Biomedical subjects

Cristian Picioreanu

Publications and source records attributed to Cristian Picioreanu.

9 recordsLinked to original sources

PubMed2006

Three-dimensional biofilm model with individual cells and continuum EPS matrix.

An innovative type of biofilm model is derived by combining an individual description of microbial particles with a continuum representation of the biofilm matrix. This hybrid model retains the advantages of each approach, while providing a more realistic description of the temporal development of biofilm structure in two or three spatial dimensions. The general model derivation takes into account any possible number of soluble components. These are substrates and metabolic products, which diffuse and react in the biofilm within individual microbial cells. The cells grow, divide, and produce extracellular polymeric substances (EPS) in a multispecies model setting. The EPS matrix is described by a continuum representation as incompressible viscous fluid, which can expand and retract due to generation and consumption processes. The cells move due to a pushing mechanism between cells in colonies and by an advective mechanism supported by the EPS dynamics. Detachment of both cells and EPS follows a continuum approach, whereas cells attach in discrete events. Two case studies are presented for model illustration. Biofilm consolidation is explained by shrinking due to EPS and cell degradation processes. This mechanism describes formation of a denser layer of cells in the biofilm depth and occurrence of an irregularly shaped biofilm surface under nutrient limiting conditions. Micro-colony formation is investigated by growth of autotrophic microbial colonies in an EPS matrix produced by heterotrophic cells. Size and shape of colonies of ammonia and nitrite-oxidizing bacteria (NOB) are comparatively studied in a standard biofilm and in biofilms aerated from a membrane side.

Biofilms↗

PubMed2005

A general description of detachment for multidimensional modelling of biofilms.

A general method for describing biomass detachment in multidimensional biofilm modelling is introduced. Biomass losses from processes acting on the entire surface of the biofilm, such as erosion, are modelled using a continuous detachment speed function F(det). Discrete detachment events, i.e. sloughing, are implicitly derived from simulations. The method is flexible to allow F(det) to take several forms, including expressions dependent on any state variables such as the local biofilm density. This methodology for biomass detachment was integrated with multidimensional (2D and 3D) particle-based multispecies biofilm models by using a novel application of the level set method. Application of the method is illustrated by trends in the dynamics of biofilms structure and activity derived from simulations performed on a simple model considering uniform biomass (case study I) and a model discriminating biomass composition in heterotrophic active mass, extracellular polymeric substances (EPS) and inert mass (case study II). Results from case study I demonstrate the effect of applied detachment forces as a fundamental factor influencing steady-state biofilm activity and structure. Trends from experimental observations reported in literature were correctly described. For example, simulation results indicated that biomass sloughing is reduced when erosion forces are increased. Case study II illustrates the application of the detachment methodology to systems with non-uniform biomass composition. Simulations carried out at different bulk concentrations of substrate show changes in biofilm structure (in terms of shape, density and spatial distribution of biomass components) and activity (in terms of oxygen and substrate consumption) as a consequence of either oxygen-limited or substrate-limited growth.

Bacterial Adhesion↗

PubMed2005

Quantification of binary diffusion in protein crystals.

The use of confocal laser scanning microscopy for visualization and quantification of binary diffusion within anisotropic porous material is described here for the first time. The dynamics of adsorption profiles of dianionic fluorescein, zwitterionic rhodamine B, and their mixture in the cationic native orthorhombic lysozyme crystal were subsequently analyzed. All data could be described by a classical pore diffusion model. There was no change in the adsorption characteristics, but diffusion decreased with the introduction of a second solute in the solution. It was found that diffusion is determined by the combination of steric and electrostatic interactions,while adsorption is dependent on electrostatic and hydrophobic interactions. Thus, it was established that the outcome of binary transport depends on the solute, protein, and crystal characteristics.

Adsorption↗

PubMed2005

Relation between pore sizes of protein crystals and anisotropic solute diffusivities.

The diffusion of a solute, fluorescein, into lysozyme protein crystals with different pore structures was investigated. To determine the diffusion coefficients, three-dimensional solute concentration fields acquired by confocal laser scanning microscopy (CLSM) during diffusion into the crystals were compared with the output of a time-dependent 3-D diffusion model. The diffusion process was found to be anisotropic, and the degree of anisotropy increased in the order: triclinic, tetragonal and orthorhombic crystal morphology. A linear correlation between the pore diffusion coefficients and the pore sizes was established. The maximum size of the solute, deduced from the established correlation of diffusion coefficients and pore size, was 0.73 +/- 0.06 nm, which was in the range of the average diameter of fluorescein (0.69 +/- 0.02 nm). This proves that size exclusion is the key mechanism for solute diffusion in protein crystals. Hence, the origin of solute diffusion anisotropy can be found in the packing of the protein molecules in the crystals, which determines the crystal pore organization.

Anisotropy↗

PubMed2005

Modeling biofilm and floc diffusion processes based on analytical solution of reaction-diffusion equations.

Biofilm modeling is often considered as a complex mathematical subject. This paper evaluates simple equations to describe the basic processes in a biofilm system with the main aim to show several interesting applications. To avoid mathematical complexity the simulations are carried out in a simple spreadsheet. Frequently, only the solution for zero-order reaction kinetics of the reaction-diffusion equation is used (better known as half-order kinetics). A weighted average of the analytical solutions for zero- and first-order reactions is proposed as basic and useful model to describe steady-state (in biofilm composition) biofilm reactors. This approach is compared with several modeling approaches, such as the simple solution for zero-order reaction and more complex ones (i) direct numerical solution for the diffusion equations, (ii) 1-D AQUASIM and (iii) 2-D modeling. The systems evaluated are single and multiple species biofilms. It is shown that for describing conversions in biofilm reactors, the zero-order solution is generally sufficient; however, for design purposes large deviations of the correct solution can occur. Additionally, the role of diffusion in flocculated and granular sludge systems is discussed. The relation between the measured (apparent) substrate affinity constant and diffusion processes is outlined.

Biofilms↗

PubMed2005

Biofilm-control strategies based on enzymic disruption of the extracellular polymeric substance matrix--a modelling study.

A kinetic model is proposed to assess the feasibility of strategies for the removal of biofilms by using substances that induce detachment by affecting the cohesiveness of the matrix of extracellular polymeric substances (EPSs). The model uses a two-state description of the EPS (natural EPS and compromised EPS) to provide a unified representation of diverse mechanisms of action of detachment-promoting agents (DPAs), which include enzymes that degrade the EPS and other agents described in the literature. A biofilm-cohesiveness factor describes local increases in detachment rates resultant from losses in cohesive strength. The kinetic model was implemented in an individual-based biofilm-modelling framework, including detachment rates dependent on local cohesiveness. The efficacy of treatments with DPAs was assessed by three-dimensional model simulations. Changes in treatment efficacy were evaluated quantitatively by using a Thiele modulus, which quantifies the relationship between diffusion of the DPA through the biofilm matrix and DPA decay rate, and a Damköhler number relating the rate of EPS reaction with a DPA and the rate of EPS production by the micro-organisms in the biofilm. This study demonstrates the feasibility and limits of implementing biofilm-control strategies based on attacking the EPS.

Bacterial Adhesion↗

PubMed2005

A framework for multidimensional modelling of activity and structure of multispecies biofilms.

Concepts from previous biofilm models were integrated to create a framework for the implementation of multidimensional (2D and 3D) multispecies biofilm models. The framework is here described at three levels: (i) mathematical representation of the processes involved in biofilm formation, (ii) numerical implementation into a computer program (freely available from our website http://www.biofilms.bt.tudelft.nl/frameworkMaterial) and (iii) using the program for the creation of biofilm models with multiple bacterial and solute species. An improved version of the individual-based modelling (IbM) that allows structured biomass was used. In this approach biomass composition may be discriminated into any number of particulate species, including extracellular polymeric substances (EPS) for which specific functionality was included. Detachment is also included, described as occurring at the biofilm surface with variable local rates derived from functions of state variables. The application of this modelling framework to a multispecies system with structured biomass is illustrated in a case study where the competition between an organism capable of accumulating polyhydroxybutyrate (PHB, an internal storage compound) and an EPS-producing organism in a two-species biofilm is analysed. Results illustrate that biofilms enriched in PHB-producing organisms may be obtained by supplying substrate intermittently in feast/famine cycles.

Bacteria↗

PubMed2004

Three-dimensional dual-morphotype species modeling of activated sludge flocs.

An individual-based model, originally developed for a biofilm system, was adapted to simulate three-dimensional formation of activated sludge flocs. The model was extended to two different bacterial morphotypes (floc-forming and filamentous bacteria), allowing spatial development of the floc according to the bacterial morphology, diffusion, reaction, and growth processes. The model needed also extension with a process for attachment of individual cells. Despite being in an early stage of development, the model is already a tool that enables us to obtain useful information about the microfloc environment. The model indicates that filamentous bacterial morphology and substrate microgradients are important aspects in the formation of bacterial structures. In mass transport-limited regimes filamentous bacterial structures prevail, whereas in growth-limited regimes irregular shaped flocs with fingerlike structures are dominant. These modeling results suggest that activated sludge flocs and biofilms might be different manifestations of the same phenomena. The model results support the hypothesis that floc-macrogradients can be the most important parameter for development of bulking sludge. The model suggests that attachment has a very strong effect on floc structure, leading to enhancement of the effect of substrate microgradients.

Bacteria, Aerobic↗

PubMed2004

Particle-based multidimensional multispecies biofilm model.

In this paper we describe a spatially multidimensional (two-dimensional [2-D] and three-dimensional [3-D]) particle-based approach for modeling the dynamics of multispecies biofilms growing on multiple substrates. The model is based on diffusion-reaction mass balances for chemical species coupled with microbial growth and spreading of biomass represented by hard spherical particles. Effectively, this is a scaled-up version of a previously proposed individual-based biofilm model. Predictions of this new particle-based model were quantitatively compared with those obtained with an established one-dimensional (1-D) multispecies model for equivalent problems. A nitrifying biofilm containing aerobic ammonium and nitrite oxidizers, anaerobic ammonium oxidizers, and inert biomass was chosen as an example. The 2-D and 3-D models generally gave the same results. If only the average flux of nutrients needs to be known, 2-D and 1-D models are very similar. However, the behavior of intermediates, which are produced and consumed in different locations within the biofilm, is better described in 2-D and 3-D models because of the multidirectional concentration gradients. The predictions of 2-D or 3-D models are also different from those of 1-D models for slowly growing or minority species in the biofilm. This aspect is related to the mechanism of biomass spreading or advection implemented in the models and should receive more attention in future experimental studies.

Anaerobiosis↗