Related papers: Active skeleton for bacteria modeling
Controlling and suppressing bacterial accumulation at solid surfaces is essential for preventing biofilm formation and biofouling. Whereas various chemical surface treatments are known to reduce cell accumulation and attachment, the role of…
Purpose: Antimicrobial resistance is a major global health concern, affecting hospital admissions and treatment success. This study aims to introduce an experimental setup for monitoring bacterial activity over time using image-based…
Many collective systems exist in nature far from equilibrium, ranging from cellular sheets up to flocks of birds. These systems reflect a form of active matter, whereby individual material components have internal energy. Under specific…
We propose a three dimensional mechanical model of embryonic tissue dynamics. Mechanically coupled adherent cells are represented as particles interconnected with elastic beams which can exert non-central forces and torques. Tissue…
Understanding large amounts of spatiotemporal data from particle-based simulations, such as molecular dynamics, often relies on the computation and analysis of aggregate measures. These, however, by virtue of aggregation, hide structural…
Recent findings suggest that shell protein distribution and morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component…
The heterogeneity of reaction fluxes present in a metabolic network within a single flux state can be exploited to construct the so-called backbone as a reduced version of metabolism. The backbone maintains all significant fluxes producing…
We propose a computational framework to study the growth and spread of bacterial biofilms on interfaces, as well as the action of antibiotics on them. Bacterial membranes are represented by boundaries immersed in a fluid matrix and subject…
The bacterial flagellar motor is a highly efficient rotary machine used by many bacteria to propel themselves. It has recently been shown that at low speeds its rotation proceeds in steps [Sowa et al. (2005) Nature 437, 916--919]. Here we…
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…
Responding mechanically to environmental requests, muscles show a surprisingly large variety of functions. The studies of in vivo cycling muscles qualified skeletal muscles into four principal locomotor patterns: motor, brake, strut, and…
Bacterial migration through confined spaces is critical for several phenomena like: biofilm formation, bacterial transport in soils, and bacterial therapy against cancer . In the present work, \textit{E. coli} (strain K12-MG1655 WT)…
Cell tracking enables data extraction from time-lapse "cell movies" and promotes modeling biological processes at the single-cell level. We introduce a new fully automated computational strategy to track accurately cells across frames in…
Recent advances in the joint processing of images have certainly shown its advantages over individual processing. Different from the existing works geared towards co-segmentation or co-localization, in this paper, we explore a new joint…
Active materials take advantage of their internal sources of energy to self-organize in an automated manner. This feature provides a novel opportunity to design micron-scale machines with minimal required control. However, self-organization…
The advent of high-throughput sequencing technologies has made data from DNA material readily available, leading to a surge of microbiome-related research establishing links between markers of microbiome health and specific outcomes.…
Biomembranes wrapping cells and organelles are not only the partitions that separate the insides but also dynamic fields for biological functions accompanied by membrane shape changes. In this review, we discuss the spatiotemporal patterns…
This paper presents a method which can track and 3D reconstruct the non-rigid surface motion of human performance using a moving RGB-D camera. 3D reconstruction of marker-less human performance is a challenging problem due to the large…
Liquid-liquid phase separation is important across biology, physics, and materials science. Although usually studied at equilibrium, active components - such as motor proteins, enzymes, and synthetic microswimmers - are increasingly…
Heterogeneous systems of active matter exhibit a range of complex emergent dynamical patterns. In particular, it is difficult to predict the properties of the mixed system based on its constituents. These considerations are particularly…