Related papers: Multiscale Computational Modeling of Biofilm
Biofilms are complex structures which are inhabited by numerous amount of different species of microorganisms. Due to their ubiquity, they influence human life on an everyday basis. It is therefore important to understand the interactions…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
We derive a physiologically structured multiscale model for biofilm development. The model has components on two spatial scales, which induce different time scales into the problem. The macroscopic behavior of the system is modeled using…
In cryo-electron microscopy (EM), molecular structures are determined from large numbers of projection images of individual particles. To harness the full power of this single-molecule information, we use the Bayesian inference of EM…
Biofilms are communities of bacteria that exhibit a multitude of multiscale biomechanical behaviors. Recent experimental advances have lead to characterizations of these behaviors in terms of measurements of the viscoelastic moduli of…
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 structure and function of biological molecules are strongly influenced by the water and dissolved ions that surround them. This aqueous solution (solvent) exerts significant electrostatic forces in response to the biomolecule's…
In this paper, we derive upscaled equations for modelling biofilm growth in porous media. The resulting macro-scale mathematical models consider permeable multi-species biofilm including water flow, transport, detachment and reactions. The…
Quantifying the action of antibiotics on biofilms is essential to devise therapies against chronic infections. Biofilms are bacterial communities attached to moist surfaces, sheltered from external aggressions by a polymeric matrix.…
The focus of this paper is the numerical solution of a pore-scale model for the growth of a permeable biofilm. The model includes water flux inside the biofilm, different biofilm components, and shear stress on the biofilm-water interface.…
The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite…
Biofilms are a cluster of bacteria embedded in extracellular polymeric substances (EPS) that contain a complex composition of polysaccharides, proteins, and extracellular DNA (eDNA). Desirable mechanical properties of the biofilms are…
Several bacteria and bacteria strands form biofilms in different environmental conditions, e.g. pH, temperature, nutrients, etc. Biofilm growth, therefore, is an extremely robust process. Because of this, while biofilm growth is a complex…
The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. Quantum mechanics/molecular mechanics (QM/MM) molecular…
The bacterium {\em Bacilus subtilis} frequently forms biofilms at the interface between the culture medium and the air. We develop a mathematical model that couples a description of bacteria as individual discrete objects to the standard…
Bacterial biofilms mechanically behave as viscoelastic media consisting of micron-sized bacteria crosslinked to a selfproduced network of extracellular polymeric substances (EPS) embedded in water. Structural principles for numerical…
In this article we propose an inverse analysis algorithm to find the best fit of multiple material parameters in different coupled multi-physics biofilm models. We use a nonlinear continuum mechanical approach to model biofilm deformation…
The goal of this work is to develop a numerical simulation that accurately captures the biomechanical response of bacterial biofilms and their associated extracellular matrix (ECM). In this, the second of a two-part effort, the primary…
From multicellular tissues to bacterial colonies, three dimensional cellular structures arise through the interaction of cellular activities and mechanical forces. Simple bacterial communities provide model systems for analyzing such…
A bacterial biofilm is an aggregate of micro-organisms growing fixed onto a solid surface, rather than floating freely in a liquid. Biofilms play a major role in various practical situations such as surgical infections and water treatment.…