Related papers: The Five Elements of Th1-Th2 System
In this work we develop a stochastic model of acute HIV infection, based on the well-known standard model, that allows us to simulate the complex mutation pathways of HIV escape from multiple CTL responses. Under this model, we describe two…
Understanding the rules underlying organismal development is a major unsolved problem in biology. Each cell in a developing organism responds to signals in its local environment by dividing, excreting, consuming, or reorganizing, yet how…
We propose a kind of reaction-diffusion equations for cell differentiation, which exhibits the Turing instability. If the diffusivity of some variables is set to be infinity, we get coupled competitive reaction-diffusion equations with a…
T1 transitions, which are localised cell rearrangements, play an important role in the fluidization of epithelial monolayers. Using a multi-phase field model and an active elastic solid model, we show that although each cell undergoes T1…
The accurate and efficient computation of the electromagnetic response of objects made from artificial materials is crucial for designing photonic functionalities and interpreting experiments. Advanced fabrication techniques can nowadays…
Statistical methods for analyzing large-scale biomolecular data are commonplace in computational biology. A notable example is phenotype prediction from gene expression data, for instance, detecting human cancers, differentiating subtypes…
We develop an agent-based model of vasculogenesis, the de novo formation of blood vessels. Endothelial cells in the vessel network are viewed as linearly elastic spheres and are of two types: vessel elements are contained within the…
Since its introduction in 1952, Turing's (pre-)pattern theory ("the chemical basis of morphogenesis") has been widely applied to a number of areas in developmental biology. The related pattern formation models normally comprise a system of…
Analysis of experimental kinetic dependences and results of the computer modeling of pairwise interactions in the heterogeneous system have shown that a character of its fractal property variation in the evolution process would be different…
Turing patterns play a fundamental role in morphogenesis and population dynamics, encoding key information about the underlying biological mechanisms. Yet, traditional inverse problems have largely relied on non-biological data such as…
The T cell arm of the adaptive immune system provides the host protection against unknown pathogens by discriminating between host and foreign material. This discriminatory capability is achieved by the creation of a repertoire of cells…
Tucker tensor decomposition offers a more effective representation for multiway data compared to the widely used PARAFAC model. However, its flexibility brings the challenge of selecting the appropriate latent multi-rank. To overcome the…
The clonal expansion of T cells during an infection is tightly regulated to ensure an appropriate immune response against invading pathogens. Although experiments have mapped the trajectory from expansion to contraction, the interplay…
The role of T-cells within the immune system is to confirm and assess anomalous situations and then either respond to or tolerate the source of the effect. To illustrate how these mechanisms can be harnessed to solve real-world problems, we…
A ternary reaction-diffusion model for early HIV infection dynamics, incorporating logistic growth of target cells, is introduced. According to in vitro and in vivo studies, random movement of target cells, infected cells, and virions and a…
Properties of a contact process in continuum for a system of two type particles one type of which is independent are considered. We study dynamics of the first and second order correlation functions, their asymptotics and dependence on…
The adaptive immune system constantly remodels its lymphocyte repertoire for better protection against future pathogens. Its ability to improve antigen recognition on the fly relies on somatic mutation and selective expansion of B…
Liquid-liquid phase separation occurs not only in bulk liquid, but also on surfaces. In physiology, the nature and function of condensates on cellular structures remain unexplored. Here, we study how the condensed protein TPX2 behaves on…
Temporal-difference (TD) networks are a class of predictive state representations that use well-established TD methods to learn models of partially observable dynamical systems. Previous research with TD networks has dealt only with…
Turn-taking behaviour is simulated in a coupled agents system. Each agent is modelled as a mobile robot with two wheels. A recurrent neural network is used to produce the motor outputs and to hold the internal dynamics. Agents are developed…