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1. Identifying Arguments of Space-Time Fractional Diffusion: Data-Driven Approach

   https://doi.org/https://doi.org/10.3389/fams.2020.00014  

   Znaidi Mohamed Ridha, Gupta Gaurav (May 2020, Frontiers in applied mathematics and statistics)

   null (Ed.)

   A plethora of complex dynamical systems from disordered media to biological systems exhibit mathematical characteristics (e.g., long-range dependence, self-similar and power law magnitude increments) that are well-fitted by fractional partial differential equations (PDEs). For instance, some biological systems displaying an anomalous diffusion behavior, which is characterized by a non-linear mean-square displacement relation, can be mathematically described by fractional PDEs. In general, the PDEs represent various physical laws or rules governing complex dynamical systems. Since prior knowledge about the mathematical equations describing complex dynamical systems in biology, healthcare, disaster mitigation, transportation, or environmental sciences may not be available, we aim to provide algorithmic strategies to discover the integer or fractional PDEs and their parameters from system's evolution data. Toward deciphering non-trivial mechanisms driving a complex system, we propose a data-driven approach that estimates the parameters of a fractional PDE model. We study the space-time fractional diffusion model that describes a complex stochastic process, where the magnitude and the time increments are stable processes. Starting from limited time-series data recorded while the system is evolving, we develop a fractional-order moments-based approach to determine the parameters of a generalized fractional PDE. We formulate two optimization problems to allow us to estimate the arguments of the fractional PDE. Employing extensive simulation studies, we show that the proposed approach is effective at retrieving the relevant parameters of the space-time fractional PDE. The presented mathematical approach can be further enhanced and generalized to include additional operators that may help to identify the dominant rule governing the measurements or to determine the degree to which multiple physical laws contribute to the observed dynamics. 

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2. Dynamic intermittent Q ‐learning–based model‐free suboptimal co‐design of ‐stabilization

   https://doi.org/10.1002/rnc.4515  

   Yang, Yongliang; Vamvoudakis, Kyriakos G.; Ferraz, Henrique; Modares, Hamidreza (March 2019, International Journal of Robust and Nonlinear Control)

   Summary This paper proposes an intermittent model‐free learning algorithm for linear time‐invariant systems, where the control policy and transmission decisions are co‐designed simultaneously while also being subjected to worst‐case disturbances. The control policy is designed by introducing an internal dynamical system to further reduce the transmission rate and provide bandwidth flexibility in cyber‐physical systems. Moreover, aQ‐learning algorithm with two actors and a single critic structure is developed to learn the optimal parameters of aQ‐function. It is shown by using an impulsive system approach that the closed‐loop system has an asymptotically stable equilibrium and that no Zeno behavior occurs. Furthermore, a qualitative performance analysis of the model‐free dynamic intermittent framework is given and shows the degree of suboptimality concerning the optimal continuous updated controller. Finally, a numerical simulation of an unknown system is carried out to highlight the efficacy of the proposed framework. 

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3. Review of chaos in hair-cell dynamics

   https://doi.org/10.3389/fneur.2024.1444617  

   Faber, Justin; Bozovic, Dolores (July 2024, Frontiers in Neurology)

   The remarkable signal-detection capabilities of the auditory and vestibular systems have been studied for decades. Much of the conceptual framework that arose from this research has suggested that these sensory systems rest on the verge of instability, near a Hopf bifurcation, in order to explain the detection specifications. However, this paradigm contains several unresolved issues. Critical systems are not robust to stochastic fluctuations or imprecise tuning of the system parameters. Further, a system poised at criticality exhibits a phenomenon known in dynamical systems theory ascritical slowing down, where the response time diverges as the system approaches the critical point. An alternative description of these sensory systems is based on the notion of chaotic dynamics, where the instabilities inherent to the dynamics produce high temporal acuity and sensitivity to weak signals, even in the presence of noise. This alternative description resolves the issues that arise in the criticality picture. We review the conceptual framework and experimental evidence that supports the use of chaos for signal detection by these systems, and propose future validation experiments. 

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4. A dynamical systems treatment of transcriptomic trajectories in hematopoiesis

   https://doi.org/10.1242/dev.201280  

   Freedman, Simon L.; Xu, Bingxian; Goyal, Sidhartha; Mani, Madhav (June 2023, Development)

   ABSTRACT Inspired by Waddington's illustration of an epigenetic landscape, cell-fate transitions have been envisioned as bifurcating dynamical systems, wherein exogenous signaling dynamics couple to the enormously complex signaling and transcriptional machinery of a cell to elicit qualitative transitions in its collective state. Single-cell RNA sequencing (scRNA-seq), which measures the distributions of possible transcriptional states in large populations of differentiating cells, provides an alternate view, in which development is marked by the variations of a myriad of genes. Here, we present a mathematical formalism for rigorously evaluating, from a dynamical systems perspective, whether scRNA-seq trajectories display statistical signatures consistent with bifurcations and, as a case study, pinpoint regions of multistability along the neutrophil branch of hematopoeitic differentiation. Additionally, we leverage the geometric features of linear instability to identify the low-dimensional phase plane in gene expression space within which the multistability unfolds, highlighting novel genetic players that are crucial for neutrophil differentiation. Broadly, we show that a dynamical systems treatment of scRNA-seq data provides mechanistic insights into the high-dimensional processes of cellular differentiation, taking a step toward systematic construction of mathematical models for transcriptomic dynamics. 

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5. Dynamical Ising model of spatially coupled ecological oscillators

   https://doi.org/10.1098/rsif.2020.0571  

   Nareddy, Vahini Reddy; Machta, Jonathan; Abbott, Karen C.; Esmaeili, Shadisadat; Hastings, Alan (October 2020, Journal of The Royal Society Interface)

   null (Ed.)

   Long-range synchrony from short-range interactions is a familiar pattern in biological and physical systems, many of which share a common set of ‘universal’ properties at the point of synchronization. Common biological systems of coupled oscillators have been shown to be members of the Ising universality class, meaning that the very simple Ising model replicates certain spatial statistics of these systems at stationarity. This observation is useful because it reveals which aspects of spatial pattern arise independently of the details governing local dynamics, resulting in both deeper understanding of and a simpler baseline model for biological synchrony. However, in many situations a system’s dynamics are of greater interest than their static spatial properties. Here, we ask whether a dynamical Ising model can replicate universal and non-universal features of ecological systems, using noisy coupled metapopulation models with two-cycle dynamics as a case study. The standard Ising model makes unrealistic dynamical predictions, but the Ising model with memory corrects this by using an additional parameter to reflect the tendency for local dynamics to maintain their phase of oscillation. By fitting the two parameters of the Ising model with memory to simulated ecological dynamics, we assess the correspondence between the Ising and ecological models in several of their features (location of the critical boundary in parameter space between synchronous and asynchronous dynamics, probability of local phase changes and ability to predict future dynamics). We find that the Ising model with memory is reasonably good at representing these properties of ecological metapopulations. The correspondence between these models creates the potential for the simple and well-known Ising class of models to become a valuable tool for understanding complex biological systems. 

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