Isometric graphing and multidimensional scaling for reaction-diffusion modeling on regular and fractal surfaces with spatiotemporal pattern recognition

Heterogeneous surface reactions exhibiting complex spatiotemporal dynamics and patterns can be studied as processes involving reaction-diffusion mechanisms. In many realistic situations, the surface has fractal characteristics. This situation is studied by isometric graphing and multidimensional scaling (IGMDS) of fractal surfaces for extracting geodesic distances (i.e., shortest scaled distances that obtain edges of neighboring surface nodes and their interconnections) and the results obtained used to model effects of surface diffusion with nonlinear reactions. Further analysis of evolved spatiotemporal patterns may be carried out by IGMDS because high-dimensional snapshot data can be efficiently projected to a transformed subspace with reduced dimensions. Validation of the IGMDS methodology is carried out by comparing results with reduction capabilities of conventional principal component analysis for simple situations of reaction and diffusion on surfaces. The usefulness of the IGMDS methodology is shown for analysis of complex patterns formed on both regular and fractal surfaces, and using generic nonlinear reaction-diffusion systems following FitzHugh Nagumo and cubic reaction kinetics. The studies of these systems with nonlinear kinetics and noise show that effects of surface disorder due to fractality can become very relevant. The relevance is shown by studying properties of dynamical invariants in IGMDS component space, viz., the Lyapunov exponents and the KS entropy for interesting situations of spiral formation and turbulent patterns.     

Relaxation dynamics of the Kuramoto model with uniformly distributed natural frequencies

The Kuramoto model describes a system of globally coupled phase-only oscillators with distributed natural frequencies. The model in the steady state exhibits a phase transition as a function of the coupling strength, between a low-coupling incoherent phase in which the oscillators oscillate independently and a high-coupling synchronized phase. Here, we consider a uniform distribution for the natural frequencies, for which the phase transition is known to be of first order. We study how the system close to the phase transition in the supercritical regime relaxes in time to the steady state while starting from an initial incoherent state. In this case, numerical simulations of finite systems have demonstrated that the relaxation occurs as a step-like jump in the order parameter from the initial to the final steady state value, hinting at the existence of metastable states. We provide numerical evidence to suggest that the observed metastability is a finite-size effect, becoming an increasingly rare event with increasing system size.     

First-passage time statistics of stochastic transcription process for time-dependent reaction rates

The European Physical Journal E - To theoretically understand force generation properties of actin filaments, many models consider growing filaments pushing against a movable obstacle or barrier....