Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins.

cAMP-response element binding (CREB) proteins are involved in transcriptional regulation in a number of cellular processes (e.g., neural plasticity and circadian rhythms). The CREB family contains activators and repressors that may interact through positive and negative feedback loops. These loops can be generated by auto- and cross-regulation of expression of CREB proteins, via CRE elements in or near their genes. Experiments suggest that such feedback loops may operate in several systems (e.g., Aplysia and rat). To understand the functional implications of such feedback loops, which are interlocked via cross-regulation of transcription, a minimal model with a positive and negative loop was developed and investigated using bifurcation analysis. Bifurcation analysis revealed diverse nonlinear dynamics (e.g., bistability and oscillations). The stability of steady states or oscillations could be changed by time delays in the synthesis of the activator (CREB1) or the repressor (CREB2). Investigation of stochastic fluctuations due to small numbers of molecules of CREB1 and CREB2 revealed a bimodal distribution of CREB molecules in the bistability region. The robustness of the stable HIGH and LOW states of CREB expression to stochastic noise differs, and a critical number of molecules was required to sustain the HIGH state for days or longer. Increasing positive feedback or decreasing negative feedback also increased the lifetime of the HIGH state, and persistence of this state may correlate with long-term memory formation. A critical number of molecules was also required to sustain robust oscillations of CREB expression. If a steady state was near a deterministic Hopf bifurcation point, stochastic resonance could induce oscillations. This comparative analysis of deterministic and stochastic dynamics not only provides insights into the possible dynamics of CREB regulatory motifs, but also demonstrates a framework for understanding other regulatory processes with similar network architecture.

Dynamics of a minimal model of interlocked positive and negative feedback loops of transcriptional regulation by cAMP-response element binding proteins.

cAMP-response element binding (CREB) proteins are involved in transcriptional regulation in a number of cellular processes (e.g., neural plasticity and circadian rhythms). The CREB family contains activators and repressors that may interact through positive and negative feedback loops. These loops can be generated by auto- and cross-regulation of expression of CREB proteins, via CRE elements in or near their genes. Experiments suggest that such feedback loops may operate in several systems (e.g., Aplysia and rat). To understand the functional implications of such feedback loops, which are interlocked via cross-regulation of transcription, a minimal model with a positive and negative loop was developed and investigated using bifurcation analysis. Bifurcation analysis revealed diverse nonlinear dynamics (e.g., bistability and oscillations). The stability of steady states or oscillations could be changed by time delays in the synthesis of the activator (CREB1) or the repressor (CREB2). Investigation of stochastic fluctuations due to small numbers of molecules of CREB1 and CREB2 revealed a bimodal distribution of CREB molecules in the bistability region. The robustness of the stable HIGH and LOW states of CREB expression to stochastic noise differs, and a critical number of molecules was required to sustain the HIGH state for days or longer. Increasing positive feedback or decreasing negative feedback also increased the lifetime of the HIGH state, and persistence of this state may correlate with long-term memory formation. A critical number of molecules was also required to sustain robust oscillations of CREB expression. If a steady state was near a deterministic Hopf bifurcation point, stochastic resonance could induce oscillations. This comparative analysis of deterministic and stochastic dynamics not only provides insights into the possible dynamics of CREB regulatory motifs, but also demonstrates a framework for understanding other regulatory processes with similar network architecture.

Amplitude response of a unilaterally constrained nonlinear micromechanical resonator

Dynamical systems that involve impacts frequently arise in engineering. This Letter reports a study of such a system at microscale that consists of a nonlinear resonator operating with an unilateral impact. The microresonators were fabricated on silicon-on-insulator wafers by using a one-mask process and then characterised by using the capacitively driving and sensing method. Numerical results concerning the dynamics of this vibro-impact system were verified by the experiments. Bifurcation analysis was used to provide a qualitative scenario of the system steady-state solutions as a function of both the amplitude and the frequency of the external driving sinusoidal voltage. The results show that the amplitude of resonant peak is levelled off owing to the impact effect and that the bandwidth of impacting is dependent upon the nonlinearity and the operating conditions.

Nonlinear dynamics of a periodically driven Duffing resonator coupled to a Van der Pol oscillator

We explore the dynamics of a periodically driven Duffing resonator coupled elastically to a van der Pol oscillator in the case of 1?:?1 internal resonance in the cases of weak and strong coupling. Whilst strong coupling leads to dominating synchronization, the weak coupling case leads to a multitude of complex behaviours. A two-time scales method is used to obtain the frequency-amplitude modulation. The internal resonance leads to an antiresonance response of the Duffing resonator and a stagnant response (a small shoulder in the curve) of the van der Pol oscillator. The stability of the dynamic motions is also analyzed. The coupled system shows a hysteretic response pattern and symmetry-breaking facets. Chaotic behaviour of the coupled system is also observed and the dependence of the system dynamics on the parameters are also studied using bifurcation analysis.

角柱列を過ぎる流れの合流現象と乱流への遷移

Interactions between the wakes in a flow past a row of square bars are investigated by numerical simulations, the linear stability analysis and the bifurcation analysis. It is assumed that the row of square bars is placed across a uniform flow. Two-dimensional and incompressible flow field is also assumed. The flow is steady and symmetric along a streamwise centerline through the center of each square bar at low Reynolds numbers. However, it becomes unsteady and periodic in time at the Reynolds numbers larger than a critical value, and then the wakes behind the square bars become oscillatory. It is found by numerical simulations that vortices are shed synchronously from every couple of adjacent square bars in the same phase or in the anti-phase depending upon the distance between the bars. The synchronous shedding of vortices is clarified to occur due to an instability of the steady symmetric flow by the linear stability analysis. The bifurcation diagram of the flow is obtained and the critical Reynolds number of the instability is evaluated numerically.

Big bang bifurcations in von Bertalanffy’s dynamics with strong and weak Allee effects

The main purpose of this work was to study population dynamic discrete models in which the growth of the population is described by generalized von Bertalanffy's functions, with an adjustment or correction factor of polynomial type. The consideration of this correction factor is made with the aim to introduce the Allee effect. To the class of generalized von Bertalanffy's functions is identified and characterized subclasses of strong and weak Allee's functions and functions with no Allee effect. This classification is founded on the concepts of strong and weak Allee's effects to population growth rates associated. A complete description of the dynamic behavior is given, where we provide necessary conditions for the occurrence of unconditional and essential extinction types. The bifurcation structures of the parameter plane are analyzed regarding the evolution of the Allee limit with the aim to understand how the transition from strong Allee effect to no Allee effect, passing through the weak Allee effect, is realized. To generalized von Bertalanffy's functions with strong and weak Allee effects is identified an Allee's effect region, to which is associated the concepts of chaotic semistability curve and Allee's bifurcation point. We verified that under some sufficient conditions, generalized von Bertalanffy's functions have a particular bifurcation structure: the big bang bifurcations of the so-called box-within-a-box type. To this family of maps, the Allee bifurcation points and the big bang bifurcation points are characterized by the symmetric of Allee's limit and by a null intrinsic growth rate. The present paper is also a significant contribution in the framework of the big bang bifurcation analysis for continuous 1D maps and unveil their relationship with the explosion birth and the extinction phenomena.

Instabilities in threshold-diffusion equations with delay

The introduction of delays into ordinary or partial differential equation models is well known to facilitate the production of rich dynamics ranging from periodic solutions through to spatio-temporal chaos. In this paper we consider a class of scalar partial differential equations with a delayed threshold nonlinearity which admits exact solutions for equilibria, periodic orbits and travelling waves. Importantly we show how the spectra of periodic and travelling wave solutions can be determined in terms of the zeros of a complex analytic function. Using this as a computational tool to determine stability we show that delays can have very different effects on threshold systems with negative as opposed to positive feedback. Direct numerical simulations are used to confirm our bifurcation analysis, and to probe some of the rich behaviour possible for mixed feedback.

Delays in activity based neural networks

In this paper we study the effect of two distinct discrete delays on the dynamics of a Wilson-Cowan neural network. This activity based model describes the dynamics of synaptically interacting excitatory and inhibitory neuronal populations. We discuss the interpretation of the delays in the language of neurobiology and show how they can contribute to the generation of network rhythms. First we focus on the use of linear stability theory to show how to destabilise a fixed point, leading to the onset of oscillatory behaviour. Next we show for the choice of a Heaviside nonlinearity for the firing rate that such emergent oscillations can be either synchronous or anti-synchronous depending on whether inhibition or excitation dominates the network architecture. To probe the behaviour of smooth (sigmoidal) nonlinear firing rates we use a mixture of numerical bifurcation analysis and direct simulations, and uncover parameter windows that support chaotic behaviour. Finally we comment on the role of delays in the generation of bursting oscillations, and discuss natural extensions of the work in this paper.

Análise estequiométrica da dinâmica não-linear de redes de reações químicas

Dissertação (mestrado)—Universidade de Brasília, Instituto de Química, Programa de Pós-Graduação em Química, 2016.

A new approach to evaluate imperfection sensitivity in asymmetric bifurcation buckling analysis

A direct procedure for the evaluation of imperfection sensitivity in bifurcation problems is presented. The problems arise in the context of the general theory of elastic stability for discrete structural systems, in which the energy criterion of stability of structures and the total potential energy formulation are employed. In cases of bifurcation buckling the sensitivity of the critical load with respect to an imperfection parameter e is singular at the state given by epsilon =0, so that, a regular perturbation expansion of the solution is not possible. In this work we describe a direct procedure to obtain the relations between the critical loads, the generalized coordinates at the critical state, the eigenvector, and the amplitude of the imperfection, using singular perturbation analysis. The expansions are assumed in terms of arbitrary powers of the imperfection parameter, so that both exponents and coefficients of the expansion are unknown. The solution of the series exponents is obtained by searching the least degenerate solution. The formulation is here applied to asymmetric bifurcations, for which explicit expressions of the coefficients are obtained. The use of the method is illustrated by a simple example, which allows consideration of the main features of the formulation.

Investigations on the Dynamics of Combination Maps and the Analysis of Bifurcation in a Discontinuous Logistic Map

This thesis is a study of discrete nonlinear systems represented by one dimensional mappings.As one dimensional interative maps represent Poincarre sections of higher dimensional flows,they offer a convenient means to understand the dynamical evolution of many physical systems.It highlighting the basic ideas of deterministic chaos.Qualitative and quantitative measures for the detection and characterization of chaos in nonlinear systems are discussed.Some simple mathematical models exhibiting chaos are presented.The bifurcation scenario and the possible routes to chaos are explained.It present the results of the numerical computational of the Lyapunov exponents (λ) of one dimensional maps.This thesis focuses on the results obtained by our investigations on combinations maps,scaling behaviour of the Lyapunov characteristic exponents of one dimensional maps and the nature of bifurcations in a discontinous logistic map.It gives a review of the major routes to chaos in dissipative systems,namely, Period-doubling ,Intermittency and Crises.This study gives a theoretical understanding of the route to chaos in discontinous systems.A detailed analysis of the dynamics of a discontinous logistic map is carried out, both analytically and numerically ,to understand the route it follows to chaos.The present analysis deals only with the case of the discontinuity parameter applied to the right half of the interval of mapping.A detailed analysis for the n –furcations of various periodicities can be made and a more general theory for the map with discontinuities applied at different positions can be on a similar footing

Bifurcation and dynamic response analysis of a rotating blade excited by upstream vortices

Acknowledgements The authors acknowledge the projects supported by the National Basic Research Program of China (973 Project)(No. 2015CB057405) and the National Natural Science Foundation of China (No. 11372082) and the State Scholarship Fund of CSC. DW thanks for the hospitality of the University of Aberdeen.

Periodic-orbit analysis and scaling laws of intermingled basins of attraction in an ecological dynamical system

Chaotic dynamical systems with two or more attractors lying on invariant subspaces may, provided certain mathematical conditions are fulfilled, exhibit intermingled basins of attraction: Each basin is riddled with holes belonging to basins of the other attractors. In order to investigate the occurrence of such phenomenon in dynamical systems of ecological interest (two-species competition with extinction) we have characterized quantitatively the intermingled basins using periodic-orbit theory and scaling laws. The latter results agree with a theoretical prediction from a stochastic model, and also with an exact result for the scaling exponent we derived for the specific class of models investigated. We discuss the consequences of the scaling laws in terms of the predictability of a final state (extinction of either species) in an ecological experiment.

Bifurcation in growth patterns for arrays of parallel Griffith, edge and sliding cracks

This paper presents the recent finding by Muhlhaus et al [1] that bifurcation of crack growth patterns exists for arrays of two-dimensional cracks. This bifurcation is a result of the nonlinear effect due to crack interaction, which is, in the present analysis, approximated by the dipole asymptotic or pseudo-traction method. The nonlinear parameter for the problem is the crack length/ spacing ratio lambda = a/h. For parallel and edge crack arrays under far field tension, uniform crack growth patterns (all cracks having same size) yield to nonuniform crack growth patterns (i.e. bifurcation) if lambda is larger than a critical value lambda(cr) (note that such bifurcation is not found for collinear crack arrays). For parallel and edge crack arrays respectively, the value of lambda(cr) decreases monotonically from (2/9)(1/2) and (2/15.096)(1/2) for arrays of 2 cracks, to (2/3)(1/2)/pi and (2/5.032)(1/2)/pi for infinite arrays of cracks. The critical parameter lambda(cr) is calculated numerically for arrays of up to 100 cracks, whilst discrete Fourier transform is used to obtain the exact solution of lambda(cr) for infinite crack arrays. For geomaterials, bifurcation can also occurs when array of sliding cracks are under compression.

Finite element analysis of steady-state natural convection problems in fluid-saturated porous media heated from below

In this paper, a progressive asymptotic approach procedure is presented for solving the steady-state Horton-Rogers-Lapwood problem in a fluid-saturated porous medium. The Horton-Rogers-Lapwood problem possesses a bifurcation and, therefore, makes the direct use of conventional finite element methods difficult. Even if the Rayleigh number is high enough to drive the occurrence of natural convection in a fluid-saturated porous medium, the conventional methods will often produce a trivial non-convective solution. This difficulty can be overcome using the progressive asymptotic approach procedure associated with the finite element method. The method considers a series of modified Horton-Rogers-Lapwood problems in which gravity is assumed to tilt a small angle away from vertical. The main idea behind the progressive asymptotic approach procedure is that through solving a sequence of such modified problems with decreasing tilt, an accurate non-zero velocity solution to the Horton-Rogers-Lapwood problem can be obtained. This solution provides a very good initial prediction for the solution to the original Horton-Rogers-Lapwood problem so that the non-zero velocity solution can be successfully obtained when the tilted angle is set to zero. Comparison of numerical solutions with analytical ones to a benchmark problem of any rectangular geometry has demonstrated the usefulness of the present progressive asymptotic approach procedure. Finally, the procedure has been used to investigate the effect of basin shapes on natural convection of pore-fluid in a porous medium. (C) 1997 by John Wiley & Sons, Ltd.