arXiv subjects

Omer Karin

Publications and source records attributed to Omer Karin.

4 recordsLinked to original sources

arXiv2026

Compositional proofreading through critical self-tuning

High-dimensional multicomponent systems, including immune and epigenetic repertoires, must selectively retain rare, beneficial components while purging a massive influx of suboptimal variants. We demonstrate that critical tuning of component control parameters through competition naturally implements proofreading in these systems. Competition for shared inputs pins the system to the marginal stability threshold of the most persistent species. This grants dominant species extended lifetimes, concentrating the population into dominant components while forcing less-stable variants into rapid drift-driven turnover. When aggregate drive exceeds a characteristic scale, this pinning fails, producing a non-selective state where component lifetimes scale as a universal power law with aggregate drive. Applying this framework to biological memory, we identify the hallmarks of this effect in plasma cell accumulation dynamics and propose that de-pinning transitions may represent failure points across biological domains, including cancer, immunodeficiencies, and the aberrant activation of harmful genomic elements during ageing.

q-bio.OT↗

arXiv2025

Self-organized hyperuniformity in a minimal model of population dynamics

By generalizing a class of models recently introduced to account for protracted transients in biological systems, we identify a novel mechanism for hyperuniformity. In this model, competition of individuals over a shared resource serves as feedback that can asymptotically guide the population towards a critical steady state with divergent individual life time. We show that, in its spatially extended form, this many-body model exhibits hyperuniform density fluctuations. Through explicit coarse-graining, we develop a hydrodynamic theory that conforms closely with the results of stochastic simulations. Unlike previous models for non-equilibrium hyperuniform states, our model does not exhibit conservation laws, even in the asymptotic regime. Instead, hyperuniformity arises from the divergence of the range of the resource-mediated interactions. These findings may find applications in engineering, cellular population dynamics, and ecology.

cond-mat.stat-mech↗

arXiv2024

Hierarchical cell identities emerge from animal gene regulatory mechanisms

The hierarchical organisation of cell identity is a fundamental feature of animal development with rich and well-characterized experimental phenomenology, yet the mechanisms driving its emergence remain unknown. The regulation of cell identity genes relies on a distinct mechanism involving higher-order interactions of transcription factors on distant regulatory regions called enhancers. These interactions are mediated by epigenetic regulators that are broadly shared between enhancers. Through the development of a new and predictive mathematical theory on the effects of epigenetic regulator activity on gene network dynamics, we demonstrate that hierarchical identities are essential emergent properties of animal-specific gene regulatory mechanisms. Hierarchical identities arise from the interplay between enhancer competition for epigenetic readers and cooperation through activation of shared transcriptional programs. We show that epigenetic regulatory mechanisms provide the network with self-similar properties that enable multilineage priming and signal-dependent control of progenitor states. The stabilisation of progenitor states is predicted to be controlled by the balance in activities between epigenetic writers and erasers. Our model quantitatively predicts lineage relationships, reconstructs all known blood progenitor states from terminal states, and explains mechanisms of cell identity dysregulation in cancer and the general differentiation effects of histone deacetylase inhibition. We identify non-specific modulation of enhancer competition as a central regulatory axis, with implications for developmental biology, cancer, and differentiation therapy.

q-bio.CB↗

arXiv2023

Perspectives on adaptive dynamical systems

Adaptivity is a dynamical feature that is omnipresent in nature, socio-economics, and technology. For example, adaptive couplings appear in various real-world systems like the power grid, social, and neural networks, and they form the backbone of closed-loop control strategies and machine learning algorithms. In this article, we provide an interdisciplinary perspective on adaptive systems. We reflect on the notion and terminology of adaptivity in different disciplines and discuss which role adaptivity plays for various fields. We highlight common open challenges, and give perspectives on future research directions, looking to inspire interdisciplinary approaches.

nlin.AO↗