相关论文: Multiscale Computational Modeling of Biofilm
The presence of bacterial biofilms in clinical and industrial settings is a major issue worldwide. A biofilm is a viscoelastic matrix, composed of bacteria producing a network of Extracellular Polymeric Substances (EPS) to which bacteria…
Multiscale models allow for the treatment of complex phenomena involving different scales, such as remodeling and growth of tissues, muscular activation, and cardiac electrophysiology. Numerous numerical approaches have been developed to…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
In this paper we derive a pore-scale model for permeable biofilm formation in a two-dimensional pore. The pore is divided in two phases: water and biofilm. The biofilm is assumed to consist of four components: water, extracellular polymeric…
A dissipative particle dynamics (DPD) model for the quantitative simulation of biofilm growth controlled by substrate (nutrient) consumption, advective and diffusive substrate transport, and hydrodynamic interactions with fluid flow…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
In this and the associated article 'BioBlender: Fast and Efficient All Atom Morphing of Proteins Using Blender Game Engine', by Zini et al., we present BioBlender, a complete instrument for the elaboration of motion (Zini et al.) and the…
We combine advanced image reconstruction techniques from computed X-ray micro tomography (XCT) with state-of-the-art discrete element method simulations (DEM) to study granular materials. This "virtual-laboratory" platform allows us to…
In this paper, a multiscale virtual particle based elastic network model (MVP-ENM) is proposed for biomolecular normal mode analysis. The multiscale virtual particle model is proposed for the discretization of biomolecular density data in…
A stochastic model is used to assess the effect of external parameters on the development of submerged biofilms on smooth and rough surfaces. The model includes basic cellular mechanisms, such as division and spreading, together with an…
It is well known that the number of particles should be scaled up to enable industrial scale simulation. The calculations are more computationally intensive when the motion of the surrounding fluid is considered. Besides the advances in…
Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive…
A multi-scale model is presented for predicting the magnitude and rate of powder blending in a rotating drum blender. The model combines particle diffusion coefficient correlations from the literature with advective flow field information…
Computational multiscale modeling encompasses a wide range of end-products and a great number of technological applications. This paper provides an overview of the computational multiscale modeling approach based on the utilization of MBN…
One essential question in material sciences is how to bridge the gap between the microscopic picture and a macroscopic description. The former involves contact forces and deformations, whereas the latter concerns tensorial quantities like…
Understanding the behaviour of biological systems requires a complex setting of in vitro and in vivo experiments, which attracts high costs in terms of time and resources. The use of mathematical models allows researchers to perform…
This study explores the application of elongated particle interaction models, traditionally used in liquid crystal phase research, in the context of early bacterial biofilm development. Through computer simulations using an agent-based…
Biofilms are complex, self-organized consortia of microorganisms that produce a functional, protective matrix of biomolecules. Physically, the structure of a biofilm can be described as an entangled polymer network which grows and changes…
Bacterial communities such as biofilms are widely recognised as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can…
Much of our mechanistic understanding of the functions of biological macromolecules is based on static structural experiments, which can be modelled either as single structures or conformational ensembles. While these provide us with…