Bifurcation analysis of bistable and oscillatory dynamics in biological networks using the root‐locus method

Most of the biological systems including gene regulatory networks can be described well by ordinary differential equation models with rational non‐linearities. These models are derived either based on the reaction kinetics or by curve fitting to experimental data. This study demonstrates the applicability of the root‐locus‐based bifurcation analysis method for studying the complex dynamics of such models. The effectiveness of the bifurcation analysis in determining the exact parameter regions in each of which the system shows a certain dynamical behaviour, such as bistability, oscillation, and asymptotically equilibrium dynamics is shown by considering two mostly studied gene regulatory networks, namely Gardner''s genetic toggle switch and p53 gene network possessing two‐phase (mono‐stable/oscillation) dynamics.Inspec keywords: oscillations, curve fitting, differential equations, bifurcation, genetics, nonlinear dynamical systemsOther keywords: nonlinearities, reaction kinetics, root‐locus‐based bifurcation analysis method, complex dynamics, exact parameter regions, dynamical behaviour, equilibrium dynamics, studied gene regulatory networks, p53 gene network, bistable dynamics, oscillatory dynamics, biological networks, root‐locus method, biological systems, ordinary differential equation models     

Influence of aerodynamics on the critical parameters of thermal ignition

A numerical analysis of the critical conditions of thermal ignition for a two-dimensional cylindrical reactor with flow field occurrence was carried out. The critical conditions of thermal ignition were defined as bifurcation points of the limit type. The dependence of the bifurcation points on aerodynamics was analysed by a sequential variation of the Peclet number. The flow field in the reactor was generated previously by a numerical solution of the Navier-Stokes equations. The nonlinear parabolic equation of heat balance and linear eigenvalue boundary problems occurring in the proposed non-stationary method for calculating the bifurcation points was solved numerically using the finite difference technique. It was shown that the critical points of thermal ignition form a surface bounded by the line of ‘limit of criticality’ in the parameter space. For large values of the Peclet number, the dependence of the critical parameter of ignition on Peclet number becomes linear.     

具有时滞和阶段结构的生态-流行病模型的稳定性及Hopf分支

本文研究一类具有时滞和阶段结构的生态-流行病模型的稳定性及其Hopf分支．给出了边界平衡点和正平衡点存在的充分条件;通过分析特征方程,运用Hurwitz判定定理,讨论了边界平衡点和正平衡点的局部稳定性,并得到了正平衡点附近存在Hopf分支的充分条件;通过构造适当的Lyapunov泛函,运用LaSall不变集原理,讨论了边界平衡点和正平衡点的全局稳定性,从而得到了该生态模型永久持续生存与灭绝的充分条件．     

Dynamical properties and synchronization of complex non-linear equations for detuned lasers

We study the dynamics and synchronization properties of a system of complex non-linear equations describing detuned lasers. These equations possess a whole circle of fixed points, while the corresponding real variable equations have only isolated fixed points. We examine the stability of their equilibrium points and determine conditions under which the complex equations have positive, negative or zero Lyapunov exponents and chaotic, quasiperiodic or periodic attractors for a wide range of parameter values. We investigate the synchronization of chaotic solutions of our detuned laser system, using as a drive a similar set of equations and applying the method of global synchronization. We find attractors whose three-dimensional projection is not at all similar to the well-known shape of the (real) Lorenz attractor. Finally, we apply complex periodic driving to the electric field equation and show that the model can exhibit a transition from chaotic to quasiperiodic oscillations. This leads us to the discovery of an exact periodic solution, whose amplitude and frequency depend on the parameters of the system. Since this solution is stable for a wide range of parameter values, it may be used to control the system by entraining it with the applied periodic forcing.     

一类离心调速器的Hopf分岔及其混沌控制

研究了受外部扰动的离心调速器系统的复杂动力学行为。通过系统运动的拉格朗日方程和牛顿第二定律,建立了离心调速器系统的动力学方程,应用Lyapunov直接方法分析了该系统平衡点的稳定性。利用相图分析了系统超混沌吸引子的特性,通过Poincaré截面和Lyapunov指数研究了系统的超混沌行为,通过仿真系统的分岔图和相图分析了系统通向混沌的道路,并且验证了该系统的分岔图与Lyapunov指数谱是完全吻合的。通过对系统施加非线性反馈控制器,并选取合适的反馈系数,可以获得各种不同的所需的稳定周期轨道。对受外部扰动的离心调速器系统施于此控制,计算机数值模拟结果表明,这种控制方法简便有效,控制范围广。     

Bifurcation and stability of a three‐hinged rod under a conservative load

The bifurcation solutions and their stability of a three‐hinged rod under conservative compressive force are investigated. The equations for the system are non‐linear, and possess some symmetry properties. The symmerty group concepts are employed to exploit these symmetry properties. The symbolic computer software, Mathematica, is used for the analytical and numerical solutions. The loci of codimension‐one singularity are plotted on a two‐dimensional control parameter space. These curves partition the parameter space into regions of qualitatively similar bifurcation diagrams. The bifurcation solutions and their stability at typical points in the parameter diagram, and the perturbation of codimension‐one singularities are discussed. Copyright © 1999 John Wiley & Sons, Ltd.     

Nonlinear dynamics of tubes carrying a pulsatile flow

The nonlinear dynamics of a cantilever tube conveying a pulsatile flow and undergoing planar motions is investigated. The mean flow is near its critical value at which the downward vertical position of the tube gets unstable by flutter and executes limit-cycle oscillations. The pulsations in the flow are assumed to be small and harmonic with frequency nearly twice that of the limit cycle. To study the nonlinear dynamics, the method of averaging is utilized and the governing partial differential equation is reduced to a dynamic system on the plane. These two first-order differential equations depend on three parameters and govern the dynamics of the amplitude of motion of the tube. The planar system is studied for its qualitative behaviour using ideas from the local bifurcation theory and a local bifurcation set in the parameter plane is constructed. Using ideas from codimension-two unfolding of singularities, this bifurcation set is further refined. The resulting partial bifurcation set and the associated phase portraits in the various regions of the flowrate-detuning parameter plane show that the averaged equations have constant as well as periodic solutions. The stabifity type and the number of these solutions changes from one region to another. This explains how periodic or 'phase-locked' oscillations of the cantilever tube bifurcate into amplitude-modulated or almost-periodic motions.     

Prediction of vapour-liquid and vapour-liquid-liquid equilibria of nitrogen-hydrocarbon mixtures used in J-T refrigerators

Nitrogen-hydrocarbon mixtures are widely used as refrigerants in J-T refrigerators operating with mixtures, as well as in natural gas liquefiers. The Peng-Robinson equation of state has traditionally been used to simulate the above cryogenic process. Multi parameter Helmholtz energy equations are now preferred for determining the properties of natural gas. They have, however, been used only to predict vapour-liquid equilibria, and not vapour-liquid-liquid equilibria that can occur in mixtures used in cryogenic mixed refrigerant processes. In this paper the vapour-liquid equilibrium of binary mixtures of nitrogen-methane, nitrogen-ethane, nitrogen-propane, nitrogen-isobutane and three component mixtures of nitrogen-methane-ethane and nitrogen-methane-propane have been studied with the Peng-Robinson and the Helmholtz energy equations of state of NIST REFPROP and compared with experimental data available in the literature.     

变惯量曲轴系统扭转振动的参数分岔分析

变惯量参数在一定程度上会影响曲轴系统扭转振动的分岔特性,然而现有研究缺乏对此参数的分岔理论分析。本文针对上述问题展开研究,分析了当曲轴系统的转动频率、不平衡激励频率与固有频率近似满足 的情况下,变惯量参数和调谐参数对系统分岔行为的影响。首先应用多尺度法得到系统共振情况下的平均方程和分岔方程;其次应用奇异性理论得到系统的稳态振幅随参数变化的分岔图,分析并求解系统发生分岔的临界点,得到系统的稳定/分岔区间;最终选取工程实际物理参数,将理论结果与数值仿真进行对比,验证了理论分析的正确性。进行变惯量曲轴系统的参数分岔分析,有助于曲轴系统的优化设计。     

不可压缩流中二元翼运动的余维二分叉

考虑二元机翼在不可压缩流作用下运动的余维二分叉问题,弹簧的非线性刚度考虑为立方型。化方程为四维一阶微分方程,解析求出了系统发生叉式分叉与HOPF分叉的临界流速的表达式和发生余维二分叉的临界流速和一次刚度。在两个参数平面上研究了系统在余维二分叉点附近的不同区域内平衡点和极限环的稳定性及其个数。最后用数值积分方法给出相应的结果。     

Symmetry and bifurcations of planar configurations of the N-body and other problems

We describe a system of equations containing a real parameter β and an integer parameter N ≥2. Equilibria of these equations are in turn asymptotic shapes of systems of repelling particles for β= 0, central configurations with equal mass of the N-body problem for β= 1, and approximate solutions of a sphere-packing problem for β large. We introduce some asymmetric equilibria of these equations for N = 6 and 7, and identify and discuss the bifurcations that occur in this system for 5 ≤ N ≤ 8.     

非定常通气超空泡分叉突变特性研究

针对非定常通气超空泡的不稳定性,采用分叉与突变理论分析通气超空泡失稳现象发生的机理。基于Logvinovich空泡截面膨胀独立性原理及通气质量平衡方程,得出联系非定常通气超空泡长度及空化数的积分方程。根据积分思想,将积分方程分解为两个第一类Volterra积分求解,得出线性小扰动系统,对静态分叉引发的状态突变进行定性分析,并通过数值仿真进行了验证。理论分析及数值仿真结果表明,非定常通气超空泡在平衡点处呈现的跨临界分叉将导致非定常通气超空泡在分叉点处产生突变。此现象揭示了稳定通气超空泡在临界值处改变通气参数所导致的空泡失稳的机理,有助于超空泡航行体稳定航行控制系统的设计。     

Population dynamics of the modified theta model: macroscopic phase reduction and bifurcation analysis link microscopic neuronal interactions to macroscopic gamma oscillation

Gamma oscillations of the local field potential are organized by collective dynamics of numerous neurons and have many functional roles in cognition and/or attention. To mathematically and physiologically analyse relationships between individual inhibitory neurons and macroscopic oscillations, we derive a modification of the theta model, which possesses voltage-dependent dynamics with appropriate synaptic interactions. Bifurcation analysis of the corresponding Fokker–Planck equation (FPE) enables us to consider how synaptic interactions organize collective oscillations. We also develop the adjoint method (infinitesimal phase resetting curve) for simultaneous equations consisting of ordinary differential equations representing synaptic dynamics and a partial differential equation for determining the probability distribution of the membrane potential. This method provides a macroscopic phase response function (PRF), which gives insights into how it is modulated by external perturbation or internal changes of parameters. We investigate the effects of synaptic time constants and shunting inhibition on these gamma oscillations. The sensitivity of rising and decaying time constants is analysed in the oscillatory parameter regions; we find that these sensitivities are not largely dependent on rate of synaptic coupling but, rather, on current and noise intensity. Analyses of shunting inhibition reveal that it can affect both promotion and elimination of gamma oscillations. When the macroscopic oscillation is far from the bifurcation, shunting promotes the gamma oscillations and the PRF becomes flatter as the reversal potential of the synapse increases, indicating the insensitivity of gamma oscillations to perturbations. By contrast, when the macroscopic oscillation is near the bifurcation, shunting eliminates gamma oscillations and a stable firing state appears. More interestingly, under appropriate balance of parameters, two branches of bifurcation are found in our analysis of the FPE. In this case, shunting inhibition can effect both promotion and elimination of the gamma oscillation depending only on the reversal potential.     

内平动齿轮副啮合综合刚度与系统的分岔特性

用机构反转法将内平动齿轮副转化为定轴齿轮副,然后用有限元方法分析了该内啮合定轴齿轮副的啮合综合刚度,并使用FFT变换得到其频谱特性,进而得到了内平动齿轮副的啮合综合刚度的频谱特性,在此基础上,考虑了齿侧间隙的非线性因素,进一步得到存在多齿接触的时变啮合刚度下内平动齿轮副的运动微分方程。然后,用经典的显式四阶Rouge-Kutta法对系统的各个参数进行了数值计算,得到系统的参数分岔图,并分析了各参数对系统动力学行为的影响。为内平动齿轮副的设计参数选择提供理论依据。     

A codimension-two resonant bifurcation from a heteroclinic cycle with complex eigenvalues

Robust heteroclinic cycles between equilibria lose stability either through local bifurcations of their equilibria or through global bifurcations. This paper considers a global loss of stability termed a 'resonant' bifurcation. This bifurcation is usually associated with the birth or death of a nearby periodic orbit, and generically occurs in either a supercritical or subcritical manner. For a specific robust heteroclinic cycle between equilibria with complex eigenvalues we examine the codimension-two point that separates the supercritical and subcritical. We investigate the bifurcation structure and show the existence of further bifurcations of periodic orbits.     

Snakes and isolas in non-reversible conservative systems

Reversible variational partial differential equations such as the Swift–Hohenberg equation can admit localized stationary roll structures whose solution branches are bounded in parameter space but unbounded in function space, with the width of the roll plateaus increasing without bound along the branch: this scenario is commonly referred to as snaking. In this work, the structure of the bifurcation diagrams of localized rolls is investigated for variational but non-reversible systems, and conditions are derived that guarantee snaking or result in diagrams that either consist entirely of isolas.