Deterministic continutation of stochastic metastable equilibria via Lyapunov equations and ellipsoids

Numerical continuation methods for deterministic dynamical systems have been one of the most successful tools in applied dynamical systems theory. Continuation techniques have been employed in all branches of the natural sciences as well as in engineering to analyze ordinary, partial and delay differential equations. Here we show that the deterministic continuation algorithm for equilibrium points can be extended to track information about metastable equilibrium points of stochastic differential equations (SDEs). We stress that we do not develop a new technical tool but that we combine results and methods from probability theory, dynamical systems, numerical analysis, optimization and control theory into an algorithm that augments classical equilibrium continuation methods. In particular, we use ellipsoids defining regions of high concentration of sample paths. It is shown that these ellipsoids and the distances between them can be efficiently calculated using iterative methods that take advantage of the numerical continuation framework. We apply our method to a bistable neural competition model and a classical predator-prey system. Furthermore, we show how global assumptions on the flow can be incorporated - if they are available - by relating numerical continuation, Kramers' formula and Rayleigh iteration.Comment: 29 pages, 7 figures [Fig.7 reduced in quality due to arXiv size restrictions]; v2 - added Section 9 on Kramers' formula, additional computations, corrected typos, improved explanation

Complex oscillations in the delayed Fitzhugh-Nagumo equation

Motivated by the dynamics of neuronal responses, we analyze the dynamics of the Fitzhugh-Nagumo slow-fast system with delayed self-coupling. This system provides a canonical example of a canard explosion for sufficiently small delays. Beyond this regime, delays significantly enrich the dynamics, leading to mixed-mode oscillations, bursting and chaos. These behaviors emerge from a delay-induced subcritical Bogdanov-Takens instability arising at the fold points of the S-shaped critical manifold. Underlying the transition from canard-induced to delay-induced dynamics is an abrupt switch in the nature of the Hopf bifurcation

Stochastic Representations of Ion Channel Kinetics and Exact Stochastic Simulation of Neuronal Dynamics

In this paper we provide two representations for stochastic ion channel kinetics, and compare the performance of exact simulation with a commonly used numerical approximation strategy. The first representation we present is a random time change representation, popularized by Thomas Kurtz, with the second being analogous to a "Gillespie" representation. Exact stochastic algorithms are provided for the different representations, which are preferable to either (a) fixed time step or (b) piecewise constant propensity algorithms, which still appear in the literature. As examples, we provide versions of the exact algorithms for the Morris-Lecar conductance based model, and detail the error induced, both in a weak and a strong sense, by the use of approximate algorithms on this model. We include ready-to-use implementations of the random time change algorithm in both XPP and Matlab. Finally, through the consideration of parametric sensitivity analysis, we show how the representations presented here are useful in the development of further computational methods. The general representations and simulation strategies provided here are known in other parts of the sciences, but less so in the present setting.Comment: 39 pages, 6 figures, appendix with XPP and Matlab cod

Duty Cycle Maintenance in an Artificial Neuron

Neuroprosthetics is at the intersection of neuroscience, biomedical engineering, and physics. A biocompatible neuroprosthesis contains artificial neurons exhibiting biophysically plausible dynamics. Hybrid systems analysis could be used to prototype such artificial neurons. Biohybrid systems are composed of artificial and living neurons coupled via real-time computing and dynamic clamp. Model neurons must be thoroughly tested before coupled with a living cell. We use bifurcation theory to identify hazardous regimes of activity that may compromise biocompatibility and to identify control strategies for regimes of activity desirable for functional behavior. We construct real-time artificial neurons for the analysis of hybrid systems and demonstrate a mechanism through which an artificial neuron could maintain duty cycle independent of variations in period

Tutorial of numerical continuation and bifurcation theory for systems and synthetic biology

Mathematical modelling allows us to concisely describe fundamental principles in biology. Analysis of models can help to both explain known phenomena, and predict the existence of new, unseen behaviours. Model analysis is often a complex task, such that we have little choice but to approach the problem with computational methods. Numerical continuation is a computational method for analysing the dynamics of nonlinear models by algorithmically detecting bifurcations. Here we aim to promote the use of numerical continuation tools by providing an introduction to nonlinear dynamics and numerical bifurcation analysis. Many numerical continuation packages are available, covering a wide range of system classes; a review of these packages is provided, to help both new and experienced practitioners in choosing the appropriate software tools for their needs.Comment: 14 pages, 2 figures, 2 table

A continuum model for the dynamics of the phase transition from slow-wave sleep to REM sleep

Previous studies have shown that activated cortical states (awake and rapid eye-movement (REM) sleep), are associated with increased cholinergic input into the cerebral cortex. However, the mechanisms that underlie the detailed dynamics of the cortical transition from slow-wave to REM sleep have not been quantitatively modeled. How does the sequence of abrupt changes in the cortical dynamics (as detected in the electrocorticogram) result from the more gradual change in subcortical cholinergic input? We compare the output from a continuum model of cortical neuronal dynamics with experimentally-derived rat electrocorticogram data. The output from the computer model was consistent with experimental observations. In slow-wave sleep, 0.5–2-Hz oscillations arise from the cortex jumping between “up” and “down” states on the stationary-state manifold. As cholinergic input increases, the upper state undergoes a bifurcation to an 8-Hz oscillation. The coexistence of both oscillations is similar to that found in the intermediate stage of sleep of the rat. Further cholinergic input moves the trajectory to a point where the lower part of the manifold in not available, and thus the slow oscillation abruptly ceases (REM sleep). The model provides a natural basis to explain neuromodulator-induced changes in cortical activity, and indicates that a cortical phase change, rather than a brainstem “flip-flop”, may describe the transition from slow-wave sleep to REM