Related papers: A dissipative particle dynamics model of biofilm g…
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…
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…
Dissipative particle dynamics (DPD) is a novel particle method for mesoscale modeling of complex fluids. DPD particles are often thought to represent packets of real atoms, and the physical scale probed in DPD models are determined by the…
The dissipative particle dynamics (DPD) simulation method has been shown to be a promising tool to study self-assembly of soft matter systems. In particular, it has been used to study block copolymer (BCP) self-assembly. However, previous…
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 study in details the fluid dynamics system proposed in Clarelli et al (2013) to model the formation of cyanobacteria biofilms. After analyzing the linear stability of the unique non trivial equilibrium of the system, we…
Dissipative particle dynamics (DPD) belongs to a class of models and computational algorithms developed to address mesoscale problems in complex fluids and soft matter in general. It is based on the notion of particles that represent…
Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in…
The spatial organization of bacteria in dense biofilms is key to their collective behaviour, and understanding it will be important for medical and technological applications. Here we study the morphology of a compact biofilm that undergoes…
Two phase solid-fluid mixture models are ubiquitous in biological applications. For instance, models for growth of tissues and biofilms combine time dependent and quasi-stationary boundary value problems set in domains whose boundary moves…
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.…
Biofilms are ubiquitous macro-colonies of bacteria that develop at various interfaces (solid-liquid, solid-gas or liquid-gas). The formation of biofilms starts with the attachment of individual bacteria to an interface, where they…
We perform mathematical anaysis of the biofilm development process. A model describing biomass growth is proposed: It arises from coupling three parabolic nonlinear equations: a biomass equation with degenerate and singular diffusion, a…
Smoothed dissipative particle dynamics (SDPD) is a widely used particle-based method for modelling soft matter systems at mesoscopic and macroscopic scales, offering thermodynamic consistency and direct control over the fluid's transport…
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…
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.…
We present a novel approach of mapping dissipative particle dynamics (DPD) into classical molecular dynamics. By introducing the invariant volume element representing the swarm of atoms we show that the interactions between the emerging…
Equations for dislocation evolution bridge the gap between dislocation properties and continuum descriptions of plastic behavior of crystalline materials. Computer simulations can help us verify these evolution equations and find their…
Dissipative particle dynamics (DPD) is a relatively new technique which has proved successful in the simulation of complex fluids. We caution that for the equilibrium achieved by the DPD simulation of a simple fluid the temperature depends…
Free boundaries of biofilms advancing on surfaces evolve according to conservation laws coupled with systems of partial differential equations for velocities, pressures and chemicals affecting cell behavior. Thin film approximations lead to…