CFD modeling of a fixed-bed biofilm reactor coupling hydrodynamics and biokinetics

Peer ReviewedPostprint (author's final draft

Invasion moving boundary problem for a biofilm reactor model

The work presents the analysis of the free boundary value problem related to the invasion model of new species in biofilm reactors. In the framework of continuum approach to mathematical modelling of biofilm growth, the problem consists of a system of nonlinear hyperbolic partial differential equations governing the microbial species growth and a system of semi-linear elliptic partial differential equations describing the substrate trends. The model is completed with a system of elliptic partial differential equations governing the diffusion and reaction of planktonic cells, which are able to switch their mode of growth from planktonic to sessile when specific environmental conditions are found. Two systems of nonlinear differential equations for the substrate and planktonic cells mass balance within the bulk liquid are also considered. The free boundary evolution is governed by a differential equation that accounts for detachment. The qualitative analysis is performed and a uniqueness and existence result is discussed. Furthermore, two special models of biological and engineering interest are discussed numerically. The invasion of Anammox bacteria in a constituted biofilm inhabiting the deammonification units of the wastewater treatment plants is simulated. Numerical simulations are run to evaluate the influence of the colonization process on biofilm structure and activity.Comment: 20 pages, 11 figures, original pape

Computational Methods and Results for Structured Multiscale Models of Tumor Invasion

We present multiscale models of cancer tumor invasion with components at the molecular, cellular, and tissue levels. We provide biological justifications for the model components, present computational results from the model, and discuss the scientific-computing methodology used to solve the model equations. The models and methodology presented in this paper form the basis for developing and treating increasingly complex, mechanistic models of tumor invasion that will be more predictive and less phenomenological. Because many of the features of the cancer models, such as taxis, aging and growth, are seen in other biological systems, the models and methods discussed here also provide a template for handling a broader range of biological problems

The Impacts of Three Flamelet Burning Regimes in Nonlinear Combustion Dynamics

Axisymmetric simulations of a liquid rocket engine are performed using a delayed detached-eddy-simulation (DDES) turbulence model with the Compressible Flamelet Progress Variable (CFPV) combustion model. Three different pressure instability domains are simulated: completely unstable, semi-stable, and fully stable. The different instability domains are found by varying the combustion chamber and oxidizer post length. Laminar flamelet solutions with a detailed chemical mechanism are examined. The $\beta$ Probability Density Function (PDF) for the mixture fraction and Dirac $\delta$ PDF for both the pressure and the progress variable are used. A coupling mechanism between the Heat Release Rate (HRR) and the pressure in an unstable cycle is demonstrated. Local extinction and reignition is investigated for all the instability domains using the full S-curve approach. A monotonic decrease in the amount of local extinctions and reignitions occurs when pressure oscillation amplitude becomes smaller. The flame index is used to distinguish between the premixed and non-premixed burning mode in different stability domains. An additional simulation of the unstable pressure oscillation case using only the stable flamelet burning branch of the S-curve is performed. Better agreement with experiments in terms of pressure oscillation amplitude is found when the full S-curve is used.Comment: 25 pages, 12 figures. Submitted to Combustion and Flame for a Special Issu

Effects of external global noise on the catalytic CO oxidation on Pt(110)

Oxidation reaction of CO on a single platinum crystal is a reaction-diffusion system that may exhibit bistable, excitable, and oscillatory behavior. We studied the effect of a stochastic signal artificially introduced into the system through the partial pressure of CO. First, the external signal is employed as a turbulence suppression tool, and second, it modifies the boundaries in the bistable transition between the CO and oxygen covered phases. Experiments using photoemission electron microscopy (PEEM) together with numerical simulations performed with the Krischer-Eiswirth-Ertl (KEE) model are presented.Comment: 15 pages, 7 figures, accepted in J. Chem. Phy

Modeling and Simulation of the Effects of Cyclic Loading on Articular Cartilage Lesion Formation

We present a model of articular cartilage lesion formation to simulate the effects of cyclic loading. This model extends and modifies the reaction-diffusion-delay model by Graham et al. 2012 for the spread of a lesion formed though a single traumatic event. Our model represents "implicitly" the effects of loading, meaning through a cyclic sink term in the equations for live cells. Our model forms the basis for in silico studies of cartilage damage relevant to questions in osteoarthritis, for example, that may not be easily answered through in vivo or in vitro studies. Computational results are presented that indicate the impact of differing levels of EPO on articular cartilage lesion abatement

Nonlinear predictive control for durability enhancement and efficiency improvement in a fuel cell power system

© . This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/In this work, a nonlinear model predictive control (NMPC) strategy is proposed to improve the efficiency and enhance the durability of a proton exchange membrane fuel cell (PEMFC) power system. The PEMFC controller is based on a distributed parameters model that describes the nonlinear dynamics of the system, considering spatial variations along the gas channels. Parasitic power from different system auxiliaries is considered, including the main parasitic losses which are those of the compressor. A nonlinear observer is implemented, based on the discretised model of the PEMFC, to estimate the internal states. This information is included in the cost function of the controller to enhance the durability of the system by means of avoiding local starvation and inappropriate water vapour concentrations. Simulation results are presented to show the performance of the proposed controller over a given case study in an automotive application (New European Driving Cycle). With the aim of representing the most relevant phenomena that affects the PEMFC voltage, the simulation model includes a two-phase water model and the effects of liquid water on the catalyst active area. The control model is a simplified version that does not consider two-phase water dynamics.Peer ReviewedPostprint (author's final draft

A phenomenological approach to the simulation of metabolism and proliferation dynamics of large tumour cell populations

A major goal of modern computational biology is to simulate the collective behaviour of large cell populations starting from the intricate web of molecular interactions occurring at the microscopic level. In this paper we describe a simplified model of cell metabolism, growth and proliferation, suitable for inclusion in a multicell simulator, now under development (Chignola R and Milotti E 2004 Physica A 338 261-6). Nutrients regulate the proliferation dynamics of tumor cells which adapt their behaviour to respond to changes in the biochemical composition of the environment. This modeling of nutrient metabolism and cell cycle at a mesoscopic scale level leads to a continuous flow of information between the two disparate spatiotemporal scales of molecular and cellular dynamics that can be simulated with modern computers and tested experimentally.Comment: 58 pages, 7 figures, 3 tables, pdf onl