Global analysis of dynamical decision-making models through local computation around the hidden saddle

Bistable dynamical switches are frequently encountered in mathematical modeling of biological systems because binary decisions are at the core of many cellular processes. Bistable switches present two stable steady-states, each of them corresponding to a distinct decision. In response to a transient signal, the system can flip back and forth between these two stable steady-states, switching between both decisions. Understanding which parameters and states affect this switch between stable states may shed light on the mechanisms underlying the decision-making process. Yet, answering such a question involves analyzing the global dynamical (i.e., transient) behavior of a nonlinear, possibly high dimensional model. In this paper, we show how a local analysis at a particular equilibrium point of bistable systems is highly relevant to understand the global properties of the switching system. The local analysis is performed at the saddle point, an often disregarded equilibrium point of bistable models but which is shown to be a key ruler of the decision-making process. Results are illustrated on three previously published models of biological switches: two models of apoptosis, the programmed cell death and one model of long-term potentiation, a phenomenon underlying synaptic plasticity. © 2012 Trotta et al.

Robotics and neuroscience: A rhythmic interaction

At the crossing between motor control neuroscience and robotics system theory, the paper presents a rhythmic experiment that is amenable both to handy laboratory implementation and simple mathematical modeling. The experiment is based on an impact juggling task, requiring the coordination of two upper-limb effectors and some phase-locking with the trajectories of one or several juggled objects. We describe the experiment, its implementation and the mathematical model used for the analysis. Our underlying research focuses on the role of sensory feedback in rhythmic tasks. In a robotic implementation of our experiment, we study the minimum feedback that is required to achieve robust control. A limited source of feedback, measuring only the impact times, is shown to give promising results. A second field of investigation concerns the human behavior in the same impact juggling task. We study how a variation of the tempo induces a transition between two distinct control strategies with different sensory feedback requirements. Analogies and differences between the robotic and human behaviors are obviously of high relevance in such a flexible setup. © 2008 Elsevier Ltd. All rights reserved.

A FEniCS-based programming framework for modeling turbulent flow by the Reynolds-averaged Navier-Stokes equations

Finding an appropriate turbulence model for a given flow case usually calls for extensive experimentation with both models and numerical solution methods. This work presents the design and implementation of a flexible, programmable software framework for assisting with numerical experiments in computational turbulence. The framework targets Reynolds-averaged Navier-Stokes models, discretized by finite element methods. The novel implementation makes use of Python and the FEniCS package, the combination of which leads to compact and reusable code, where model- and solver-specific code resemble closely the mathematical formulation of equations and algorithms. The presented ideas and programming techniques are also applicable to other fields that involve systems of nonlinear partial differential equations. We demonstrate the framework in two applications and investigate the impact of various linearizations on the convergence properties of nonlinear solvers for a Reynolds-averaged Navier-Stokes model. © 2011 Elsevier Ltd.

Improved jet noise modeling using a new time-scale.

To calculate the noise emanating from a turbulent flow using an acoustic analogy knowledge concerning the unsteady characteristics of the turbulence is required. Specifically, the form of the turbulent correlation tensor together with various time and length-scales are needed. However, if a Reynolds Averaged Navier-Stores calculation is used as the starting point then one can only obtain steady characteristics of the flow and it is necessary to model the unsteady behavior in some way. While there has been considerable attention given to the correct way to model the form of the correlation tensor less attention has been given to the underlying physics that dictate the proper choice of time-scale. In this paper the authors recognize that there are several time dependent processes occurring within a turbulent flow and propose a new way of obtaining the time-scale. Isothermal single-stream flow jets with Mach numbers 0.75 and 0.90 have been chosen for the present study. The Mani-Gliebe-Balsa-Khavaran method has been used for prediction of noise at different angles, and there is good agreement between the noise predictions and observations. Furthermore, the new time-scale has an inherent frequency dependency that arises naturally from the underlying physics, thus avoiding supplementary mathematical enhancements needed in previous modeling.

Modeling nonlinearities in MEMS oscillators

We present a mathematical model of a microelectromechanical system (MEMS) oscillator that integrates the nonlinearities of the MEMS resonator and the oscillator circuitry in a single numerical modeling environment. This is achieved by transforming the conventional nonlinear mechanical model into the electrical domain while simultaneously considering the prominent nonlinearities of the resonator. The proposed nonlinear electrical model is validated by comparing the simulated amplitude¿frequency response with measurements on an open-loop electrically addressed flexural silicon MEMS resonator driven to large motional amplitudes. Next, the essential nonlinearities in the oscillator circuit are investigated and a mathematical model of a MEMS oscillator is proposed that integrates the nonlinearities of the resonator. The concept is illustrated for MEMS transimpedance-amplifier-based square-wave and sine-wave oscillators. Closed-form expressions of steady-state output power and output frequency are derived for both oscillator models and compared with experimental and simulation results, with a good match in the predicted trends in all three cases. © 1986-2012 IEEE.