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Cell division, aging, and stress recovery triggers spatial reorganization of cellular components in the cytoplasm, including membrane bound organelles, with molecular changes in their compositions and structures. However, it is not clear…
We introduce a bisimulation learning algorithm for non-deterministic transition systems. We generalise bisimulation learning to systems with bounded branching and extend its applicability to model checking branching-time temporal logic,…
Stochasticity is a defining feature of the pairwise forces governing interactions in biological systems-from molecular motors to cell-cell adhesion-yet its consequences on large-scale dynamics remain poorly understood. Here, we show that…
We study the channel output distribution induced by a rate-$R$ random code via statistical physics. The partition function is $Z_n(\beta|\mathcal{C}) = \sum_{y^n}[P_{Y^n|\mathcal{C}}(y^n)]^\beta$, where $\mathcal{C}$ is the code and $\beta…
The well-known issue of reconstructing regulatory networks from gene expression measurements has been somewhat disrupted by the emergence and rapid development of single-cell data. Indeed, the traditional way of seeing a gene regulatory…
Periodic reversals of the direction of motion in systems of self-propelled rod shaped bacteria enable them to effectively resolve traffic jams formed during swarming and maximize their swarming rate. In this paper, a connection is found…
Margination, a fundamental process in which leukocytes migrate from the flowing blood to the vessel wall, is well-documented in physiology. However, it is still an open question on how the differences in cell size and stiffness of white and…
An analytical model based on variational principles for a thin-walled stiffened plate subjected to axial compression is presented. A system of nonlinear differential and integral equations is derived and solved using numerical continuation.…
Cell-to-cell variability is inherent to numerous biological processes, including cell migration. Quantifying and characterizing the variability of migrating cells is challenging, as it requires monitoring many cells for long time windows…
Germ order is a non-standard stochastic order defined through the comparison of the generating functions of the processes. This order was first introduced for branching random walks with a constant breeding law and independent dispersal of…
In this paper, we introduce a novel framework using inhomogeneous Branching Random Walks (BRWs) to model growth processes, specifically introducing genealogy-dependence in branching rates and displacement distributions to model phenomena…
Experiments of in vitro formation of blood vessels show that cells randomly spread on a gel matrix autonomously organize to form a connected vascular network. We propose a simple model which reproduces many features of the biological…
Basic problems for the construction of a scenario for the Life are discussed. To study the problems in terms of dynamical systems theory, a scheme of intra-inter dynamics is presented. It consists of internal dynamics of a unit, interaction…
Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across the millions of cells…
Stochastic branching processes are a classical model for describing random trees, which have applications in numerous fields including biology, physics, and natural language processing. In particular, they have recently been proposed to…
We study sequences of partitions of the unit interval into subintervals, starting from the trivial partition, in which each partition is obtained from the one before by splitting its subintervals in two, according to a given rule, and then…
In this paper homogenization of a mathematical model for biomechanics of a plant tissue with randomly distributed cells is considered. Mechanical properties of a plant tissue are modelled by a strongly coupled system of…
We introduce a novel top-down end-to-end formulation of document-level discourse parsing in the Rhetorical Structure Theory (RST) framework. In this formulation, we consider discourse parsing as a sequence of splitting decisions at token…
Stochastic neural networks are a prototypical computational device able to build a probabilistic representation of an ensemble of external stimuli. Building on the relationship between inference and learning, we derive a synaptic plasticity…
We study the limiting behavior of an interacting particle system evolving on the lattice $Z^{d}$ for $d\ge 3$. The model is known as the contact process with rapid stirring. The process starts with a single particle at the origin. Each…