Network analysis of complex biological systems : boundedness of weakly reversible chemical reaction networks and conditions for synchronisation of coupled oscillators

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Stability of a chain of phase oscillators

We study a chain of N + 1 phase oscillators with asymmetric but uniform coupling. This type of chain possesses 2 N ways to synchronize in so-called traveling wave states, i.e., states where the phases of the single oscillators are in relative equilibrium. We show that the number of unstable dimensions of a traveling wave equals the number of oscillators with relative phase close to π . This implies that only the relative equilibrium corresponding to approximate in-phase synchronization is locally stable. Despite the presence of a Lyapunov-type functional, periodic or chaotic phase slipping occurs. For chains of lengths 3 and 4 we locate the region in parameter space where rotations (corresponding to phase slipping) are present

Self-organized escape of oscillator chains in nonlinear potentials

We present the noise free escape of a chain of linearly interacting units from a metastable state over a cubic on-site potential barrier. The underlying dynamics is conservative and purely deterministic. The mutual interplay between nonlinearity and harmonic interactions causes an initially uniform lattice state to become unstable, leading to an energy redistribution with strong localization. As a result a spontaneously emerging localized mode grows into a critical nucleus. By surpassing this transition state, the nonlinear chain manages a self-organized, deterministic barrier crossing. Most strikingly, these noise-free, collective nonlinear escape events proceed generally by far faster than transitions assisted by thermal noise when the ratio between the average energy supplied per unit in the chain and the potential barrier energy assumes small values

Statistical Mechanics of Recurrent Neural Networks I. Statics

A lecture notes style review of the equilibrium statistical mechanics of recurrent neural networks with discrete and continuous neurons (e.g. Ising, coupled-oscillators). To be published in the Handbook of Biological Physics (North-Holland). Accompanied by a similar review (part II) dealing with the dynamics.Comment: 49 pages, LaTe

Symmetry-broken dissipative exchange flows in thin-film ferromagnets with in-plane anisotropy

Planar ferromagnetic channels have been shown to theoretically support a long-range ordered and coherently precessing state where the balance between local spin injection at one edge and damping along the channel establishes a dissipative exchange flow, sometimes referred to as a spin superfluid. However, realistic materials exhibit in-plane anisotropy, which breaks the axial symmetry assumed in current theoretical models. Here, we study dissipative exchange flows in a ferromagnet with in-plane anisotropy from a dispersive hydrodynamic perspective. Through the analysis of a boundary value problem for a damped sine-Gordon equation, dissipative exchange flows in a ferromagnetic channel can be excited above a spin current threshold that depends on material parameters and the length of the channel. Symmetry-broken dissipative exchange flows display harmonic overtones that redshift the fundamental precessional frequency and lead to a reduced spin pumping efficiency when compared to their symmetric counterpart. Micromagnetic simulations are used to verify that the analytical results are qualitatively accurate, even in the presence of nonlocal dipole fields. Simulations also confirm that dissipative exchange flows can be driven by spin transfer torque in a finite-sized region. These results delineate the important material parameters that must be optimized for the excitation of dissipative exchange flows in realistic systems.Comment: 20 pages, 5 figure

Hamiltonian formalism of fractional systems

In this paper we consider a generalized classical mechanics with fractional derivatives. The generalization is based on the time-clock randomization of momenta and coordinates taken from the conventional phase space. The fractional equations of motion are derived using the Hamiltonian formalism. The approach is illustrated with a simple-fractional oscillator in a free state and under an external force. Besides the behavior of the coupled fractional oscillators is analyzed. The natural extension of this approach to continuous systems is stated. The interpretation of the mechanics is discussed.Comment: 16 pages, 5 figure