Related papers: A Calculus of Located Entities
We are interested in modeling some two-level population dynamics, resulting from the interplay of ecological interactions and phenotypic variation of individuals (or hosts) and the evolution of cells (or parasites) of two types living in…
Causal ordering of key events in the cell cycle is essential for proper functioning of an organism. Yet, it remains a mystery how a specific temporal program of events is maintained despite ineluctable stochasticity in the biochemical…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
Fascinating and puzzling phenomena, such as landmark vector cells, splitter cells, and event-specific representations to name a few, are regularly discovered in the hippocampus. Without a unifying principle that can explain these divergent…
Originally motivated by the morphogenesis of bacterial microcolonies, the aim of this article is to explore models through different scales for a spatial population of interacting, growing and dividing particles. We start from a microscopic…
Knowing a biomolecule's structure is inherently linked to and a prerequisite for any detailed understanding of its function. Significant effort has gone into developing technologies for structural characterization. These technologies do not…
Stochastic resetting models diverse phenomena across numerous scientific disciplines. Current understanding stems from the renewal framework, which relates systems subject to global resetting to their non-resetting counterparts. Yet, in…
Despite the central role of self-assembled groups in animal and human societies, statistical tools to explain their composition are limited. We introduce a statistical framework for cross-sectional observations of groups with exclusive…
Cells exhibit a wide variety of different shapes. This diversity poses a challenge for computational approaches that attempt to shed light on the role cell geometry plays in regulating cell physiology and behavior. The simulation platform…
In the framework of model-based clustering, a model allowing several latent class variables is proposed. This model assumes that the distribution of the observed data can be factorized into several independent blocks of variables. Each…
Probabilistic inference provides a language for describing how organisms may learn from and adapt to their environment. The computations needed to implement probabilistic inference often require specific representations, akin to having the…
We consider hexagonal cellular automata with immediate cell neighbourhood and three cell-states. Every cell calculates its next state depending on the integral representation of states in its neighbourhood, i.e. how many neighbours are in…
We describe a new phenomenon in quantum cosmology: self-organised localisation. When the fundamental parameters of a theory are functions of a scalar field subject to large fluctuations during inflation, quantum phase transitions can act as…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
Place Recognition enables the estimation of a globally consistent map and trajectory by providing non-local constraints in Simultaneous Localisation and Mapping (SLAM). This paper presents Locus, a novel place recognition method using 3D…
Stochastic agent-based models can account for millions of cells with spatiotemporal movement that can be a function of different factors. However, these simulations can be computationally expensive. In this work, we develop a novel…
We present a method for enhanced sampling of molecular dynamics simulations using stochastic resetting. Various phenomena, ranging from crystal nucleation to protein folding, occur on timescales that are unreachable in standard simulations.…
Cells of the human body have nearly identical genome but exhibit very different phenotypes that allow them to carry out specific functions and react to changes in their surrounding environment. This division of labour is achieved by…
Visual segmentation is a key perceptual function that partitions visual space and allows for detection, recognition and discrimination of objects in complex environments. The processes underlying human segmentation of natural images are…