INDIVIDUAL-BASED MODELLING OF MICROBIAL COLONY DYNAMICS ON FOOD SURFACES IN A PARALLEL SIMULATOR

International audienceThroughout the whole food processing and distribution chain, an accurate assessment and control of microbiological food safety is indispensable to avoid large outbreaks of foodborne diseases. For this reason, mathematical models are developed in predictive microbiology to describe the growth and survival of food spoiling and pathogenic microorganisms as a function of the environmental conditions during food processing and distribution. Traditionally, these models are representative for the planktonic growth of axenic microbial cultures in perfectly mixed liquid media. However, most food products are characterised by a semi-solid structure, where the contaminating cells grow out as colonies. Diffusion limitations emerge in these colonies due to the high local cell density. Hence, it is most appropriate to simulate microbial colonies at a microscopic level, considering the cell as basic modelling unit in an individual-based modelling approach. Within this respect, the MICRODIMS model has been developed at the BioTeC+ research group. However, over the last years, it became clear that the implementation of this individual-based model in the standard Repast Simphony toolkit is rather slow for the simulation of mature colonies containing a large number of cells. For this reason, MICRODIMS has been ported to the TransProg library, which uses modern general-purpose multicore and multiprocessor computers to their fullest potential. This transfer enables the simulation of mature colony dynamics in three dimensions. In this paper, the branched morphology of colonies growing on the surface of a food substrate is investigated. It is demonstrated that the emergence of this pattern is dependent on the thickness of the food substrate and structural heterogeneities at the food surface

Beitrag zur Physiologie des N. Vagus. I. Mitteilung : Uber die Funktion des N. vagus auf die Atmung

1) Der Gaswechsel und der Respirationsquotient des Einrecurrenskaninchens (Lungenvagusfreienkaninchens, vgl. II. Mitteilung) scheint fast keinen Unterschied im Vergleich mit den normalen und Kontrolltieren zu zeigen. Beim Versuch wurde der von Saeki (1931) am hiesigen Institut verbesserte Haldensche Apparat angewendet. Aus diesem Resultat gelangt der Verfasser zu dem Schluss, dass die Ausschaltung des Lungenvagus auf den Gaswechsel und den Respirationsquotienten fast keinen Einfluss ausubt. 2) Bei der Durchschneidungsmethode, die sicher den Lungenvagus auschaltet, tritt immer die typische Vagusatmung auf. 3) Was die Vagusatmung des Einrecurrenskaninchens nach der Operation betrifft, so kehrt wieder allmahlich im Verlauf der Zeit ersichtlich der normale Atmungszustand zuruck, aber durch eine leichte Storung, z. B. durch die Anlegung der Gasmaske, kann die typische Vagusatmung hervorgerufen werden. Um an wiedererholte Erhaltung des normalen Atmungszustandes nach der Ausschaltung des Lungenvagus zu denken, muss man voraussetzen, dass es anstatt des Lungenvagus noch einen anderen Regulations-mechanismus fur den normalen Atmungszustand geben; falls der Regulationsmechanismus durch eine leichte Storung gestort wird, tritt die Vagusatmung auf. Es ist sehr schwer zu denken, an welchem Ort und auf welche Weise die Regulation ausgeubt wird, aber der Verfasser vermutet, dass das Atemzentrum durch die centripetalen Impulse von uberangestrengtem Atemmuskel und Zwerchfell nach der Lungenvagusaus-schaltung wieder die regulatorische centrifugale Wirkung zum Atemmuskel und Zwerchfell sendet, wodurch der Regulationsmechanismus entsteht. 4) Die Abnahme der Atmungszahl nach der doppelseitigen Vagotomie am Halse kann nicht durch die Schafersche Glottislahmungstheorie oder Hymansche Aorten-Sinusnervenlahmungstheorie erklart werden, sondern durch die Ausschaltung des Lungen-vagus selbst. 5) Beim Einrecurrenskaninchen sieht man keine Apnoe beim Einblasen der Lunge. Es gilt als eine Bestatigung dafur, dass alle Vagusaste nach der Lunge

GASDS: A kinetic-based package for biomass and coal gasification

In this paper, a simulation package called GASDS is introduced. It is particularly suited to evaluate the pyrolysis, gasification and combustion of biomass and coal feedstocks. The aim of this work is to describe the package from a numerical point of view and its interface. Additionally, experimental results for a countercurrent fixed-bed biomass gasification reactor are reproduced. The influence of reactor and particle discretizations are investigated with respect to accuracy and computational time. Some differences are present between experimental and simulation results. In order to improve the agreement between simulation and experimental results it is suggested to improve the kinetic scheme of the solid phase and gas-solid reactions. The negligible differences in terms of predictions, instead, do not justify the adoption of finer discretizations for the particle and reactor, which imply longer computational times

Towards Online Model Predictive Control on a Programmable Logic Controller: Practical Considerations

Given the growing computational power of embedded controllers, the use of model predictive control (MPC) strategies on this type of devices becomes more and more attractive. This paper investigates the use of online MPC, in which at each step, an optimization problem is solved, on both a programmable automation controller (PAC) and a programmable logic controller (PLC). Three different optimization routines to solve the quadratic program were investigated with respect to their applicability on these devices. To this end, an air heating setup was built and selected as a small-scale multi-input single-output system. It turns out that the code generator (CVXGEN) is not suited for the PLC as the required programming language is not available and the programming concept with preallocated memory consumes too much memory. The Hildreth and qpOASES algorithms successfully controlled the setup running on the PLC hardware. Both algorithms perform similarly, although it takes more time to calculate a solution for qpOASES. However, if the problem size increases, it is expected that the high number of required iterations when the constraints are hit will cause the Hildreth algorithm to exceed the necessary time to present a solution. For this small heating problem under test, the Hildreth algorithm is selected as most useful on a PLC

Multi-objective dynamic optimisation of cyclic chemical reactors with distributed parameters

The dynamic optimisation and optimal control of innovative cyclic chemical processes are challenging because these problems involve apart from temporal periodicity constraints often also Partial Differential Equation (PDE) models and multiple objectives. To allow a fast and efficient generation of the Pareto set, this paper presents a deterministic approach that integrates accurate scalarisation methods for multi-objective optimisation as Normal Boundary Intersection (NBI) and (Enhanced) Normalised Normal Constraint (E)NNC, with a fast direct multiple shooting approach for optimal control. The feasibility of the proposed approach is presented for a reverse flow reactor involving conflicting conversion and energy objectives. In addition, advantages of the NBI and (E)NNC methods over the classic Weighted Sum of the individual objectives have been illustrated. © 2012 Elsevier Ltd.status: publishe

Novel insights for multi-objective optimisation in engineering using Normal Boundary Intersection and (Enhanced) Normalised Normal Constraint

Normal Boundary Intersection (NBI) and (Enhanced) Normalised Normal Constraint (E)NNC are attractive and popular approaches to generate an approximation of the Pareto set in nonlinear multi-objective optimisation problems. All three methods are based on similar ideas, but do not always yield identical results, which may confuse practitioners. Hence, the current paper provides theoretical insights in the conditions under which identical results are obtained. Typically, NBI and ENNC are able to generate the same candidate Pareto points, if all additional inequalities in the ENNC subproblem are active. In general, NBI and NNC do not return the same points when three or more objectives are considered. Equivalence relations between the resulting lagrange multipliers for the additional NBI and ENNC (in)equality constraints have been derived. Moreover, the obtained relations have lead to novel criteria for detecting non-Pareto optimal points that in adverse situations maybe generated by these methods. The major advantage is that the removal criteria do not rely on a time-consuming pairwise comparison but only need matrix multiplications. A Matlab implementation has been added for completeness. The insights are illustrated for a general nonlinear bi-objective and three-objective optimisation problem, and a dynamic three-objective tubular reactor optimisation problem from chemical engineering. Finally, practical guidelines are added. © Springer-Verlag 2011.status: publishe

Bi-objective optimization of dynamic systems by continuation methods

© 2016 Elsevier Ltd As a proof of concept the properties of path-following methods are studied for multi-objective optimization problems involving dynamic systems (also called multi-objective dynamic optimization or multi-objective optimal control problems), which have never been presented before. Two case studies with two objectives are considered to cover convex, as well as non-convex trade-off curves or Pareto sets. In order for the method to be applicable, the infinite dimensional dynamic problems have to be discretized and scalarization parameters have to be introduced, which leads to large-scale parametric nonlinear optimization problems. For both the chemical tubular reactor and the fed-batch bioreactor case study it is found that a path-following continuation approach is able to compute the Pareto fronts accurately and efficiently. A branch switching technique is required whenever a constraint switches from active to inactive or vice versa. When dealing with non-convex problems, a technique for detecting inflection points is required. Simple switching techniques are suggested and have been tested successfully.publisher: Elsevier articletitle: Bi-objective optimization of dynamic systems by continuation methods journaltitle: Computers & Chemical Engineering articlelink: http://dx.doi.org/10.1016/j.compchemeng.2016.11.025 content_type: article copyright: © 2016 Elsevier Ltd. All rights reserved.status: publishe

Dynamic estimation of specific fluxes in metabolic networks using non-linear dynamic optimization

BACKGROUND: Metabolic network models describing the biochemical reaction network and material fluxes inside microorganisms open interesting routes for the model-based optimization of bioprocesses. Dynamic metabolic flux analysis (dMFA) has lately been studied as an extension of regular metabolic flux analysis (MFA), rendering a dynamic view of the fluxes, also in non-stationary conditions. Recent dMFA implementations suffer from some drawbacks, though. More specifically, the fluxes are not estimated as specific fluxes, which are more biologically relevant. Also, the flux profiles are not smooth, and additional constraints like, e.g., irreversibility constraints on the fluxes, cannot be taken into account. Finally, in all previous methods, a basis for the null space of the stoichiometric matrix, i.e., which set of free fluxes is used, needs to be chosen. This choice is not trivial, and has a large influence on the resulting estimates. RESULTS: In this work, a new methodology based on a B-spline parameterization of the fluxes is presented. Because of the high degree of non-linearity due to this parameterization, an incremental knot insertion strategy has been devised, resulting in a sequence of non-linear dynamic optimization problems. These are solved using state-of-the-art dynamic optimization methods and tools, i.e., orthogonal collocation, an interior-point optimizer and automatic differentiation. Also, a procedure to choose an optimal basis for the null space of the stoichiometric matrix is described, discarding the need to make a choice beforehand. The proposed methodology is validated on two simulated case studies: (i) a small-scale network with 7 fluxes, to illustrate the operation of the algorithm, and (ii) a medium-scale network with 68 fluxes, to show the algorithm's capabilities for a realistic network. The results show an accurate correspondence to the reference fluxes used to simulate the measurements, both in a theoretically ideal setting with no experimental noise, and in a realistic noise setting. CONCLUSIONS: Because, apart from a metabolic reaction network and the measurements, no extra input needs to be given, the resulting algorithm is a systematic, integrated and accurate methodology for dynamic metabolic flux analysis that can be run online in real-time if necessary.status: publishe