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We introduce a class of 2D lattice models that describe the dynamics of intertwiners, or, in a condensed matter interpretation, the fusion and splitting of anyons. We identify different families and instances of triangulation invariant,…
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…
Traditional top-down robotic design often lacks the adaptability needed to handle real-world complexities, prompting the need for more flexible approaches. Therefore, this study introduces a novel cellular plasticity model tailored for…
Tumor Necrosis Factor alpha (TNF) initiates a complex series of biochemical events in the cell upon binding to its type R1 receptor (TNF-R1). Recent experimental work has unravelled the molecular regulation of the recruitment of initial…
Semiflexible polymers such as filamentous actin play a vital role in the mechanical behavior of cells, yet the basic properties of cross-linked F-actin networks remain poorly understood. To address this issue, we have performed numerical…
Turing patterns in reaction-diffusion (RD) systems have classically been studied only in RD systems which do not explicitly depend on independent variables such as space. In practise, many systems for which Turing patterning is important…
We address the role of topology in the energy transport process that occurs in networks of photosynthetic complexes. We take inspiration from light harvesting networks present in purple bacteria and simulate an incoherent dissipative energy…
An interesting interplay between two different modifiers and the surface of titanium dioxide leads to a significant change in photoelectrochemical properties of the designed hybrid materials. The semiconductor is photosensitized by one of…
Mechanisms of immunity, and of the host-pathogen interactions in general are among the most fundamental problems of medicine, ecology, and evolution studies. Here, we present a microscopic, protein-level, sequence-based model of immune…
Motivated by neuronal models from neuroscience, we consider the system identification of simple feedback structures whose behaviors include nonlinear phenomena such as excitability, limit-cycles and chaos. We show that output feedback is…
Connecting the dynamics of biomolecular networks to experimentally measurable cell phenotypes remains a central challenge in systems biology. Here we introduce a model-based definition of phenotype as a partial steady state that is…
We study the dynamic properties of a model for wetting with two competing adsorbates on a planar substrate. The two species of particles have identical properties and repel each other. Starting with a flat interface one observes the…
Quantitative modeling has become an essential tool in modern biophysics, driven by advances in both experimental techniques and theoretical frameworks. Powerful high-resolution techniques now provide detailed datasets spanning molecular to…
We consider a two dimensional Turing like system with two diffusing species which interact with each other. Considering the species to be charged, we include the effect of an electric field along a given direction which can lead to a drift…
Tuberculosis (TB) is a major global health challenge, and is compounded by co-morbidities such as HIV, diabetes, and anemia, which complicate treatment outcomes and contribute to heterogeneous patient responses. Traditional models of TB…
Many systems exhibit complex interactions between their components: some features or actions amplify each other's effects, others provide redundant information, and some contribute independently. We present a simple geometric method for…
Naive human T cells are produced in the thymus, which atrophies abruptly and severely in response to physical or psychological stress. To understand how an instance of stress affects the size and "diversity" of the peripheral naive T cell…
We investigate the behaviour of a system of particles with the different character of interaction. The approach makes it possible to describe systems of interacting particles by statistical methods taking into account a spatial…
Building on the phenomenological and microscopic models reviewed in Part I, this second part focuses on network-level mechanisms that generate emergent temperature response curves. We review deterministic models in which temperature…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…