Relevant bibliographies by topics / Cell behaviour modelling

Contents

  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers

Academic literature on the topic 'Cell behaviour modelling'

Author: Grafiati
Published: 4 June 2021
Last updated: 1 February 2022

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Journal articles on the topic "Cell behaviour modelling"

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C. Markham, Deborah, Ruth E. Baker, and Philip K. Maini. "Modelling collective cell behaviour." Discrete & Continuous Dynamical Systems - A 34, no. 12 (2014): 5123–33. http://dx.doi.org/10.3934/dcds.2014.34.5123.

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Schwarz, U. S., and I. B. Bischofs. "Modelling cell behaviour in compliant environments." Journal of Biomechanics 39 (January 2006): S397. http://dx.doi.org/10.1016/s0021-9290(06)84605-1.

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Vosniakos, George Christopher, Emmanuel Levedianos, and Xenofon V. Gogouvitis. "Streamlining virtual manufacturing cell modelling by behaviour modules." International Journal of Manufacturing Research 10, no. 1 (2015): 17. http://dx.doi.org/10.1504/ijmr.2015.067616.

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Song, Zhuoyi, Robert W. Banks, and Guy S. Bewick. "Modelling the mechanoreceptor's dynamic behaviour." Journal of Anatomy 227, no. 2 (June 25, 2015): 243–54. http://dx.doi.org/10.1111/joa.12328.

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Butler, George, Jonathan Rudge, and Philip R. Dash. "Mathematical modelling of cell migration." Essays in Biochemistry 63, no. 5 (October 2019): 631–37. http://dx.doi.org/10.1042/ebc20190020.

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Abstract The complexity of biological systems creates challenges for fully understanding their behaviour. This is particularly true for cell migration which requires the co-ordinated activity of hundreds of individual components within cells. Mathematical modelling can help understand these complex systems by breaking the system into discrete steps which can then be interrogated in silico. In this review, we highlight scenarios in cell migration where mathematical modelling can be applied and discuss what types of modelling are most suited. Almost any aspect of cell migration is amenable to mathematical modelling from the modelling of intracellular processes such as chemokine receptor signalling and actin filament branching to larger scale processes such as the movement of individual cells or populations of cells through their environment. Two common ways of approaching this modelling are the use of models based on differential equations or agent-based modelling. The application of both these approaches to cell migration are discussed with specific examples along with common software tools to facilitate the process for non-mathematicians. We also highlight the challenges of modelling cell migration and the need for rigorous experimental work to effectively parameterise a model.
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Bray, Dennis. "Cell biology: Computer modelling of the behaviour of actin gels." Nature 313, no. 6005 (February 1985): 738. http://dx.doi.org/10.1038/313738a0.

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Bown, James L., Michael A. Idowu, Hilal S. Khalil, Alexey Goltsov, Yusuf Deeni, Nikolai Zhelev, Simon P. Langdon, and David J. Harrison. "Process-based vs. data-driven modelling of cancer cell behaviour." Journal of Biotechnology 185 (September 2014): S13. http://dx.doi.org/10.1016/j.jbiotec.2014.07.048.

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Vassaux, M., and J. L. Milan. "Stem cell mechanical behaviour modelling: substrate’s curvature influence during adhesion." Biomechanics and Modeling in Mechanobiology 16, no. 4 (February 21, 2017): 1295–308. http://dx.doi.org/10.1007/s10237-017-0888-4.

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Bruce, David M. "Mathematical modelling of the cellular mechanics of plants." Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 358, no. 1437 (July 30, 2003): 1437–44. http://dx.doi.org/10.1098/rstb.2003.1337.

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The complex mechanical behaviour of plant tissues reflects the complexity of their structure and material properties. Modelling has been widely used in studies of how cell walls, single cells and tissue respond to loading, both externally applied loading and loads on the cell wall resulting from changes in the pressure within fluid–filled cells. This paper reviews what approaches have been taken to modelling and simulation of cell wall, cell and tissue mechanics, and to what extent models have been successful in predicting mechanical behaviour. Advances in understanding of cell wall ultrastructure and the control of cell growth present opportunities for modelling to clarify how growth–related mechanical properties arise from wall polymeric structure and biochemistry.
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Browning, Alexander P., Wang Jin, Michael J. Plank, and Matthew J. Simpson. "Identifying density-dependent interactions in collective cell behaviour." Journal of The Royal Society Interface 17, no. 165 (April 2020): 20200143. http://dx.doi.org/10.1098/rsif.2020.0143.

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Scratch assays are routinely used to study collective cell behaviour in vitro . Typical experimental protocols do not vary the initial density of cells, and typical mathematical modelling approaches describe cell motility and proliferation based on assumptions of linear diffusion and logistic growth. Jin et al. (Jin et al . 2016 J. Theor. Biol. 390 , 136–145 ( doi:10.1016/j.jtbi.2015.10.040 )) find that the behaviour of cells in scratch assays is density-dependent, and show that standard modelling approaches cannot simultaneously describe data initiated across a range of initial densities. To address this limitation, we calibrate an individual-based model to scratch assay data across a large range of initial densities. Our model allows proliferation, motility, and a direction bias to depend on interactions between neighbouring cells. By considering a hierarchy of models where we systematically and sequentially remove interactions, we perform model selection analysis to identify the minimum interactions required for the model to simultaneously describe data across all initial densities. The calibrated model is able to match the experimental data across all densities using a single parameter distribution, and captures details about the spatial structure of cells. Our results provide strong evidence to suggest that motility is density-dependent in these experiments. On the other hand, we do not see the effect of crowding on proliferation in these experiments. These results are significant as they are precisely the opposite of the assumptions in standard continuum models, such as the Fisher–Kolmogorov equation and its generalizations.
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Dissertations / Theses on the topic "Cell behaviour modelling"

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Zhang, Xiliang. "Modelling and identification of neutrophil cell dynamic behaviour." Thesis, University of Sheffield, 2016. http://etheses.whiterose.ac.uk/13828/.

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This thesis is focussed on the shape analysis and tracking of neutrophil cells to facilitate the understanding of their behaviour. Neutrophil, one of the important type of white blood cell, protects humans and animals from infections and inflammations. The underlying mechanism is believed to be that when inflammation happens, a changing chemotaxis field causes neutrophils to move to inflammatory sites. During this migration process, neutrophils also change shapes. For example, pseudopod protrusions are formed on the boundary in response to the local gradient of the chemotactic field. After inflammation resolution, some neutrophils go to "sleep" and some move back but what drives these mechanisms are still not fully understood. If the mechanisms were known, it would be helpful to accelerate or slow down the process of treating some diseases. The thesis attempts to provide a quantitative analysis based on time lapse microscopic images of in vivo zebrafish animal models. The underlying premise governing the analysis is to identify if cell states from their motion and shape. The thesis begins with cell centroid tracking and uses three common kinematic models commonly used in the target tracking literature. The interacting multiple model framework, which is underpinned by multiple Kalman filters, is used to determine probabilities of most likely model to explain the cell motility pattern. These different models are then compared to identify if the motion pattern (motility) can be attributed to different cell behaviours. This is then followed by cell shape tracking to characterise not only the cell shape but also to identify regions of protrusions. It addresses the problem of estimating the chemotactic field that acts to recruit neutrophil cells to the inflammation sites based only on observed cell tracks, without any direct measurement associated with the external cell environment. By assuming that the cell velocity is proportional to the local chemotactic gradient, a least squares method in combination with the Kalman filter, was used to estimate this field. Results on a set of real data show the estimated field. Cell shapes were modelled as B-spline parametric active contours. By casting the parametric active contour model in state space form, Kalman filter was employed to track the shapes. Shape tracking required solving the problem of cell boundary association between two time frames which required identification of correspondence points at cell boundaries. This required improvement to a nearest neighbour filter method to give continuity of the cell shapes of the same neutrophils across the different frames. Characterisation of cell shape was carried out by employing Fourier descriptors from which two features, magnitude of the highest descriptor and the magnitude of the lowest frequency, were chosen as proxy for associating cell shapes with cell states. These features for instance are associated with cell roundedness. Both tracking methods, cell centroid and shape tracking, are employed on the real data and results shown to demonstrate the effectiveness of the methods. This thesis makes the following novel contributions. Firstly, a new framework was established to solve the cell centroid and shape tracking towards characterising cell shape behaviour. Secondly, the nearest neighbourhood filter employed to solve the association problem was improved to solve the problem of neutrophil cells disappearing and reappearing in image frames. Thirdly, the low frequency Fourier descriptor, combined with other methodologies, was successfully implemented in detecting the modes of neutrophil behaviour. In addition, the chemotactic field was estimated by using the centroid velocities. Furthermore, the multiple model filter was used for behavioural mode detection of cells.
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Myerscough, Mary Ruth. "A chemotactic model of biological pattern formation." Thesis, University of Oxford, 1988. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.329983.

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Roberts, Suzanne. "Characterising the Behaviour of an Electromagnetic Levitation Cell using Numerical Modelling." Diss., University of Pretoria, 2016. http://hdl.handle.net/2263/61552.

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Experimental investigations of high temperature industrial processes, for example the melting and smelting processes taking place inside furnaces, are complicated by the high temperatures and the chemically reactive environment in which they take place. Fortunately, mathematical models can be used in conjunction with the limited experimental results that are available to gain insight into these high temperature processes. However, mathematical models of high temperature processes require high temperature material properties, which are difficult to measure experimentally since container materials are often unable to withstand high enough temperatures, and sample contamination often occurs. These difficulties can be overcome by employing containerless processing techniques such as electromagnetic levitation melting to allow for characterisation of high temperature material properties. Efficient design of electromagnetic levitation cells is challenging since the effects of changes in coil design, sample size and sample material on levitation force and sample temperature are not yet well understood. In this work a numerical model of the electromagnetic levitation cell is implemented and used to investigate the sensitivity of levitation cell operation to variations in coil design, sample material and sample size. Various levitation cell modelling methods in literature are reviewed and a suitable model is chosen, adapted for the current application, and implemented in Python. The finite volume electromagnetic component of the model is derived from Maxwell’s equations, while heat transfer is modelled using a lumped parameter energy balance based on the first law of thermodynamics. The implemented model is verified for a simple case with a known analytical solution, and validated against published experimental results. It is found that a calibrated model can successfully predict the lifting force inside the levitation cell, as well as the sample temperature at low coil currents. The validated model is used to characterise the operation of a levitation cell for a number of different sample materials and sample sizes, and for variations in coil geometry and coil current. The model can be used in this way to investigate a variety of cases and hence to support experimental levitation cell design. Based on model results, a number of operating procedure recommendations are also made.
Dissertation (MEng)--University of Pretoria, 2016.
Mechanical and Aeronautical Engineering
MEng
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Erben, Dan. "Analysis and modelling of immune cell behaviour in lymph nodes based on multi-photon imaging." Thesis, University of Glasgow, 2016. http://theses.gla.ac.uk/7285/.

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This thesis presents quantitative studies of T cell and dendritic cell (DC) behaviour in mouse lymph nodes (LNs) in the naive state and following immunisation. These processes are of importance and interest in basic immunology, and better understanding could improve both diagnostic capacity and therapeutic manipulations, potentially helping in producing more effective vaccines or developing treatments for autoimmune diseases. The problem is also interesting conceptually as it is relevant to other fields where 3D movement of objects is tracked with a discrete scanning interval. A general immunology introduction is presented in chapter 1. In chapter 2, I apply quantitative methods to multi-photon imaging data to measure how T cells and DCs are spatially arranged in LNs. This has been previously studied to describe differences between the naive and immunised state and as an indicator of the magnitude of the immune response in LNs, but previous analyses have been generally descriptive. The quantitative analysis shows that some of the previous conclusions may have been premature. In chapter 3, I use Bayesian state-space models to test some hypotheses about the mode of T cell search for DCs. A two-state mode of movement where T cells can be classified as either interacting to a DC or freely migrating is supported over a model where T cells would home in on DCs at distance through for example the action of chemokines. In chapter 4, I study whether T cell migration is linked to the geometric structure of the fibroblast reticular network (FRC). I find support for the hypothesis that the movement is constrained to the fibroblast reticular cell (FRC) network over an alternative 'random walk with persistence time' model where cells would move randomly, with a short-term persistence driven by a hypothetical T cell intrinsic 'clock'. I also present unexpected results on the FRC network geometry. Finally, a quantitative method is presented for addressing some measurement biases inherent to multi-photon imaging. In all three chapters, novel findings are made, and the methods developed have the potential for further use to address important problems in the field. In chapter 5, I present a summary and synthesis of results from chapters 3-4 and a more speculative discussion of these results and potential future directions.
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da, Silva Barbara Luisa. "Glioblastoma cell behaviour : a study of chemically-induced cellular connectivity and 3D modelling of cellular migration." Thesis, University of Leeds, 2018. http://etheses.whiterose.ac.uk/22479/.

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Glioblastoma multiforme (GBM) is the most common and deadliest brain cancer in adults. Despite considerable efforts at both bench and bedside, the average survival for GBM patients is only 14-15 months. This dismal prognosis stems from challenges in treatment and a malignant tumour biology. A key need in addressing GBM is to better understand and therapeutically target GBM cell invasion into the surrounding healthy brain tissue. Cytoskeletal remodelling and dynamics, mediated by ROCK effector proteins, play an important role in the ability of GBM cells to migrate. ROCK inhibition is being considered as potential cancer therapy; however, there is insufficient data examining a chemical pan-ROCK inhibition effect in the cellular context of GBM. I address this gap in the context of undifferentiated patient-derived brain tumour stem cell (BTSC) models. My results show that chemical ROCK pathway inhibition with several different compounds led to a reversible neurite-like outgrowth phenotype across three different patient-derived cell models. This phenotype was accompanied by a decrease in BTSCs motility, which enabled the cells to form an interactive multicellular network. Interestingly, ROCK inhibition did not alter the self-renewal ability or proliferation capacity of BTSCs. To further investigate this diffusive nature of GBM cells, I developed an in vitro 3D model that allows the study of GBM infiltration in real-time. My work demonstrates the ability of GBM spheres to spontaneously fuse with, and infiltrate, neural-like early-stage cerebral organoids (eCOs) with the use of stem cell culture-based organoid methodology. In addition, this 'hybrid' GBM tumour organoid possessed an invasive tumour compartment, which was specific to GBM cells. Thus, this self-assembly GBM tumour organoid may be used to identify anti-GBM invasion treatment approaches.
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Sahli, Mehdi. "Simulation and modelling of thermal and mechanical behaviour of silicon photovoltaic panels under nominal and real-time conditions." Thesis, Strasbourg, 2019. http://www.theses.fr/2019STRAD036.

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Le travail présenté dans cette thèse porte sur le développement d’un modèle multi-physique numérique, destiné à étudier le comportement optique, électrique et thermique d’un module photovoltaïque. Le comportement optique a été évalué en utilisant des chaines de Markov. Le comportement électrique est obtenu pour les panneaux en Silicium à l’aide d’une méthode d’optimisation numérique. Le comportement thermique est développé en 1D sur l’épaisseur du module, et le modèle multi-physique a été faiblement couplé sous MATLAB. Le comportement sous des conditions nominales d’opération a été validé en utilisant les données déclarées par les constructeurs. Ce modèle a été utilisé pour effectuer une étude paramétrique sur l’effet des irradiances solaires en régime permanent. Le modèle a été validé pour des conditions d’utilisations réelles en comparant avec des mesures expérimentales de température et de puissance électrique. Une étude thermomécanique en 2D sous ABAQUS/CAE et se basant sur le modèle multi-physique a été effectué en conditions nominales d’opération, ainsi qu’en cycle de fatigue selon la norme 61215 pour prédire les contraintes qui sont imposées sur le panneau dans les deux cas mentionnés précédemment
The work presented in this thesis deals with the development of a numerical multi-physics model, designed to study the optical, electrical and thermal behaviour of a photovoltaic module. The optical behaviour was evaluated using stochastic modelling based on Markov chains, whereas the electrical behaviour was drawn specifically for Silicon based photovoltaic panels using numerical optimization methods. The thermal behaviour was developed in 1D over the thickness of the module, and the multi-physics module was weakly coupled in MATLAB. The behaviour of commercial panels under nominal operation conditions was validated using data declared by the manufacturers. This model was used to perform a parametric study on the effect of solar irradiances in steady state. It was also validated for real use conditions by comparing it to experimental temperature and electrical power output. A thermomechanical study in 2D in ABAQUS/CAE based in the multi-physics model was carried out in nominal operating conditions, as well as in fatigue thermal cycling according to the IEC 61215 Standard to predict the stresses that are imposed on the panel
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Byrne, Philip. "Mathematical modelling and experimental simulation of chlorate and chlor-alkali cells." Doctoral thesis, Stockholm, 2001. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-3182.

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Gubner, Andreas. "Modelling of high temperature fuel cells : the thermal, chemical, electrochemical and fluidmechanical behaviour of solid oxide fuel cells operating with internal reforming of methane." Thesis, University of Portsmouth, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.336474.

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Since only little is known in the field of Solid Oxide Fuel Cell (SOFC) operation about internal reforming of methane at present, the aim of this thesis study is to conduct a detailed investigation delivering the basis for further experimental and theoretical work. Also information is required if the concept of internal reforming has technical development potential. The thesis is arranged into two major parts being a thermodynamic investigation and an application of a suitable kinetic model. Pure methane tends to decompose at the high operation temperatures of the SOFC (about 950°C) thus forming solid carbon. Therefore it is necessary to include a fuel preparation process delivering H2 and CO that can be utilized by the SOFC. The fuel processing can either be carried out by steam reforming or partial oxidation. It is shown by a thermodynamic investigation that fuel processing by partial oxidation yields a fuel gas of inferior quality than fuel processing by steam reforming. The kinetic part contains the application of a model describing the chemical and electrochemical conversion occuring in the SOFC as detailed as possible at present. This model is used to investigate the thermal behaviour of an SOFC process referring to technical operation parameters. It is shown that internal reforming has technical development potential although a lot of care must be paid to the heat management. Particular operation conditions might exist where the highly endothermic steam reforming process could cause a breakdown of the complete fuel cell process due to its enormous local cooling effect.
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Hamsa, Ahmed [Verfasser], Sascha [Akademischer Betreuer] Schäfer, and Carsten [Akademischer Betreuer] Agert. "Performance Optimization of Cu(In1-x,Gax)(Se1-y,Sy)2 Thin-Film Solar Cells by Characterization and Modelling of Temperature and Low-Light Behavior / Ahmed Hamsa ; Sascha Schäfer, Carsten Agert." Oldenburg : BIS der Universität Oldenburg, 2021. http://d-nb.info/1236691849/34.

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Mahesh, C. "Prediction Of The Mechanical Behaviour Of A Closed Cell Aluminium Foam Using Advanced Nonlinear Finite Element Modelling." Thesis, 2012. http://etd.iisc.ernet.in/handle/2005/2537.

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Cellular materials like aluminum foam which is the subject of interest here are generally characterized by high energy absorption capacity per unit weight. Materials of this category can be ideal for applications such as packaging and vehicle body structures for enhanced impact safety. A particularly well-known variety of closed-cell aluminum foam is designated as Alporas, which is studied here. From a viewpoint of mechanical behavior, the foam being considered can be represented using either a detailed cellular approach capturing the voids present in foam structure or a phenomenological approach in which experimental stress-strain response is assigned a-priori to solid elements filling up the space occupied by a foam geometry. Both modeling approaches are studied in the present work. It has been shown for the first time that stress-strain behavior under compression including densification can be predicted well with a Kelvin cell-based model, although scope for further improvement exists. Based on a novel combination of compression tests at low strain rates in a UTM and medium strain rates in low velocity impact tests, a relation between foam strength and strain rate has been proposed. This effect of strain rate on strength is captured in a finite element model for analysis using an explicit code with contact simulation capabilities and the predictions for projectile impact tests at higher strain rates using a gas gun-based device have been found to match commendably with results obtained from the said tests.
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Books on the topic "Cell behaviour modelling"

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Gubner, Andreas. Modelling of high temperature fuel cells: The thermal, chemical, electrochemical and fluidmechanical behaviour of solid oxide fuel cells operating with internal reforming of methane : a thesis. Portsmouth: University of Portsmouth, 1996.

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(Editor), T. Kumazawa, L. Kruger (Editor), and K. Mizumura (Editor), eds. The Polymodal Receptor - A Gateway to Pathological Pain (Progress in Brain Research). Elsevier Science, 1996.

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Takao, Kumazawa, Kruger Lawrence, and Mizumura Kazue, eds. The polymodal receptor: A gateway to pathological pain. Amsterdam: Elsevier, 1996.

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Book chapters on the topic "Cell behaviour modelling"

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Fortin, S., M. Gerhardt, and A. J. Gesing. "Physical Modelling of Bubble Behaviour and Gas Release from Aluminum Reduction Cell Anodes." In Essential Readings in Light Metals, 385–95. Hoboken, NJ, USA: John Wiley & Sons, Inc., 2013. http://dx.doi.org/10.1002/9781118647851.ch55.

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Fortin, S., M. Gerhardt, and A. J. Gesing. "Physical Modelling of Bubble Behaviour and Gas Release from Aluminum Reduction Cell Anodes." In Essential Readings in Light Metals, 385–95. Cham: Springer International Publishing, 2016. http://dx.doi.org/10.1007/978-3-319-48156-2_55.

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Crețu, M., L. Darabant, and A. Răcășan. "Modelling the Passive Behavior of the Nervous Cell. Influence of Electric Parameters Variation." In International Conference on Advancements of Medicine and Health Care through Technology; 12th - 15th October 2016, Cluj-Napoca, Romania, 159–64. Cham: Springer International Publishing, 2017. http://dx.doi.org/10.1007/978-3-319-52875-5_36.

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Louzazni, Mohamed, Ahmed Khouya, Khalid Amechnoue, Marco Mussetta, and Rachid Herbazi. "Analytical Modelling and Analysis of Thermal Behavior for Series Resistance of Solar Cell." In Advances in Intelligent Systems and Computing, 21–29. Cham: Springer International Publishing, 2019. http://dx.doi.org/10.1007/978-3-030-12065-8_3.

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Večeř, Jaroslav, and Petr Heřman. "Kinetic Behavior of Potential-Sensitive Fluorescent Redistribution Probes: Modelling of the Time Course of Cell Staining." In Fluorescence Microscopy and Fluorescent Probes, 145–49. Boston, MA: Springer US, 1996. http://dx.doi.org/10.1007/978-1-4899-1866-6_20.

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Joldes, Grand R., George C. Bourantas, Adam Wittek, Karol Miller, David W. Smith, and Bruce S. Gardiner. "A Discrete Element Method for Modelling Cell Mechanics: Application to the Simulation of Chondrocyte Behavior in the Growth Plate." In Computational Biomechanics for Medicine, 93–103. Cham: Springer International Publishing, 2018. http://dx.doi.org/10.1007/978-3-319-75589-2_9.

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Attia, M. S., S. A. Meguid, and K. M. Liew. "Multiscale modelling of crush behaviour of closed-cell aluminium foam." In Computational Fluid and Solid Mechanics 2003, 68–71. Elsevier, 2003. http://dx.doi.org/10.1016/b978-008044046-0.50018-x.

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Deepak, Gerard, Ayush Kumar, Santhanavijayan A., Pushpa C. N., Thriveni J., and Venugopal K. R. "Pedagogical Ontology Modelling for Cell Biology Domain With an Algorithm for Question Generation." In Machine Learning Approaches for Improvising Modern Learning Systems, 144–68. IGI Global, 2021. http://dx.doi.org/10.4018/978-1-7998-5009-0.ch006.

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In this chapter, an ontology that structures all the cell organelles and their parts are modelled to cognitively model domain knowledge by explicitly establishing relationships among them. The ontologies are modelled depicting the cell as a system and the parts of the cell as the subclasses of the cell along with various functionalities and behavior. The model further focuses on education pedagogy to generate questions based on the modelled ontologies. Furthermore, the defined ontologies are made consistent by defining the classes and the relationship between them, initializing the instances and axiomatizing the developed ontological content. The modelled ontologies are semiotically evaluated using various learners and domain experts. An overall reuse ratio of 0.91 has been achieved, and the proposed ontology has been differentiated from the existing cell ontologies by focusing on an educational pedagogy. Ultimately, an ontology-focused algorithm for multiple choice question generation has been proposed for cell biology as a domain of choice with an accuracy of 90.03%.
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Montagna, Sara, and Andrea Omicini. "Agent-Based Modelling in Multicellular Systems Biology." In Advances in Computational Intelligence and Robotics, 159–78. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1756-6.ch007.

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This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.
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Montagna, Sara, and Andrea Omicini. "Agent-Based Modelling in Multicellular Systems Biology." In Data Analytics in Medicine, 369–89. IGI Global, 2020. http://dx.doi.org/10.4018/978-1-7998-1204-3.ch020.

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This chapter aims at discussing the content of multi-agent based simulation (MABS) applied to computational biology i.e., to modelling and simulating biological systems by means of computational models, methodologies, and frameworks. In particular, the adoption of agent-based modelling (ABM) in the field of multicellular systems biology is explored, focussing on the challenging scenarios of developmental biology. After motivating why agent-based abstractions are critical in representing multicellular systems behaviour, MABS is discussed as the source of the most natural and appropriate mechanism for analysing the self-organising behaviour of systems of cells. As a case study, an application of MABS to the development of Drosophila Melanogaster is finally presented, which exploits the ALCHEMIST platform for agent-based simulation.
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Conference papers on the topic "Cell behaviour modelling"

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Wilson, Jim R., and Neil A. Duncan. "Modelling the Ion Channel Behaviour of Articular Chondrocytes." In ASME 2002 International Mechanical Engineering Congress and Exposition. ASMEDC, 2002. http://dx.doi.org/10.1115/imece2002-32661.

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All cells have a membrane potential; this voltage difference arises from the different intracellular and extracellular ion concentrations. In excitable tissue the cell membranes contain ion channels which control the movement of ions and hence control the cell’s membrane potential. Extensive measurements of the electrophysiology of excitable cells has allowed considerable understanding of the ion channels. The Hodgkin-Huxley model [1] was developed from measurements on a squid nerve axon, and it quantifies the changes in membrane conductance due to the opening and closing of specific ion channels. This model has been very successful in describing the electrical behaviour of neurons. Ion channels also exist in non-excitable tissue cells. Patch clamp experiments have demonstrated that ion channels in chondrocytes influence cell’s membrane potential [2]; controls the influx of Ca2+ [3] and may regulate cell proliferation [2]. The objective of this research was to develop a model of ion channel behaviour for connective tissue cells based on the Hodgkin-Huxley model, and to apply this model to reported patch clamp measurements of articular chondrocytes.
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Tholen, Christoph, Lars Nolle, and Oliver Zielinski. "On The Effect Of Neighborhood Schemes And Cell Shape On The Behaviour Of Cellular Automata Applied To The Simulation Of Submarine Groundwater Discharge." In 31st Conference on Modelling and Simulation. ECMS, 2017. http://dx.doi.org/10.7148/2017-0255.

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Rosli, M. I., M. Pourkashanian, D. B. Ingham, L. Ma, D. Borman, and M. S. Ismail. "Transparent PEM Fuel Cells for Direct Visualisation Experiments." In ASME 2009 7th International Conference on Fuel Cell Science, Engineering and Technology. ASMEDC, 2009. http://dx.doi.org/10.1115/fuelcell2009-85089.

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This paper reviews some of the previous research works on direct visualisation inside PEM fuel cells via a transparent single cell for the water behaviour investigation. Several papers which have employed the method have been selected and summarised and a comparison between the design of the cell, materials, methods and visual results are presented. The important aspects, advantages of the method and a summary on the previous work are discussed. Some initial work on transparent PEM fuel cell design using a single serpentine flow-field pattern is described. The results show that the direct visualisation via transparent PEM fuel cells could be one potential technique for investigating the water behavior inside the channels and a very promising way forward to provide useful data for validation in PEM fuel cell modelling and simulation.
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Caballero, L. J., A. Martinez, P. Sanchez-Friera, M. A. Vazquez, and J. Alonso. "Front grid design in industrial silicon solar cells: Modelling to evaluate the behaviour of three vs. two buses cell patterns." In 2008 33rd IEEE Photovolatic Specialists Conference (PVSC). IEEE, 2008. http://dx.doi.org/10.1109/pvsc.2008.4922435.

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Minutillo, Mariagiovanna, and Elio Jannelli. "Modelling and Testing a PEM Fuel Cell Fuelled by a Steam Reforming System." In ASME 2006 4th International Conference on Fuel Cell Science, Engineering and Technology. ASMEDC, 2006. http://dx.doi.org/10.1115/fuelcell2006-97151.

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In this paper the performance of a natural gas power system has been discussed. The power generation unit is composed by a fuel cell and a fuel processor integrated in a compact system. The hydrogen generator uses the steam reforming technology. A CO shift converter and a preferential oxidation reactor are used to minimize the CO concentration in the reformate gas. The hydrogen dilution in the reformate gas calls for a modification of the fuel cell feeding system. The dead-end mode is not practicable for the fuel cell operation, but it is necessary to open the anode flow channels. In order to increase the efficiency of the integrated system, the anode off gas mass flow is burned to supply heat for the reforming reaction. The fuel cell performance has been evaluated using the test bed of the University of Cassino. The experimental activity has been focused to evaluate the performance in different operating conditions. A semi-empirical model of the fuel cell has been employed to forecast the fuel cell behaviour with pure hydrogen and reformate gas feeding. The semi-empirical coefficients of the model have been fitted by using the experimental data. The target of the fuel cell modelling has been to develop a tool capable of predicting the performance in different operating conditions. The same tool can be used to identify the areas for design improvements.
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Schlüter, Dominik, Robert P. Grewe, Fabian Wartzek, Alexander Liefke, Jan Werner, Christian Kunkel, and Volker Gümmer. "Reduced-Order Modelling of Rotating Stall." In ASME Turbo Expo 2020: Turbomachinery Technical Conference and Exposition. American Society of Mechanical Engineers, 2020. http://dx.doi.org/10.1115/gt2020-14459.

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Abstract Rotating stall is a non-axisymmetric disturbance in axial compressors arising at operating conditions beyond the stability limit of a stage. Although well-known, its driving mechanisms determining the number of stall cells and their rotational speed are still marginally understood. Numerical studies applying full-wheel 3D unsteady RANS calculations require weeks per operating point. This paper quantifies the capability of a more feasible quasi-2D approach to reproduce 3D rotating stall and related sensitivities. The first part of the paper deals with the validation of a numerical baseline the simplified model is compared to in detail. Therefore, 3D computations of a state-of-the-art transonic compressor are conducted. At steady conditions the single-passage RANS CFD matches the experimental results within an error of 1% in total pressure ratio and mass flow rate. At stalled conditions, the full-wheel URANS computation shows the same spiketype disturbance as the experiment. However, the CFD underpredicts the stalling point by approximately 7% in mass flow rate. In deep stall, the computational model correctly forecasts a single-cell rotating stall. The stall cell differs by approximately 21% in rotational speed and 18% in circumferential size from the experimental findings. As the 3D model reflects the compressor behaviour sufficiently accurate, it is considered valid for physical investigations. In the second part of the paper, the validated baseline is reduced in radial direction to a quasi-2D domain only resembling the compressor tip area. Four model variations regarding span-wise location and extent are numerically investigated. As the most promising model matches the 3D flow conditions in the rotor tip region, it correctly yields a single-cell rotating stall. The cell differs by only 7% in circumferential size from the 3D results. Due to the impeded radial migration in the quasi-2D slice, however, the cell exhibits an increased axial extent. It is assumed, that the axial expansion into the adjacent rows causes the difference in cell speed by approximately 24%. Further validation of the reduced model against experimental findings reveals, that it correctly reflects the sensitivity of circumferential cell size to flow coefficient and individual cell speed to compressor shaft speed. As the approach reduced the wall clock time by 92%, it can be used to increase the physical understanding of rotating stall at much lower costs.
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Abu-Muharib, Andrew, Andrey P. Jivkov, Peter James, and John R. Yates. "Cleavage Fracture Modelling for RPV Steels: Discrete Model for Collective Behaviour of Micro-Cracks." In ASME 2013 Pressure Vessels and Piping Conference. American Society of Mechanical Engineers, 2013. http://dx.doi.org/10.1115/pvp2013-97431.

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The ability to predict variations in cleavage fracture toughness behaviour of ferritic RPV steels, accounting for the effects of irradiation and defect geometry, is vital to safety assessment and life extension decisions. Local approaches to cleavage fracture offer a promising methodology to accomplish such calculations. However, the limited progress achieved by improving the local failure probability expression suggests that the methodology for calculating global cleavage might not be adequately representing real material. The basis for the existing methodology is the weakest-link assumption that all individual failure events are independent and non-interacting. Here an approach is considered which utilises a microstructure-informed model incorporating the experimental knowledge needed to postulate deterministic criteria for particle rupture and micro-crack propagation, whilst accounting for the probabilistic distribution of particle sizes. This is then used in a lattice model that can help detail the evolution of the formation of micro-cracks on global failure, therefore inferring the suitability of the weakest-link assumption. Predicting the probability of cleavage fracture requires such models, as the macroscopic cleavage phenomenon is governed by a number of micro-structural features. The material microstructure is represented by a regular lattice of truncated octahedral cells forming a computational site-bond model, with sites located at the cell centres and connected by two distinct sets of bonds. These bonds are modelled with structural beam elements, which represent all the possible relative deformations between coordinated sites. Particles of various sizes are distributed in the bonds, based on an experimentally determined distribution of cleavage initiating particles in RPV steel (Euro Material A). Although only elastic deformations are considered here, the results demonstrate that the interactions between individual failure events could potentially have a strong effect on the way global failure is reached. Nucleation of micro-cracks by rupturing second-phase particles affects their subsequent formation. In particular, it was found that once formed there is a reduced probability of further development of micro-cracks at particles outside the crack planes and an enhanced probability of formation at particles along the crack planes. This will therefore influence the distribution of micro-crack sizes that could in principle be used to calculate the global probability of failure, and could lead to substantially different distributions of particle sizes, then used in the current local approach methods.
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Jelodarian, Peyman, and Abdolnabi Kosarian. "Modeling of the Effect of p-Layer and i-Layer Properties on the Electrical Behaviour of a-Si:H/a-SiGe:H Thin Film Hetero-Structure Solar Cell." In 2011 Third International Conference on Computational Intelligence, Modelling and Simulation (CIMSiM). IEEE, 2011. http://dx.doi.org/10.1109/cimsim.2011.81.

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Trasino, Francesco, Michele Bozzolo, Loredana Magistri, and Aristide F. Massardo. "Modelling and Performance Analysis of the Rolls-Royce Fuel Cell Systems Limited: 1 MW Plant." In ASME Turbo Expo 2009: Power for Land, Sea, and Air. ASMEDC, 2009. http://dx.doi.org/10.1115/gt2009-59328.

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This paper is focused on the performance of the 1MW plant designed and developed by Rolls-Royce Fuel Cell Systems Limited. The system consists of a two stage turbogenerator coupled with pressure vessels containing the fuel cell stack, internal reformer, cathode ejector, anode ejector and off gas burner. While the overall scheme is relatively simple, due to the limited number of components, the interaction between the components is complex and the system behaviour is determined by many parameters. In particular two important subsystems such as the cathode and the anode recycle loops must be carefully analyzed also considering their interaction with and influence on the turbogenerator performance. The system performance model represents the whole and each physical component is modelled in detail as a sub-system. The component models have been validated or are under verification. The model provides all the operating parameters in each characteristic point of the plant and a complete distribution of thermodynamics and chemical parameters inside the SOFC stack and reformer. In order to characterise the system behaviour, its operating envelope has been calculated taking into account the effect of ambient temperature and pressure as described in the paper. Given the complexity of the system various constraints have to be considered in order to obtain a safe operating condition not only for the system as a whole but also for each of its parts. In particular each point calculated has to comply with several constraints such as stack temperature distribution, maximum and minimum temperatures and high and low pressure spool maximum rotational speeds. The model developed and the results presented in the paper provide important information for the definition of an appropriate control strategy and a first step in the development of a robust and optimized control system.
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Hedjazi, Lotfi, Christophe L. Martin, Sofiane Guessasma, Guy Della Valle, and Rémy Dendievel. "Application of Discrete Element Simulation to the Crushing of a Food Biopolymer Foam for Mastication Modelling." In ASME 2012 11th Biennial Conference on Engineering Systems Design and Analysis. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/esda2012-82953.

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The fragmentation behaviour of brittle airy cereal foods is studied both numerically and experimentally. The food item is subjected to severe compression until densification stage. Experimental evidence of typical cellular material behaviour is pointed out by elasticity, cell collapse and densification regimes. Using an accurate description of the cellular structure determined by X-ray tomography, a numerical approach based on discrete element method is proposed in order to better explain the resulting fragmentation. The approach allows to reproduce the deformation stages and predicted results show good agreement with experimental mechanical responses, in terms of maximum force. Moreover, large size fragments are found to form as a consequence of small rupture events.
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