Related papers: Multiscale Computational Modeling of Biofilm
Bacteria generally live in complicated structures called biofilms, consisting of communicating bacterial colonies and extracellular polymeric substance (EPS). Since biofilms are related to detrimental effects such as infection or antibiotic…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, an open-source software package that enables to simulate operational light-sheet microscopes by combining data…
The extracellular matrix of biofilms presents a dense and intricate architecture. Numerous biophysical properties of the matrix surrounding microbial cells contribute to the heterogeneity of biofilms and their functions at the microscale.…
Using bioimaging technology, biologists have attempted to identify and document analytical interpretations that underlie biological phenomena in biological cells. Theoretical biology aims at distilling those interpretations into knowledge…
Developing complex biomolecular workflows is not always straightforward. It requires tedious developments to enable the interoperability between the different biomolecular simulation and analysis tools. Moreover, the need to execute the…
This review summarizes recent progress in investigating polymer systems by using Differential dynamic microscopy (DDM), a rapidly emerging approach that transforms a commercial microscope by combining real-space information with the…
Low-energy electron microscopy (LEEM) is a surface science method that works primarily in the UHV environment. It provides information complementary to the other established techniques: it extends the limited view of scanning probe…
Biofilms are bacterial aggregates that grow on moist surfaces. Thin homogeneous biofilms naturally formed on the walls of conducts may serve as biosensors, providing information on the status of microsystems (MEMS) without disrupting them.…
Bacterial cellulose biofilms are complex networks of strong interwoven nanofibers that control transport and protect bacterial colonies in the film. Design of diverse applications of bacterial cellulose films also relies on understanding…
The promise of machine learning has been explored in a variety of scientific disciplines in the last few years, however, its application on first-principles based computationally expensive tools is still in nascent stage. Even with the…
Usage, manipulation, transport, delivery, and mixing of granular or particulate media, comprised of spherical or polyhedral particles, is commonly encountered in industrial sectors of construction (cement and rock fragments), pharmaceutics…
The XDEM multi-physics and multi-scale simulation platform roots in the Ex- tended Discrete Element Method (XDEM) and is being developed at the In- stitute of Computational Engineering at the University of Luxembourg. The platform is an…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Biomembranes adopt varying morphologies that are vital to cellular functions. Many studies use computational modeling to understand how various mechanochemical factors contribute to membrane shape transformations. Compared to…
Biofilms, bacteria cells surrounded by a self-produced polymeric matrix, are common on medical devices and lead to many hospital infections. The biofilm lifecycle includes disassembly and dispersion, where bacteria clusters detach from the…
Mathematical models are vital interpretive and predictive tools used to assist in the understanding of cell migration. There are typically two approaches to modelling cell migration: either micro-scale, discrete or macro-scale, continuum.…
Biofilm growth changes many physical properties of porous media such as porosity, permeability and mass transport parameters. The growth depends on various environmental conditions, and in particular, on flow rates. Modeling the evolution…
Electrostatic forces play many important roles in molecular biology, but are hard to model due to the complicated interactions between biomolecules and the surrounding solvent, a fluid composed of water and dissolved ions. Continuum model…
Microscopic organisms, such as bacteria, have the ability of colonizing surfaces and developing biofilms that can determine diseases and infections. Most bacteria secrete a significant amount of extracellular polymer substances that are…