Related papers: Modelling Diffuse Subcellular Protein Structures a…

The formation and regulation of macromolecular complexes provides the backbone of most cellular processes, including gene regulation and signal transduction. The inherent complexity of assembling macromolecular structures makes current…

Internally generated active stresses drive soft materials into architectures inaccessible to thermal self-assembly. We use a microtubule-based active fluid to assemble and irreversibly restructure actin-fascin networks. Subsequently, we…

In this paper a lattice model for diffusional transport of particles in the interphase cell nucleus is proposed. Dense networks of chromatin fibers are created by three different methods: randomly distributed, non-interconnected obstacles,…

Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…

The advent and proliferation of social media have led to the development of mathematical models describing the evolution of beliefs/opinions in an ecosystem composed of socially interacting users. The goal is to gain insights into…

Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…

Many dynamic processes such as telecommunication and transport networks can be described through discrete time series of graphs. Modelling the dynamics of such time series enables prediction of graph structure at future time steps, which…

The integration and transmission of information in the brain are dependent on the interplay between structural and dynamical properties. Implicit in any pursuit aimed at understanding neural dynamics from appropriate sets of mathematically…

Diffusion models have been shown to be capable of generating high-quality images, suggesting that they could contain meaningful internal representations. Unfortunately, the feature maps that encode a diffusion model's internal information…

Understanding the mutual interdependence between the behavior of dynamical processes on networks and the underlying topologies promises new insight for a large class of empirical networks. We present a generic approach to investigate this…

Visual microscopic study of diseased tissue by pathologists has been the cornerstone for cancer diagnosis and prognostication for more than a century. Recently, deep learning methods have made significant advances in the analysis and…

Inspired by recent experimental observation of patterning at the membrane of a living cell, we propose a generic model for the dynamics of a fluctuating interface driven by particle-like inclusions which stimulate its growth. We find that…

Dynamics of protein self-assembly on the inorganic surface and the resultant geometric patterns are visualized using high-speed atomic force microscopy. The time dynamics of the classical macroscopic descriptors such as 2D Fast Fourier…

We present Brownian dynamics simulations of the facilitated diffusion of a protein, modelled as a sphere with a binding site on its surface, along DNA, modelled as a semi-flexible polymer. We consider both the effect of DNA organisation in…

Biochemical processes in cells are governed by complex networks of many chemical species interacting stochastically in diverse ways and on different time scales. Constructing microscopically accurate models of such networks is often…

As a granular material is compressed, the particles and forces within the system arrange to form complex heterogeneous structures. Force chains are a prime example and are thought to constrain bulk properties such as mechanical stability…

Discrete-time modeling of acoustic, mechanical and electrical systems is a prominent topic in the musical signal processing literature. Such models are mostly derived by discretizing a mathematical model, given in terms of ordinary or…

The spatial structure of the cell is highly organized at all levels: from small complexes and assemblies, to local nano- and micro-clusters, to global, micrometer scales across and between cells. We suggest that this multiscale spatial cell…

A temporal network -- a collection of snapshots recording the evolution of a network whose links appear and disappear dynamically -- can be interpreted as a trajectory in graph space. In order to characterize the complex dynamics of such…

Recently, the potential of dynamic brain networks as a neuroimaging biomarkers for mental illnesses is being increasingly recognized. However, there are several unmet challenges in developing such biomarkers, including the need for methods…