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The polymerization of actin via branching at a cell membrane containing nucleation-promoting factors is simulated using a stochastic-growth methodology. The polymerized-actin distribution displays three types of behavior: a) traveling…
In the absence of environmental cues, a migrating cell performs an isotropic random motion. Recently, the breaking of this isotropy has been observed when cells move in the presence of asymmetric adhesive patterns. However, up to now the…
In this research, the application of the Physics-Informed Neural Network (PINN) model is explored to solve transport equation-based Partial Differential Equations (PDEs). The primary objective is to analyze the impact of different…
Despite simplicity, the synchronous cellular automaton [D.A. Young, Math. Biosci. 72, 51 (1984)] enables reconstructing basic features of patterns of skin. Our extended model allows studying the formatting of patterns and their temporal…
In this paper we consider the multiscale modelling of water transport in vegetated soil. In the microscopic model we distinguish between subdomains of soil and plant tissue, and use the Richards equation to model the water transport through…
We show how a gradient in the motility properties of non-interacting point-like active particles can cause a pressure gradient that pushes a large inert object. We calculate the force on an object inside a system of active particles with…
Many different proteins self-aggregate into insoluble fibrils growing apically by reversible addition of elementary building blocks. But beyond this common principle, the modalities of fibril formation are very disparate, with various…
Bacterial colonies can form a wide variety of shapes and structures based on ambient and internal conditions. To help understand the mechanisms that determine the structure of and the diversity within these colonies, various numerical…
In many important cellular processes, including mRNA translation, gene transcription, phosphotransfer, and intracellular transport, biological "particles" move along some kind of "tracks". The motion of these particles can be modeled as a…
Transport in molecular electronic devices is different from that in semiconductor mesoscopic devices in two important aspects: (1) the effect of the electronic structure and (2) the effect of the interface to the external contact. A…
In multi-cellular organisms, cells differentiate into multiple types as they divide. States of these cell types, as well as their numbers, are known to be robust to external perturbations; as conceptualized by Waddington's epigenetic…
We study the effect of discreteness on various models for patterning in bacterial colonies. In a bacterial colony with branching pattern, there are discrete entities - bacteria - which are only two orders of magnitude smaller than the…
Vegetation patterns are abundant in arid and semiarid ecosystems, but how they form remains unclear. One of the most extended theories lies in the existence of scale-dependent feedbacks (SDF) in plant-to-plant and plant-water interactions.…
A model of pattern formation in living systems is presented. The pattern is achieved by the sequential interaction of two signaling pathways. The coupling of the pattern to the (thick) epithelial sheet changes is given, when the Gauss…
In the field of pharmacokinetics and pharmacodynamics (PKPD) modeling, which plays a pivotal role in the drug development process, traditional models frequently encounter difficulties in fully encapsulating the complexities of drug…
The paper introduces a PDE model for the growth of a tree stem or a vine. The equations describe the elongation due to cell growth, and the response to gravity and to external obstacles. An additional term accounts for the tendency of a…
Many theoretical works have attempted to coarse grain gene expression at the level of transcription and translation via frameworks based on exclusion processes. Usually in these models the three-dimensional conformation of the substrates…
This paper is a step-by-step, self-contained guide to the complete training cycle of a Physics-Informed Neural Network (PINN) -- a topic that existing tutorials and guides typically delegate to automatic differentiation libraries without…
We consider transport of passive particles in steady laminar plane flows of incompressible viscous fluids. While drifting along the streamlines, the particles experience alternating accelerations and slowdowns. For an ensemble of particles,…
The orientation of cell division is a major determinant of three-dimensional plant morphogenesis. Whether and how a simple division orientation rule explains the establishment of symmetric body plans is a fundamental question. Testing such…