting can be considerably buffered at the protein level, limiting the effect of noisy mRNAs at a more global regulation level. This raises a question as to what constructive role noisy mRNAs can play in the system-level dynamics. In this study, we have addressed this question using the computational models that extend the conventional transcriptional bursting model with a post-transcriptional regulation step. Surprisingly, by comparing this stochastic model with the corresponding deterministic model, we find that intrinsic fluctuations can substantially increase the expected mRNA level. Because effects of a higher mRNA level can be transmitted to the protein level even with slow protein degradation rates, this finding suggests that an increase in the protein level is another potential effect of transcriptional bursting. Here...

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## Dynamics of Random Boolean Networks under Fully Asynchronous Stochastic Update Based on Linear Representation

Fonte: Public Library of Science
Publicador: Public Library of Science

Tipo: Artigo de Revista Científica

Publicado em 13/06/2013
Português

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A novel algebraic approach is proposed to study dynamics of asynchronous random Boolean networks where a random number of nodes can be updated at each time step (ARBNs). In this article, the logical equations of ARBNs are converted into the discrete-time linear representation and dynamical behaviors of systems are investigated. We provide a general formula of network transition matrices of ARBNs as well as a necessary and sufficient algebraic criterion to determine whether a group of given states compose an attractor of length in ARBNs. Consequently, algorithms are achieved to find all of the attractors and basins in ARBNs. Examples are showed to demonstrate the feasibility of the proposed scheme.

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## Stochastic environmental fluctuations drive epidemiology in experimental host–parasite metapopulations

Fonte: The Royal Society
Publicador: The Royal Society

Tipo: Artigo de Revista Científica

Publicado em 22/10/2013
Português

Relevância na Pesquisa

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Environmental fluctuations are important for parasite spread and persistence. However, the effects of the spatial and temporal structure of environmental fluctuations on host–parasite dynamics are not well understood. Temporal fluctuations can be random but positively autocorrelated, such that the environment is similar to the recent past (red noise), or random and uncorrelated with the past (white noise). We imposed red or white temporal temperature fluctuations on experimental metapopulations of Paramecium caudatum, experiencing an epidemic of the bacterial parasite Holospora undulata. Metapopulations (two subpopulations linked by migration) experienced fluctuations between stressful (5°C) and permissive (23°C) conditions following red or white temporal sequences. Spatial variation in temperature fluctuations was implemented by exposing subpopulations to the same (synchronous temperatures) or different (asynchronous temperatures) temporal sequences. Red noise, compared with white noise, enhanced parasite persistence. Despite this, red noise coupled with asynchronous temperatures allowed infected host populations to maintain sizes equivalent to uninfected populations. It is likely that this occurs because subpopulations in permissive conditions rescue declining subpopulations in stressful conditions. We show how patterns of temporal and spatial environmental fluctuations can impact parasite spread and host population abundance. We conclude that accurate prediction of parasite epidemics may require realistic models of environmental noise.

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## GADIA: A Greedy Asynchronous Distributed Interference Avoidance Algorithm

Fonte: Institute of Electrical and Electronics Engineers
Publicador: Institute of Electrical and Electronics Engineers

Tipo: Artigo de Revista Científica

Português

Relevância na Pesquisa

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#cognitive radios#distributed algorithms#dynamic spectrum allocation#Glauber dynamics#interference avoidance

In this paper, the problem of distributed dynamic frequency allocation is considered for a canonical communication network, which spans several networks such as cognitive radio networks and digital subscriber lines (DSLs). A greedy asynchronous distributed interference avoidance (GADIA) algorithm for horizontal spectrum sharing has been proposed that achieves performance close to that of a centralized optimal algorithm. The convergence of the GADIA algorithm to a near-optimal frequency allocation strategy is proved and several asymptotic performance bounds have been established for various spatial configurations of the network nodes. Furthermore, the near-equilibrium dynamics of the GADIA algorithm has been studied using the Glauber dynamics, by identifying the problem with the antiferromagnetic inhomogeneous long-range Potts model. Using the near-equilibrium dynamics and methods from stochastic analysis, the robustness of the algorithm with respect to time variations in the activity of network nodes is studied. These analytic results along with simulation studies reveal that the performance is close to that of an optimum centralized frequency allocation algorithm. Further simulation studies confirm that our proposed algorithm outperforms the iterative water-filling algorithm in the low signal-to-interference-plus-noise ratio (SINR) regime...

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## Controllability of time-delayed Boolean multiplex control networks under asynchronous stochastic update

Fonte: Nature Publishing Group
Publicador: Nature Publishing Group

Tipo: Artigo de Revista Científica

Publicado em 17/12/2014
Português

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In this article, the controllability of asynchronous Boolean multiplex control networks (ABMCNs) with time delay is studied. Firstly, dynamical model of Boolean multiplex control networks is constructed, which is assumed to be under Harvey' asynchronous update and time delay is introduced both in states and controls. By using of semi-tensor product (STP) approach, the logical dynamics is converted into an equivalent algebraic form by obtaining the control-depending network transition matrices of delayed system. Secondly, a necessary and sufficient condition is proved that only control-depending fixed points of the studied dynamics can be controlled with probability one. Thirdly, respectively for two types of controls, the controllability of dynamical control system is investigated. When initial states and time delay are given, formulae are obtained to show a) the reachable set at time s under specified controls; b) the reachable set at time s under arbitrary controls; c) the reachable probabilities to different destination states. Furthermore, an approach is discussed to find a precise control sequence which can steer dynamical system into a specified target with the maximum reachable probability. Examples are shown to illustrate the feasibility of the proposed scheme.

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## Asynchronous stochastic dynamics and the spatial prisioner's dilemma game

Fonte: Springer
Publicador: Springer

Tipo: Conferência ou Objeto de Conferência

Publicado em //2007
Português

Relevância na Pesquisa

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We argue that intermediate levels of asynchronism should
be explored when one uses evolutionary games to model biological and
sociological systems. Usually, only perfect synchronism and continuous
asynchronism are used, assuming that it is enough to test the model under
these two opposite update methods. We believe that biological and
social systems lie somewhere between these two extremes and that we
should inquire how the models used in these situations behave when the
update method allows more than one element to be active at the same
time but not necessarily all of them. Here, we use an update method
called Asynchronous Stochastic Dynamics which allows us to explore
intermediate levels of asynchronism and we apply it to the Spatial Prisoner’s
Dilemma game. We report some results concerning the way the
system changes its behaviour as the synchrony rate of the update method
varies.

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## The influence of asynchronous dynamics in the spatial prisioner's dilemma game

Fonte: Springer
Publicador: Springer

Tipo: Conferência ou Objeto de Conferência

Publicado em //2008
Português

Relevância na Pesquisa

27.85045%

We examine the influence of asynchronism in the Spatial
Prisoner’s Dilemma game. Previous studies reported that less cooperation
is achieved with the asynchronous version of the game than with
the synchronous one. Here, we show that, in general, the opposite is the
most common outcome. This conclusion is only possible because a larger
number of scenarios was tested, namely, different interaction topologies,
a transition rule that can be tuned to emulate different levels of determinism
in the choice of the next strategy to be adopted and different
rates of asynchronism. The influence of stochastic and deterministic periodic
updating in the outcome of the system is also compared. We found
that these two update disciplines lead basically to the same result. This
is an important issue in the simulation of social and biological behavior.

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## Learning Stationary Correlated Equilibria in Constrained General-Sum Stochastic Games

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Português

Relevância na Pesquisa

38.388315%

We study constrained general-sum stochastic games with unknown Markovian
dynamics. A distributed constrained no-regret Q-learning scheme (CNRQ) is
presented to guarantee convergence to the set of stationary correlated
equilibria of the game. Prior art addresses the unconstrained case only, is
structured with nested control loops, and has no convergence result. CNRQ is
cast as a single-loop three-timescale asynchronous stochastic approximation
algorithm with set-valued update increments. A rigorous convergence analysis
with differential inclusion arguments is given which draws on recent extensions
of the theory of stochastic approximation to the case of asynchronous recursive
inclusions with set-valued mean fields. Numerical results are given for the
exemplary application of CNRQ to decentralized resource control in
heterogeneous wireless networks (HetNets).; Comment: 25 pages, 2 figures, 5 tables in IEEE Transactions on Cybernetics,
Vol. XX, No. XX, 2015

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## Power, Levy, Exponential and Gaussian Regimes in Autocatalytic Financial Systems

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 02/08/2000
Português

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We study by theoretical analysis and by direct numerical simulation the
dynamics of a wide class of asynchronous stochastic systems composed of many
autocatalytic degrees of freedom. We describe the generic emergence of
truncated power laws in the size distribution of their individual elements. The
exponents $\alpha$ of these power laws are time independent and depend only on
the way the elements with very small values are treated. These truncated power
laws determine the collective time evolution of the system. In particular the
global stochastic fluctuations of the system differ from the normal Gaussian
noise according to the time and size scales at which these fluctuations are
considered. We describe the ranges in which these fluctuations are
parameterized respectively by: the Levy regime $\alpha < 2$, the power law
decay with large exponent ($\alpha > 2$), and the exponential decay. Finally we
relate these results to the large exponent power laws found in the actual
behavior of the stock markets and to the exponential cut-off detected in
certain recent measurement.; Comment: 9 pages with 5 figures; Proceedings of EPS conference "Applications
of Physics in Financial Analysis 2", 13 to 15 July 2000 Liege, Belgium (to
appear in Eur. Phys. J. B)

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## The dynamics of critical Kauffman networks under asynchronous stochastic update

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 05/01/2005
Português

Relevância na Pesquisa

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We show that the mean number of attractors in a critical Boolean network
under asynchronous stochastic update grows like a power law and that the mean
size of the attractors increases as a stretched exponential with the system
size. This is in strong contrast to the synchronous case, where the number of
attractors grows faster than any power law.; Comment: submitted to PRL

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## Approach to Fixation for Zero-Temperature Stochastic Ising Models on the Hexagonal Lattice

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 14/11/2001
Português

Relevância na Pesquisa

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#Mathematics - Probability#Condensed Matter - Statistical Mechanics#60K35, 82C22, 60K37, 37B15, 82C20

We investigate zero-temperature dynamics on the hexagonal lattice H for the
homogeneous ferromagnetic Ising model with zero external magnetic field and a
disordered ferromagnetic Ising model with a positive external magnetic field h.
We consider both continuous time (asynchronous) processes and, in the
homogeneous case, also discrete time synchronous dynamics (i.e., a
deterministic cellular automaton), alternating between two sublattices of H.
The state space consists of assignments of -1 or +1 to each site of H, and the
processes are zero-temperature limits of stochastic Ising ferromagnets with
Glauber dynamics and a random (i.i.d. Bernoulli) spin configuration at time 0.
We study the speed of convergence of the configuration $\sigma^t$ at time t to
its limit $\sigma^{\infty}$ and related issues.; Comment: 20 pages, to appear in "In and out of equilibrium: probability with a
physics flavor", Progress in Probability, Birkhauser

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## Transient Information Flow in a Network of Excitatory and Inhibitory Model Neurons: Role of Noise and Signal Autocorrelation

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 23/02/2005
Português

Relevância na Pesquisa

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We investigate the performance of sparsely-connected networks of
integrate-and-fire neurons for ultra-short term information processing. We
exploit the fact that the population activity of networks with balanced
excitation and inhibition can switch from an oscillatory firing regime to a
state of asynchronous irregular firing or quiescence depending on the rate of
external background spikes.
We find that in terms of information buffering the network performs best for
a moderate, non-zero, amount of noise. Analogous to the phenomenon of
stochastic resonance the performance decreases for higher and lower noise
levels. The optimal amount of noise corresponds to the transition zone between
a quiescent state and a regime of stochastic dynamics. This provides a
potential explanation on the role of non-oscillatory population activity in a
simplified model of cortical micro-circuits.; Comment: 27 pages, 7 figures, to appear in J. Physiology (Paris) Vol. 98

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## Progresses in the Analysis of Stochastic 2D Cellular Automata: a Study of Asynchronous 2D Minority

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 17/06/2007
Português

Relevância na Pesquisa

28.292976%

Cellular automata are often used to model systems in physics, social
sciences, biology that are inherently asynchronous. Over the past 20 years,
studies have demonstrated that the behavior of cellular automata drastically
changed under asynchronous updates. Still, the few mathematical analyses of
asynchronism focus on one-dimensional probabilistic cellular automata, either
on single examples or on specific classes. As for other classic dynamical
systems in physics, extending known methods from one- to two-dimensional
systems is a long lasting challenging problem.
In this paper, we address the problem of analysing an apparently simple 2D
asynchronous cellular automaton: 2D Minority where each cell, when fired,
updates to the minority state of its neighborhood. Our experiments reveal that
in spite of its simplicity, the minority rule exhibits a quite complex response
to asynchronism. By focusing on the fully asynchronous regime, we are however
able to describe completely the asymptotic behavior of this dynamics as long as
the initial configuration satisfies some natural constraints. Besides these
technical results, we have strong reasons to believe that our techniques
relying on defining an energy function from the transition table of the
automaton may be extended to the wider class of threshold automata.

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## Does brain activity stem from high-dimensional chaotic dynamics? Evidence from the human electroencephalogram, cat cerebral cortex and artificial neuronal networks

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 27/04/2009
Português

Relevância na Pesquisa

48.28648%

Nonlinear time series analyses have suggested that the human
electroencephalogram (EEG) may share statistical and dynamical properties with
chaotic systems. During slow-wave sleep or pathological states like epilepsy,
correlation dimension measurements display low values, while in awake and
attentive subjects, there is not such low dimensionality, and the EEG is more
similar to a stochastic variable. We briefly review these results and contrast
them with recordings in cat cerebral cortex, as well as with theoretical
models. In awake or sleeping cats, recordings with microelectrodes inserted in
cortex show that global variables such as local field potentials (local EEG)
are similar to the human EEG. However, in both cases, neuronal discharges are
highly irregular and exponentially distributed, similar to Poisson stochastic
processes. To attempt reconcile these results, we investigate models of
randomly-connected networks of integrate-and-fire neurons, and also contrast
global (averaged) variables, with neuronal activity. The network displays
different states, such as "synchronous regular" (SR) or "asynchronous
irregular" (AI) states. In SR states, the global variables display coherent
behavior with low dimensionality, while in AI states...

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## Asynchronous Event-Driven Particle Algorithms

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Português

Relevância na Pesquisa

28.27418%

We present, in a unifying way, the main components of three asynchronous
event-driven algorithms for simulating physical systems of interacting
particles. The first example, hard-particle molecular dynamics, is well-known.
We also present a recently-developed diffusion kinetic Monte Carlo algorithm,
as well as a novel stochastic molecular-dynamics algorithm that builds on the
Direct Simulation Monte Carlo. We explain how to effectively combine
asynchronous event-driven with classical time-driven or with synchronous
event-driven handling. Finally, we discuss some promises and challenges for
event-driven simulation of realistic physical systems.; Comment: To appear in Simulation: Transactions of the Society for Modeling and
Simulation International, 2008

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## Stochastic Minority on Graphs

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 23/11/2010
Português

Relevância na Pesquisa

27.815007%

#Nonlinear Sciences - Cellular Automata and Lattice Gases#Computer Science - Distributed, Parallel, and Cluster Computing#Computer Science - Discrete Mathematics#Mathematics - Combinatorics#Mathematics - Probability

Cellular automata have been mainly studied on very regular graphs carrying
the vertices (like lines or grids) and under synchronous dynamics (all vertices
update simultaneously). In this paper, we study how the asynchronism and the
graph act upon the dynamics of the classical Minority rule. Minority has been
well-studied for synchronous updates and is thus a reasonable choice to begin
with. Yet, beyond its apparent simplicity, this rule yields complex behaviors
when asynchronism is introduced. We investigate the transitory part as well as
the asymptotic behavior of the dynamics under full asynchronism (also called
sequential: only one random vertex updates at each time step) for several types
of graphs. Such a comparative study is a first step in understanding how the
asynchronous dynamics is linked to the topology (the graph).
Previous analyses on the grid [1,2] have observed that Minority seems to
induce fast stabilization. We investigate here this property on arbitrary
graphs using tools such as energy, particles and random walks. We show that the
worst case convergence time is, in fact, strongly dependent on the topology. In
particular, we observe that the case of trees is non trivial.

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## Asynchronous Networks and Event Driven Dynamics

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 14/09/2015
Português

Relevância na Pesquisa

29.009565%

Real-world networks in physics, biology and technology often exhibit dynamics
that cannot be adequately reproduced using network models given by smooth
dynamical systems and a fixed network topology. Asynchronous networks give a
theoretical and conceptual framework for the study of network dynamics where
nodes can evolve independently of one another, be constrained, stop, and later
restart, and where the interaction between different components of the network
may depend on time, state, and stochastic effects. This framework is
sufficiently general to encompass a wide range of applications ranging from
engineering to neuroscience. Typically, dynamics is piecewise smooth and there
are relationships with Filippov systems. We make the notion of a functional
asynchronous network rigorous, discuss the phenomenon of dynamical locks, and
present a theorem about the spatiotemporal factorization of the dynamics for a
class of deadlock free functional asynchronous networks of feedforward type. We
conclude with some examples and applications related to asynchronous networks
with a stochastic connection structure.

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## Activity-dependent stochastic resonance in recurrent neuronal networks

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 10/06/2008
Português

Relevância na Pesquisa

27.726086%

We use a biophysical model of a local neuronal circuit to study the
implications of synaptic plasticity for the detection of weak sensory stimuli.
Networks with fast plastic coupling show behavior consistent with stochastic
resonance. Addition of an additional slow coupling that accounts for the
asynchronous release of neurotransmitter results in qualitatively different
properties of signal detection, and also leads to the appearance of transient
post-stimulus bistability. Our results suggest testable hypothesis with regard
to the self-organization and dynamics of local neuronal circuits.; Comment: 4 pages, 4 figures, published in Physical Review E

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## Stable stochastic dynamics in yeast cell cycle

Fonte: Universidade Cornell
Publicador: Universidade Cornell

Tipo: Artigo de Revista Científica

Publicado em 11/07/2007
Português

Relevância na Pesquisa

37.878696%

Chemical reactions in cell are subject to intense stochastic fluctuations. An
important question is how the fundamental physiological behavior of cell is
kept stable against those noisy perturbations. In this paper a stochastic model
of cell cycle of budding yeast is constructed to analyze the effects of noise
on the cell cycle oscillation. The model predicts intense noise in levels of
mRNAs and proteins, and the simulated protein levels explain the observed
statistical tendency of noise in populations of synchronous and asynchronous
cells. In spite of intense noise in levels of proteins and mRNAs, cell cycle is
stable enough to bring the largely perturbed cells back to the physiological
cyclic oscillation. The model shows that consecutively appearing fixed points
are the origin of this stability of cell cycle.; Comment: main text, 2 supporting texts, 3 supplementary tables

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