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Simulating transition dynamics between metastable states is a fundamental challenge in dynamical systems and stochastic processes with wide real-world applications in understanding protein folding, chemical reactions and neural activities.…
Mutualistic communities have an internal structure that makes them resilient to external per- turbations. Late research has focused on their stability and the topology of the relations between the different organisms to explain the reasons…
How do we capture the breadth of behavior in animal movement, from rapid body twitches to aging? Using high-resolution videos of the nematode worm $C. elegans$, we show that a single dynamics connects posture-scale fluctuations with…
A fundamental goal of microbial ecology is to understand what determines the diversity, stability, and structure of microbial ecosystems. The microbial context poses special conceptual challenges because of the strong mutual influences…
Collective behavior of active elements inspired by mass of biological organisms is addressed. Especially, two topics are focused on among amazing behaviors performed by colony of ants. First, task allocation phenomena are treated from the…
Adaptation is used by biological sensory systems to respond to a wide range of environmental signals, by adapting their response properties to the statistics of the stimulus in order to maximize information transmission. We derive rules of…
We propose a theoretical approach to estimate the permeability coefficient of substrates (permeants) for crossing membranes from donor (D) phase to acceptor (A) phase by means of molecular dynamics (MD) simulation. A fundamental aspect of…
In this paper, we propose a mathematical framework that governs the evolution of epidemic dynamics, encompassing both intra-population dynamics and inter-population mobility within a metapopulation network. By linearizing this dynamical…
Measurement in biological systems became a subject of concern as a consequence of numerous reports on limited reproducibility of experimental results. To reveal origins of this inconsistency, we have examined general features of biological…
Complex institutions are typically characterized by meso-scale structures which are fundamental for the successful coordination of multiple agents. Here we introduce a framework to study the temporal dynamics of the node-community…
Many biological ecosystems exhibit chaotic behavior, demonstrated either analytically using parameter choices in an associated dynamical systems model or empirically through analysis of experimental data. In this paper, we provide a…
Communication-enabled devices routinely carried by individuals have become pervasive, opening unprecedented opportunities for collecting digital metadata about the mobility of large populations. In this paper, we propose a novel methodology…
Spreading processes on top of active dynamics provide a novel theoretical framework for capturing emerging collective behavior in living systems. I consider run-and-tumble dynamics coupled with coagulation/decoagulation reactions that lead…
In a cellular medium, the plasmic membrane is a place of interactions between the cell and its direct external environment. A classic model describes it as a fluid mosaic. The fluid phase of the membrane allows a lateral degree of freedom…
The computational study of conformational transitions in RNA and proteins with atomistic molecular dynamics often requires suitable enhanced sampling techniques. We here introduce a novel method where concurrent metadynamics are integrated…
Movement is fundamental to life, shaping population dynamics, biodiversity patterns, and ecosystem structure. Recent advances in tracking technology have enabled fundamental questions about movement to be tackled, leading to the development…
A central concern across the natural sciences is a quantitative understanding of the mechanism governing rare transitions between two metastable states. Recent research has uncovered a fundamental equality between the time-reversal…
Immigration can rescue local populations from extinction, helping to stabilise a metapopulation. Local population dynamics is important for determining the strength of this rescue effect, but the mechanistic link between local demographic…
Adaptive control in biological systems, such as intestinal immunity, remains poorly understood despite detailed knowledge of underlying regulatory networks. We propose an alternative framework based on stochastic martingale turnover, in…
Complex systems with nonreciprocal interactions are often stratified into layers. Ecosystems are a prime example, where species at one trophic level grow by consuming those at another. Yet the dynamical consequences of such stratified…