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Antonio Matas-Gil

Publications and source records attributed to Antonio Matas-Gil.

4 recordsLinked to original sources

How nature discovers rare Turing islands: exploration by common limit cycles

Turing patterns are a cornerstone of biological self-organization, yet their emergence typically requires finely tuned parameters occupying narrow regions of high-dimensional space. This poses a fundamental challenge: how can evolving biological systems reliably find and exploit such rare conditions? In this work, we propose that common biochemical limit cycles, such as those arising from genetic feedback loops, can act as natural explorers of Turing space. By coupling a reaction-diffusion system to an orbit that modulates some of its parameters, we show that the system can dynamically sweep through Turing-permissive regimes and generate transient spatial patterns. We use an entropy-based measure in Fourier space to quantify pattern formation and demonstrate how cycles enhance the detectability and robustness of Turing islands. We further explore how coupling to positional gradients increases reproducibility, suggesting a route from oscillatory dynamics to stable developmental programs. Our results highlight a powerful mechanism by which nature might bootstrap complex spatial structure from simple temporal motifs.

q-bio.CB

From Toggle to Tuning: Controlling Turing Patterns in Gene Circuits

Controlling spatial patterns in synthetic biological systems remains challenging due to poor parameter robustness and limited experimental tunability. We introduce two complementary mechanisms-the pattern switch and the pattern dial-to systematically control Turing pattern formation in gene circuits. The switch toggles pattern onset via a single parameter, while the dial enables transitions between distinct pattern types using weakly nonlinear amplitude equations. Analyzing network size reveals a key trade-off: small networks are easier to control but less robust, while larger networks gain robustness at the cost of tunability-suggesting a sweet spot for both evolvability and designability. Our results offer practical design rules for engineering programmable patterns in living systems.

physics.bio-ph

Optimal network sizes for most robust Turing patterns

Many cellular patterns exhibit a reaction-diffusion component, suggesting that Turing instability may contribute to pattern formation. However, biological gene-regulatory pathways are more complex than simple Turing activator-inhibitor models and generally do not require fine-tuning of parameters as dictated by the Turing conditions. To address these issues, we employ random matrix theory to analyze the Jacobian matrices of larger networks with robust statistical properties. Our analysis reveals that Turing patterns are more likely to occur by chance than previously thought and that the most robust Turing networks have an optimal size, surprisingly consisting only of a handful of molecular species, thus significantly increasing their identifiability in biological systems. This optimal size emerges from a tradeoff between the highest stability in small networks and the greatest instability with diffusion in large networks. Furthermore, we find that with multiple immobile nodes, differential diffusion ceases to be important for Turing patterns. Our findings may inform future synthetic biology approaches and provide insights into bridging the gap to complex developmental pathways.

q-bio.MN

Unraveling biochemical spatial patterns: machine learning approaches to the inverse problem of Turing patterns

The diffusion-driven Turing instability is a potential mechanism for spatial pattern formation in numerous biological and chemical systems. However, engineering these patterns and demonstrating that they are produced by this mechanism is challenging. To address this, we aim to solve the inverse problem in artificial and experimental Turing patterns. This task is challenging since high levels of noise corrupt the patterns and slight changes in initial conditions can lead to different patterns. We used both least squares to explore the problem and physics-informed neural networks to build a noise-robust method. We elucidate the functionality of our network in scenarios mimicking biological noise levels and showcase its application through a prototype involving an experimentally obtained chemical pattern. The findings reveal the significant promise of machine learning in steering the creation of synthetic patterns in bioengineering, thereby advancing our grasp of morphological intricacies within biological systems while acknowledging existing limitations.

physics.bio-ph