Tootfinder

Design, Modelling and Analysis of a Bio-inspired Spiking Temperature Regulator
J. M. Rosito, E. Petri, E. Steur, W. P. M. H. Heemels
https://arxiv.org/abs/2509.01300 https://

Design, Modelling and Analysis of a Bio-inspired Spiking Temperature Regulator
In biology, homeostasis is the process of maintaining a stable internal environment, which is crucial for optimal functioning of organisms. One of the key homeostatic mechanisms is thermoregulation that allows the organism to maintain its core temperature within tight bounds despite being exposed to a wide range of varying external temperatures. Instrumental in thermoregulation is the presence of thermosensitive neurons at multiple places throughout the body, including muscles, the spinal cord,…

Correlated cell movements drive epithelial finger formation
Sander C. Kammeraat, Yann-Edwin Keta, Paul Appleton, Ian P. Newton, Tanniemola B. Liverpool, Rastko Sknepnek, Inke N\"athke, Silke Henkes
https://arxiv.org/abs/2508.01046

Correlated cell movements drive epithelial finger formation
Epithelia form protective barriers in multicellular organisms. To maintain homeostasis, they must be able to regenerate and heal damaged areas. This occurs through collective cell migration, during which finger-like protrusions commonly appear. Whether these protrusions are driven by specialised leader cells, biochemical cues, or generic physical interactions remains unclear. Integrating in vitro imaging, agent-based simulations, and continuum modelling, we show that correlated active cell moti…

Rapid Single-Cell Measurement of Transient Transmembrane Water Flow under Osmotic Gradient
Hong Jiang, Jinnawat Jongkhumkrong, Y. J. Chao, Qian Wang, Guiren Wang
https://arxiv.org/abs/2508.00104

Rapid Single-Cell Measurement of Transient Transmembrane Water Flow under Osmotic Gradient
While aquaporin (AQP) gating dynamically regulates transmembrane water permeability for cellular homeostasis, its mechanisms remain poorly understood compared to ion channels. A central challenge is the lack of methods to measure water flow through AQPs with the spatiotemporal resolution and sensitivity equivalent to patch-clamp recordings of ion fluxes, a limitation stemming from the electrically silent nature of water transport. We introduce a technique to rapidly detect cytoplasmic flows ind…

Self-regulated emergence of heavy-tailed weight distributions in evolving complex network architectures
Jia Li, Cees van Leeuwen, Roman Bauer, Ilias Rentzeperis
https://arxiv.org/abs/2508.21445

Self-regulated emergence of heavy-tailed weight distributions in evolving complex network architectures
Brain networks continually adjust the weights of their connections, resulting in heavy-tailed distributions of their connection weights, a few strong connections among many weaker ones. At the same time, these connections undergo structural plasticity, forming a complex network topology. Although mechanisms producing either heavy-tailed distributions or complex topologies have been proposed, it has remained unclear whether a single mechanism can produce both. We consider homeostasis as the driv…

Could Living Cells Use Phase Transitions to Process Information?
Arvind Murugan, David Zwicker, Charlotta Lorenz, Eric R. Dufresne
https://arxiv.org/abs/2507.23384 https://

Could Living Cells Use Phase Transitions to Process Information?
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how networks of physical interactions could contribute to the processing of information inside cells. In particular, we focus on the impact of biomolecular condensation, a structural phase transition found in cells. Biomolecular condensation has recently been im…

Beyond Imaging: Vision Transformer Digital Twin Surrogates for 3D T Biological Tissue Dynamics
Kaan Berke Ugurlar, Joaqu\'in de Navascu\'es, Michael Taynnan Barros
https://arxiv.org/abs/2508.15883

Beyond Imaging: Vision Transformer Digital Twin Surrogates for 3D+T Biological Tissue Dynamics
Understanding the dynamic organization and homeostasis of living tissues requires high-resolution, time-resolved imaging coupled with methods capable of extracting interpretable, predictive insights from complex datasets. Here, we present the Vision Transformer Digital Twin Surrogate Network (VT-DTSN), a deep learning framework for predictive modeling of 3D+T imaging data from biological tissue. By leveraging Vision Transformers pretrained with DINO (Self-Distillation with NO Labels) and employ…

[Social] Allostasis: Or, How I Learned To Stop Worrying and Love The Noise
Imran Khan
https://arxiv.org/abs/2508.12791 https://arxiv.org/pdf/2508.12791

[Social] Allostasis: Or, How I Learned To Stop Worrying and Love The Noise
The notion of homeostasis typically conceptualises biological and artificial systems as maintaining stability by resisting deviations caused by environmental and social perturbations. In contrast, (social) allostasis proposes that these systems can proactively leverage these very perturbations to reconfigure their regulatory parameters in anticipation of environmental demands, aligning with von Foerster's ``order through noise'' principle. This paper formulates a computational model of allostat…

A control theoretical approach to gene regulation raises quantitative constraints for dynamic homeostasis in stochastic gene expression
Guilherme Giovanini, Cyro von Zuben de Valega Negr\~ao, Ammar Alsinai, Alexandre Ferreira Ramos
https://arxiv.org/abs/2508.09038

A control theoretical approach to gene regulation raises quantitative constraints for dynamic homeostasis in stochastic gene expression
Cell phenotype dynamic homeostasis contrasts with the inherent randomness of intracellular reactions. Although feedback control of master regulatory genes (MRG) is a key strategy for maintaining gene network expression ranges limited, understanding the quantitative constraints and corresponding mechanisms enabling such a dynamic stability under noise remains elusive. Here we model MRG expression as a stochastic process and downstream genes as sensors which response conditionally induce MRG acti…

Stochastic modelling reveals that chromatin folding buffers epigenetic landscapes against sirtuin depletion during DNA damage
Daria Stepanova, Helen M. Byrne, Tom\'as Alarc\'on
https://arxiv.org/abs/2508.16548

Stochastic modelling reveals that chromatin folding buffers epigenetic landscapes against sirtuin depletion during DNA damage
Epigenetic landscapes, represented by patterns of chemical modifications on histone tails, are essential for maintaining cell identity and tissue homeostasis. These landscapes are shaped by multiple factors, including local biochemical signals and the three-dimensional organisation of chromatin. However, their response to genomic stress, such as DNA double-strand breaks (DSBs), remains incompletely understood. Here, we use a stochastic model of histone modification dynamics integrated with chro…

Emergence of Active Inference from a Chemical Oscillator: A Constructive Approach to Pre-genetic Homeostasis
Takeshi Ishida
https://arxiv.org/abs/2508.06323 https://

Emergence of Active Inference from a Chemical Oscillator: A Constructive Approach to Pre-genetic Homeostasis
How could primordial life, before the evolution of genetic systems, adapt to fluctuating environments and achieve homeostasis? This study proposes a minimal, chemically plausible model where homeostasis emerges from a simple chemical reaction network. It utilizes an internal Lotka-Volterra chemical oscillator as a "search engine" to periodically vary a protocell's pigmentation. The system then optimizes its internal state by evaluating the temporal correlation between these internal fluctuation…

Thiol post-translational modifications modulate allosteric regulation of the OpcA-G6PDH complex through conformational gate control
Hoshin Kim, Song Feng, Pavlo Bohutskyi, Xiaolu Li, Daniel Mejia-Rodriguez, Tong Zhang, Wei-Jun Qian, Margaret S. Cheung
https://arxiv.org/abs/2507.21336

Thiol post-translational modifications modulate allosteric regulation of the OpcA-G6PDH complex through conformational gate control
Cyanobacteria require ultra-fast metabolic switching to maintain reducing power balance during environmental fluctuations. Glucose-6-phosphate dehydrogenase (G6PDH), catalyzing the rate-limiting step of the oxidative pentose phosphate pathway (OPPP), provides essential NADPH and metabolic intermediates for biosynthetic processes and redox homeostasis. In cyanobacteria, the unique redox-sensitive protein OpcA acts as a metabolic switch for G6PDH, enabling rapid adjustment of reducing power gener…

Linking Homeostasis to Reinforcement Learning: Internal State Control of Motivated Behavior
Naoto Yoshida, Henning Sprekeler, Boris Gutkin
https://arxiv.org/abs/2507.04998

Linking Homeostasis to Reinforcement Learning: Internal State Control of Motivated Behavior
For living beings, survival depends on effective regulation of internal physiological states through motivated behaviors. In this perspective we propose that Homeostatically Regulated Reinforcement Learning (HRRL) as a framework to describe biological agents that optimize internal states via learned predictive control strategies, integrating biological principles with computational learning. We show that HRRL inherently produces multiple behaviors such as risk aversion, anticipatory regulation,…

Homeostatic Adaptation of Optimal Population Codes under Metabolic Stress
Yi-Chun Hung, Gregory Schwartz, Emily A. Cooper, Emma Alexander
https://arxiv.org/abs/2507.07874

Homeostatic Adaptation of Optimal Population Codes under Metabolic Stress
Information processing in neural populations is inherently constrained by metabolic resource limits and noise properties, with dynamics that are not accurately described by existing mathematical models. Recent data, for example, shows that neurons in mouse visual cortex go into a "low power mode" in which they maintain firing rate homeostasis while expending less energy. This adaptation leads to increased neuronal noise and tuning curve flattening in response to metabolic stress. We have develo…

Simple biological controllers drive the evolution of soft modes
Christopher Joel Russo, Kabir Husain, Rama Ranganathan, David Pincus, Arvind Murugan
https://arxiv.org/abs/2507.11973

Simple biological controllers drive the evolution of soft modes
Biological systems, with many interacting components, face high-dimensional environmental fluctuations, ranging from diverse nutrient deprivations to toxins, drugs, and physical stresses. Yet, many biological control mechanisms are `simple' -- they restore homeostasis through low-dimensional representations of the system's high-dimensional state. How do low-dimensional controllers maintain homeostasis in high-dimensional systems? We develop an analytically tractable model of integral feedback f…

Replaced article(s) found for q-bio.CB. https://arxiv.org/list/q-bio.CB/new
[1/1]:
- The transition from homeostasis to stochasticity induced catastrophe
Rudro R. Biswas, Charles S. Wright, Kunaal Joshi, Srividya Iyer-Biswas

Phase separation in a mixture of proliferating and motile active matter
Lukas Hupe, Joanna M. Materska, David Zwicker, Ramin Golestanian, Bartlomiej Waclaw, Philip Bittihn
https://arxiv.org/abs/2506.05288

Phase separation in a mixture of proliferating and motile active matter
Proliferation and motility are ubiquitous drivers of activity in biological systems. Here, we study a dense binary mixture of motile and proliferating particles with exclusively repulsive interactions, where homeostasis in the proliferating subpopulation is maintained by pressure-induced removal. Using computer simulations, we show that phase separation emerges naturally in this system at high density and weak enough self-propulsion. We show that condensation is caused by interactions between m…

Replaced article(s) found for q-bio.CB. https://arxiv.org/list/q-bio.CB/new
[1/1]:
- The transition from homeostasis to stochasticity induced catastrophe
Rudro R. Biswas, Charles S. Wright, Kunaal Joshi, Srividya Iyer-Biswas