Journal articles: '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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Mina, Petros, Mario di Bernardo, Nigel J. Savery, and Krasimira Tsaneva-Atanasova. "Modelling emergence of oscillations in communicating bacteria: a structured approach from one to many cells." Journal of The Royal Society Interface 10, no. 78 (January 6, 2013): 20120612. http://dx.doi.org/10.1098/rsif.2012.0612.

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Population-level measurements of phenotypic behaviour in biological systems may not necessarily reflect individual cell behaviour. To assess qualitative changes in the behaviour of a single cell, when alone and when part of a community, we developed an agent-based model describing the metabolic states of a population of quorum-coupled cells. The modelling is motivated by published experimental work of a synthetic genetic regulatory network (GRN) used in Escherichia coli cells that exhibit oscillatory behaviour across the population. To decipher the mechanisms underlying oscillations in the system, we investigate the behaviour of the model via numerical simulation and bifurcation analysis. In particular, we study the effect of an increase in population size as well as the spatio-temporal behaviour of the model. Our results demonstrate that oscillations are possible only in the presence of a high concentration of the coupling chemical and are due to a time scale separation in key regulatory components of the system. The model suggests that the population establishes oscillatory behaviour as the system's preferred stable state. This is achieved via an effective increase in coupling across the population. We conclude that population effects in GRN design need to be taken into consideration and be part of the design process. This is important in planning intervention strategies or designing specific cell behaviours.

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Babtie, Ann C., and Michael P. H. Stumpf. "How to deal with parameters for whole-cell modelling." Journal of The Royal Society Interface 14, no. 133 (August 2017): 20170237. http://dx.doi.org/10.1098/rsif.2017.0237.

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Dynamical systems describing whole cells are on the verge of becoming a reality. But as models of reality, they are only useful if we have realistic parameters for the molecular reaction rates and cell physiological processes. There is currently no suitable framework to reliably estimate hundreds, let alone thousands, of reaction rate parameters. Here, we map out the relative weaknesses and promises of different approaches aimed at redressing this issue. While suitable procedures for estimation or inference of the whole (vast) set of parameters will, in all likelihood, remain elusive, some hope can be drawn from the fact that much of the cellular behaviour may be explained in terms of smaller sets of parameters. Identifying such parameter sets and assessing their behaviour is now becoming possible even for very large systems of equations, and we expect such methods to become central tools in the development and analysis of whole-cell models.

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Fanelli, Pierluigi, Andrea Evangelisti, Pietro Salvini, and Francesco Vivio. "Modelling and characterization of structural behaviour of Al open-cell foams." Materials & Design 114 (January 2017): 167–75. http://dx.doi.org/10.1016/j.matdes.2016.10.052.

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Borovinšek, M., and Z. Ren. "Computational modelling of irregular open-cell foam behaviour under impact loading." Materialwissenschaft und Werkstofftechnik 39, no. 2 (February 2008): 114–20. http://dx.doi.org/10.1002/mawe.200700270.

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Gerlee, P., and A. R. A. Anderson. "Modelling evolutionary cell behaviour using neural networks: Application to tumour growth." Biosystems 95, no. 2 (February 2009): 166–74. http://dx.doi.org/10.1016/j.biosystems.2008.10.007.

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Liu, Cheng Jun, Yi Xia Zhang, and Chun Hui Yang. "Representative Volume Element-Based Modelling of Closed-Cell Aluminum Foams ." Applied Mechanics and Materials 846 (July 2016): 530–34. http://dx.doi.org/10.4028/www.scientific.net/amm.846.530.

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This paper presents a representative volume element (RVE)-based modelling method to capture the mechanical behaviour of aluminum foams under compressive loadings. Octadecahedron is selected as a geometric basis shape to form closed cells of the aluminum foams in the microstructured RVE model to simulate the mechanical behaviour under compressive loadings. The stress-strain relationship obtained from the numerical modelling is compared to that from experimental study and agreements between these results demonstrate the validity of the proposed RVE model. Through observing the deformation evolution of cells during a compressive loading process, the failure modes of aluminum foams are identified and analysed using the proposed RVE model. Further the influence of strain rate on the mechanical behaviour of aluminum foams under compressive loadings is numerically studied via a parametric study.

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Neuhäuserová, Michaela, and Petr Koudelka. "NUMERICAL MODELLING OF COMPRESSIVE CHARACTERISTICS OF AUXETIC STRUCTURES." Acta Polytechnica CTU Proceedings 18 (October 23, 2018): 38. http://dx.doi.org/10.14311/app.2018.18.0038.

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The paper is focused on numerical analysis of mechanical behaviour of auxetic structures with re-entrant tetrakaidecahedral unit cell subjected to uni-axial quasi-static compression. The mechanical behaviour was evaluated inversely with respect to selected geometrical parameters of the unit cell and two different loading modes. Finite element method was used for the numerical analysis of the problem. A set of fully parametric tools has been developed, which enabled automated execution and evaluation of virtual experiments. From results of the simulations, Young’s modulus, the characteristics of the Poisson’s ratio function, and the deformation energy density were estimated. The relation between these characteristics and geometry of the unit cell, particularly the re-entrant angle and the relative density, was evaluated. Results of the numerical simulations for the unit cell and representative volume element of its three-dimensional periodic assembly are presented.

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Qiu, Xiu Mei, and Han Bing Bian. "Numerical Modelling of the THM Behaviour of Underground Radioactive Waste Storages Cell." Advanced Materials Research 378-379 (October 2011): 187–90. http://dx.doi.org/10.4028/www.scientific.net/amr.378-379.187.

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In this paper, a storage cell for the high level radioactive wastes is studied in order to identify and demonstrate the coupled phenomena evolving in the high level radioactive wastes (HLW) storage. According to the various important processes in the storage structures, special attention is paid on the coupling elastoplastic and viscoplastic damage processes in short and long term. In the calculations, the complicated thermo-hydro-mechanical coupling process has been taken into consideration. These numerical calculations allow us to obtain some quantitative results describing the mechanical behaviour and coupling thermo-hydro-mechanical processes for a short-and long-term in the storage cell.

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Vengatachalam, B., L. H. Poh, Z. S. Liu, Q. H. Qin, and S. Swaddiwudhipong. "Three dimensional modelling of closed-cell aluminium foams with predictive macroscopic behaviour." Mechanics of Materials 136 (September 2019): 103067. http://dx.doi.org/10.1016/j.mechmat.2019.103067.

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Abdullah, Khalaf Al, and Bashar Bakour. "Modelling of the Behaviour of Solar Cell Under High Injection Effect Conditions." Energy Procedia 19 (2012): 15–22. http://dx.doi.org/10.1016/j.egypro.2012.05.177.

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Jebur, Qusai Hatem, Philip Harrrison, Zao Yang Guo, Gerlind Schubert, and Vincent Navez. "Characterisation and Modelling of a Melt-Extruded LDPE Closed Cell Foam." Applied Mechanics and Materials 70 (August 2011): 105–10. http://dx.doi.org/10.4028/www.scientific.net/amm.70.105.

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This paper describes uniaxial compression tests on a melt-extruded closed-cell Low-Density Polyethylene (LDPE) foam. The stress-strain response shows the mechanical behaviour of the foam is predominantly transversely isotropic viscoelastic and compressible. Images analysis is used to estimate the Poisson’s ratio under large strains. When the deformation is less than 5 percent, the kinematics and mechanical response of the polymer foam can be well-described by a linear compressible transversely isotropic elastic model. For large strain, a method of manipulating experimental data obtained from testing in the principal and transverse directions (stress vs strain and Poisson’s ratio) in order to estimate the uniaxial compression response of the foam at any arbitrary orientation is proposed. An isotropic compressible hyperfoam model is then used to implement this behaviour in a finite element code.

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Nitoi, Dan, Florin Samer, Constantin Gheorghe Opran, and Constantin Petriceanu. "Finite Element Modelling of Thermal Behaviour of Solar Cells." Materials Science Forum 957 (June 2019): 493–502. http://dx.doi.org/10.4028/www.scientific.net/msf.957.493.

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Engineering Science Based on Modelling and Simulation (M & S) is defined as the discipline that provides the scientific and mathematical basis for simulation of engineering systems. These systems range from microelectronic devices to automobiles, aircraft, and even oilfield and city infrastructure. In a word, M & S combines knowledge and techniques in the fields of traditional engineering - electrical, mechanical, civil, chemical, aerospace, nuclear, biomedical and materials science - with the knowledge and techniques of fields such as computer science, mathematics and physics, and social sciences. One of the problems that arise during solar cell operation is that of heating them because of permanent solar radiation. Since the layers of which they are made are very small and thick it is almost impossible to experimentally determine the temperature in each layer. In this sense, the finite element method comes and provides a very good prediction and gives results impossible to obtain by other methods. This article models and then simulates the thermal composition of two types of solar cells, one of them having an additional layer of silicon carbide that aims to lower the temperature in the lower layer, where the electronic components stick to degradable materials under the influence of heat.

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Deutsch, Andreas, Josué Manik Nava-Sedeño, Simon Syga, and Haralampos Hatzikirou. "BIO-LGCA: A cellular automaton modelling class for analysing collective cell migration." PLOS Computational Biology 17, no. 6 (June 15, 2021): e1009066. http://dx.doi.org/10.1371/journal.pcbi.1009066.

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Collective dynamics in multicellular systems such as biological organs and tissues plays a key role in biological development, regeneration, and pathological conditions. Collective tissue dynamics—understood as population behaviour arising from the interplay of the constituting discrete cells—can be studied with on- and off-lattice agent-based models. However, classical on-lattice agent-based models, also known as cellular automata, fail to replicate key aspects of collective migration, which is a central instance of collective behaviour in multicellular systems. To overcome drawbacks of classical on-lattice models, we introduce an on-lattice, agent-based modelling class for collective cell migration, which we call biological lattice-gas cellular automaton (BIO-LGCA). The BIO-LGCA is characterised by synchronous time updates, and the explicit consideration of individual cell velocities. While rules in classical cellular automata are typically chosen ad hoc, rules for cell-cell and cell-environment interactions in the BIO-LGCA can also be derived from experimental cell migration data or biophysical laws for individual cell migration. We introduce elementary BIO-LGCA models of fundamental cell interactions, which may be combined in a modular fashion to model complex multicellular phenomena. We exemplify the mathematical mean-field analysis of specific BIO-LGCA models, which allows to explain collective behaviour. The first example predicts the formation of clusters in adhesively interacting cells. The second example is based on a novel BIO-LGCA combining adhesive interactions and alignment. For this model, our analysis clarifies the nature of the recently discovered invasion plasticity of breast cancer cells in heterogeneous environments.

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Jacques, Nicolas, and Romain Barthélémy. "Modelling of the behaviour of metal foams under shock compression." EPJ Web of Conferences 183 (2018): 01041. http://dx.doi.org/10.1051/epjconf/201818301041.

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A theoretical modelling is proposed to describe the shock response of foam materials. This model is based on micromechanical and energetic arguments, and takes into account the contribution of microscale inertia. Within this framework, an analytical expression of the Hugoniot stress-strain curve is proposed for elastic-plastic cellular materials. The predictions derived from the proposed model are in excellent agreement with experimental data for open-cell aluminium foams. The case of viscoplastic foams is also considered.

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Dong, M., and S. Schmauder. "Transverse mechanical behaviour of fiber reinforced composites — FE modelling with embedded cell models." Computational Materials Science 5, no. 1-3 (February 1996): 53–66. http://dx.doi.org/10.1016/0927-0256(95)00058-5.

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Wynn, Michelle L., Paul M. Kulesa, and Santiago Schnell. "Computational modelling of cell chain migration reveals mechanisms that sustain follow-the-leader behaviour." Journal of The Royal Society Interface 9, no. 72 (January 4, 2012): 1576–88. http://dx.doi.org/10.1098/rsif.2011.0726.

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Follow-the-leader chain migration is a striking cell migratory behaviour observed during vertebrate development, adult neurogenesis and cancer metastasis. Although cell–cell contact and extracellular matrix (ECM) cues have been proposed to promote this phenomenon, mechanisms that underlie chain migration persistence remain unclear. Here, we developed a quantitative agent-based modelling framework to test mechanistic hypotheses of chain migration persistence. We defined chain migration and its persistence based on evidence from the highly migratory neural crest model system, where cells within a chain extend and retract filopodia in short-lived cell contacts and move together as a collective. In our agent-based simulations, we began with a set of agents arranged as a chain and systematically probed the influence of model parameters to identify factors critical to the maintenance of the chain migration pattern. We discovered that chain migration persistence requires a high degree of directional bias in both lead and follower cells towards the target. Chain migration persistence was also promoted when lead cells maintained cell contact with followers, but not vice-versa. Finally, providing a path of least resistance in the ECM was not sufficient alone to drive chain persistence. Our results indicate that chain migration persistence depends on the interplay of directional cell movement and biased cell–cell contact.

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KING, J. R., and J. M. OLIVER. "Thin-film modelling of poroviscous free surface flows." European Journal of Applied Mathematics 16, no. 4 (August 2005): 519–53. http://dx.doi.org/10.1017/s095679250500584x.

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Thin-film models for the flow of a low reduced-Reynolds-number poroviscous droplet over a planar substrate are developed. One of the formulations is used to develop a minimal model for active animal cell motion in which the microscopic mechanisms of polymerisation and depolymerisation near the outer cell periphery are modelled by specifying the rate of mass transfer between the phases at the contact-line in terms of the velocity of the latter. An asymptotic analysis in the limit corresponding to strong cell-substrate adhesion is shown to lead to a novel class of multi-valued contact-line laws, a qualitative analysis of which leads in two dimensions to some intriguing behaviour, including (i) periodic contraction and expansion (pulsation), (ii) steady propagation at a contant speed, (iii) an unsteady combination of pulsation and propagation, and (iv) a bistable regime in which both non-motile and motile solutions are admissible, each of them being stable to sufficiently small perturbations, but with sufficiently large perturbations being able to ‘prod’ a stationary cell into motion or halt a moving one; these qualitative predictions are where possible compared with experiment. The contact-line behaviour is likely to be highly sensitive to environmental signals; the formulation may, therefore, provide a useful ‘minimal’ modelling framework for investigation of chemotactic effects at the cell scale. The corresponding extensional flow formulations are also noted.

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Rampino, Celestino, Claudio Mancuso, and Filippo Vinale. "Experimental behaviour and modelling of an unsaturated compacted soil." Canadian Geotechnical Journal 37, no. 4 (August 1, 2000): 748–63. http://dx.doi.org/10.1139/t00-004.

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This paper reports the experimental study and modelling of the mechanical response of a silty sand used in the core of the Metramo dam, Italy. Specimens were prepared by compacting the soil at optimum water content conditions using the modified Proctor technique. Tests were performed under suction-controlled conditions by a stress path triaxial cell and an oedometer. The experimental program consists of 23 tests carried out in the suction range of 0-400 kPa. The findings indicate the strong influence of suction on compressibility, stiffness, and shear strength. The mechanical properties of the soil improve with suction following an exponential law with decreasing gradient. Furthermore, the soil exhibited collapsible behaviour upon wetting even at low stress levels. Interesting results were also achieved in elastoplastic modelling as well. The results led to characterization of soil behaviour with reference to widely accepted modelling criteria for unsaturated soils, providing noteworthy suggestions about their applicability for granular materials with a non-negligible fine component. Finally, some remarks are made for the extension under unsaturated conditions of the "Nor sand" model for saturated granular soils. The proposed approach yields improved predictions of deviator soil response of the tested soil when Cambridge-type frameworks prove invalid.Key words: unsaturated soils, stress state variables, triaxial tests, oedometer tests, constitutive model.

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Brockwell, Peter J. "Stochastic models in cell kinetics." Journal of Applied Probability 25, A (1988): 91–111. http://dx.doi.org/10.2307/3214149.

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We discuss the role of stochastic processes in modelling the life-cycle of a biological cell and the growth of cell populations. Results for multiphase age-dependent branching processes have proved invaluable for the interpretation of many of the basic experimental studies of the life-cycle. Moreover problems from cell kinetics, in particular those related to diurnal rhythm in cell-growth, have stimulated research into ‘periodic' renewal theory, and the asymptotic behaviour of populations of cells with periodic death rate.

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Brockwell, Peter J. "Stochastic models in cell kinetics." Journal of Applied Probability 25, A (1988): 91–111. http://dx.doi.org/10.1017/s0021900200040286.

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We discuss the role of stochastic processes in modelling the life-cycle of a biological cell and the growth of cell populations. Results for multiphase age-dependent branching processes have proved invaluable for the interpretation of many of the basic experimental studies of the life-cycle. Moreover problems from cell kinetics, in particular those related to diurnal rhythm in cell-growth, have stimulated research into ‘periodic' renewal theory, and the asymptotic behaviour of populations of cells with periodic death rate.

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Jiang, Janna, and Per Nylén. "Numerical Modelling of the Compression Behaviour of Single-Crystalline MAX-Phase Materials." Advanced Materials Research 89-91 (January 2010): 262–67. http://dx.doi.org/10.4028/www.scientific.net/amr.89-91.262.

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In this article a numerical model to describe the mechanical behaviour of nanophased singlecrystalline Ti3SiC2 is proposed. The approach is a two dimensional finite element periodic unit cell consisting of an elastic matrix interlayered with shear deformable slip planes which obey the Hill’s yield criterion. The periodic unit cell is used to predict compression material behaviour of Ti3SiC2 crystals with arbitrary slip plane orientations. Stress strain relationships are derived for Ti3SiC2, and the effect of slip plane volume fraction as well as orientation of the slip planes are investigated. The two main deformation mechanisms of the material namely; ordinary slip and so called kinking are considered in the study.

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Reder, Christine. "Transient behaviour of a Galton–Watson process with a large number of types." Journal of Applied Probability 40, no. 04 (December 2003): 1007–30. http://dx.doi.org/10.1017/s002190020002026x.

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Modelling the distribution of mutations of mitochondrial DNA in exponentially growing cell cultures leads to the study of a multitype Galton–Watson process during its transient phase. The number of types corresponds to the number of mtDNA per cell and may be considered as large. By taking advantage of this fact we prove that the stochastic process is deterministic-like on the set of nonextinction. On this set almost all trajectories are well approximated by the unique solution of a partial differential problem. This result allows also the comparison of trajectories corresponding to different modelling assumptions, for instance different values of the number of types.

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Reder, Christine. "Transient behaviour of a Galton–Watson process with a large number of types." Journal of Applied Probability 40, no. 4 (September 2003): 1007–30. http://dx.doi.org/10.1239/jap/1067436097.

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Modelling the distribution of mutations of mitochondrial DNA in exponentially growing cell cultures leads to the study of a multitype Galton–Watson process during its transient phase. The number of types corresponds to the number of mtDNA per cell and may be considered as large. By taking advantage of this fact we prove that the stochastic process is deterministic-like on the set of nonextinction. On this set almost all trajectories are well approximated by the unique solution of a partial differential problem. This result allows also the comparison of trajectories corresponding to different modelling assumptions, for instance different values of the number of types.

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Deutsch, Andreas, Peter Friedl, Luigi Preziosi, and Guy Theraulaz. "Multi-scale analysis and modelling of collective migration in biological systems." Philosophical Transactions of the Royal Society B: Biological Sciences 375, no. 1807 (July 27, 2020): 20190377. http://dx.doi.org/10.1098/rstb.2019.0377.

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Collective migration has become a paradigm for emergent behaviour in systems of moving and interacting individual units resulting in coherent motion. In biology, these units are cells or organisms. Collective cell migration is important in embryonic development, where it underlies tissue and organ formation, as well as pathological processes, such as cancer invasion and metastasis. In animal groups, collective movements may enhance individuals' decisions and facilitate navigation through complex environments and access to food resources. Mathematical models can extract unifying principles behind the diverse manifestations of collective migration. In biology, with a few exceptions, collective migration typically occurs at a ‘mesoscopic scale’ where the number of units ranges from only a few dozen to a few thousands, in contrast to the large systems treated by statistical mechanics. Recent developments in multi-scale analysis have allowed linkage of mesoscopic to micro- and macroscopic scales, and for different biological systems. The articles in this theme issue on ‘Multi-scale analysis and modelling of collective migration’ compile a range of mathematical modelling ideas and multi-scale methods for the analysis of collective migration. These approaches (i) uncover new unifying organization principles of collective behaviour, (ii) shed light on the transition from single to collective migration, and (iii) allow us to define similarities and differences of collective behaviour in groups of cells and organisms. As a common theme, self-organized collective migration is the result of ecological and evolutionary constraints both at the cell and organismic levels. Thereby, the rules governing physiological collective behaviours also underlie pathological processes, albeit with different upstream inputs and consequences for the group. This article is part of the theme issue ‘Multi-scale analysis and modelling of collective migration in biological systems’.

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Wiggert, Jerry D., Eileen E. Hofmann, and Gustav-Adolf Paffenhöfer. "A modelling study of developmental stage and environmental variability effects on copepod foraging." ICES Journal of Marine Science 65, no. 3 (February 25, 2008): 379–98. http://dx.doi.org/10.1093/icesjms/fsm193.

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Abstract Wiggert, J. D., Hofmann, E. E., and Paffenhöfer, G-A. 2008. A modelling study of developmental stage and environmental variability effects on copepod foraging. – ICES Journal of Marine Science, 65: 379–398. We used a stochastic Lagrangian model to study how behaviour contributes to copepod grazing success. The model simulates distinct foraging behaviours of Clausocalanus furcatus, Paracalanus aculeatus, and Oithona plumifera. Three sets of simulations were performed to investigate the effects of (a) prey-size preference; (b) variation in prey-size spectra; and (c) turbulence intensity on these species’ grazing rates. The size preference simulations demonstrate that, compared with copepodites, mature females have cell ingestion rates that are an order of magnitude lower, while carbon uptake is reduced by 35%. A prey spectrum that is skewed towards cells <6 µm promotes copepodite success because the basal metabolic needs of the adult females require a prey concentration of 850–1000 cells ml−1. Variations in turbulence intensity reveal distinct ecological niches, with stronger mixing favouring O. plumifera and stable conditions favouring C. furcatus. Differences in theoretically derived and simulated prey-encounter rates demonstrate that the hopping behaviour of O. plumifera provides an order of magnitude increase in prey encounter, whereas the feeding behaviour of C. furcatus can result in localized depletion of prey. These simulations highlight the importance of species-specific feeding behaviour in defining oceanic copepod distributions.

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Koubaâ, Karama, and Moez Feki. "Discrete-time modelling and behaviour analysis of an N-cell DC/DC buck converter." International Journal of Engineering Systems Modelling and Simulation 8, no. 1 (2016): 54. http://dx.doi.org/10.1504/ijesms.2016.073319.

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Mai, Vinh Q., and Martin Meere. "Modelling the Phosphorylation of Glucose by Human hexokinase I." Mathematics 9, no. 18 (September 18, 2021): 2315. http://dx.doi.org/10.3390/math9182315.

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In this paper, we develop a comprehensive mathematical model to describe the phosphorylation of glucose by the enzyme hexokinase I. Glucose phosphorylation is the first step of the glycolytic pathway, and as such, it is carefully regulated in cells. Hexokinase I phosphorylates glucose to produce glucose-6-phosphate, and the cell regulates the phosphorylation rate by inhibiting the action of this enzyme. The cell uses three inhibitory processes to regulate the enzyme: an allosteric product inhibitory process, a competitive product inhibitory process, and a competitive inhibitory process. Surprisingly, the cellular regulation of hexokinase I is not yet fully resolved, and so, in this study, we developed a detailed mathematical model to help unpack the behaviour. Numerical simulations of the model produced results that were consistent with the experimentally determined behaviour of hexokinase I. In addition, the simulations provided biological insights into the abstruse enzymatic behaviour, such as the dependence of the phosphorylation rate on the concentration of inorganic phosphate or the concentration of the product glucose-6-phosphate. A global sensitivity analysis of the model was implemented to help identify the key mechanisms of hexokinase I regulation. The sensitivity analysis also enabled the development of a simpler model that produced an output that was very close to that of the full model. Finally, the potential utility of the model in assisting experimental studies is briefly indicated.

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Binder, Benjamin J., and Matthew J. Simpson. "Cell density and cell size dynamics during in vitro tissue growth experiments: Implications for mathematical models of collective cell behaviour." Applied Mathematical Modelling 40, no. 4 (February 2016): 3438–46. http://dx.doi.org/10.1016/j.apm.2015.01.016.

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Nadell, Carey D., Vanni Bucci, Knut Drescher, Simon A. Levin, Bonnie L. Bassler, and João B. Xavier. "Cutting through the complexity of cell collectives." Proceedings of the Royal Society B: Biological Sciences 280, no. 1755 (March 22, 2013): 20122770. http://dx.doi.org/10.1098/rspb.2012.2770.

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Via strength in numbers, groups of cells can influence their environments in ways that individual cells cannot. Large-scale structural patterns and collective functions underpinning virulence, tumour growth and bacterial biofilm formation are emergent properties of coupled physical and biological processes within cell groups. Owing to the abundance of factors influencing cell group behaviour, deriving general principles about them is a daunting challenge. We argue that combining mechanistic theory with theoretical ecology and evolution provides a key strategy for clarifying how cell groups form, how they change in composition over time, and how they interact with their environments. Here, we review concepts that are critical for dissecting the complexity of cell collectives, including dimensionless parameter groups, individual-based modelling and evolutionary theory. We then use this hybrid modelling approach to provide an example analysis of the evolution of cooperative enzyme secretion in bacterial biofilms.

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Kulkarni, Shraddha Suhas, Filip Vysoudil, and Thomas Vietor. "Evaluation of Modelling and Simulation Strategies to Investigate the Mechanical Integrity of a Battery Cell Using Finite Element Methods." Energies 14, no. 11 (May 21, 2021): 2976. http://dx.doi.org/10.3390/en14112976.

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The mechanical integrity of a lithium ion battery cell can be evaluated using finite element (FE) simulation techniques. In this study, different FE modelling approaches including heterogeneous, homogeneous, hybrid and sandwich methods are presented and analysed. The basic capabilities of the FE-methods and their suitability to simulate a real mechanical safety test procedures on battery cells are investigated by performing a simulation of a spherical indentation test on a sample pouch cell. For each modelling approach, one battery cell model was created. In order to observe the system behaviour, relevant parametric studies involving coefficient of friction and failure strain of separator were performed. This studied showed that these parameters can influence the maximum force and the point of failure of the cell. Furthermore, the influence of an anisotropic separator on the results was also investigated. The advantages and disadvantages of each modelling approach are discussed and a simplified approach with a partial cell modelling is suggested to further reduce the simulation time and complexity.

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Mullen, C. A., T. J. Vaughan, M. C. Voisin, M. A. Brennan, P. Layrolle, and L. M. McNamara. "Cell morphology and focal adhesion location alters internal cell stress." Journal of The Royal Society Interface 11, no. 101 (December 6, 2014): 20140885. http://dx.doi.org/10.1098/rsif.2014.0885.

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Extracellular mechanical cues have been shown to have a profound effect on osteogenic cell behaviour. However, it is not known precisely how these cues alter intracellular mechanics to initiate changes in cell behaviour. In this study, a combination of in vitro culture of MC3T3-E1 cells and finite-element modelling was used to investigate the effects of passive differences in substrate stiffness on intracellular mechanics. Cells on collagen-based substrates were classified based on the presence of cell processes and the dimensions of various cellular features were quantified. Focal adhesion (FA) density was quantified from immunohistochemical staining, while cell and substrate stiffnesses were measured using a live-cell atomic force microscope. Computational models of cell morphologies were developed using an applied contraction of the cell body to simulate active cell contraction. The results showed that FA density is directly related to cell morphology, while the effect of substrate stiffness on internal cell tension was modulated by both cell morphology and FA density, as investigated by varying the number of adhesion sites present in each morphological model. We propose that the cells desire to achieve a homeostatic stress state may play a role in osteogenic cell differentiation in response to extracellular mechanical cues.

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Ziebell, Frederik, Ana Martin-Villalba, and Anna Marciniak-Czochra. "Mathematical modelling of adult hippocampal neurogenesis: effects of altered stem cell dynamics on cell counts and bromodeoxyuridine-labelled cells." Journal of The Royal Society Interface 11, no. 94 (May 6, 2014): 20140144. http://dx.doi.org/10.1098/rsif.2014.0144.

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In the adult hippocampus, neurogenesis—the process of generating mature granule cells from adult neural stem cells—occurs throughout the entire lifetime. In order to investigate the involved regulatory mechanisms, knockout (KO) experiments, which modify the dynamic behaviour of this process, were conducted in the past. Evaluating these KOs is a non-trivial task owing to the complicated nature of the hippocampal neurogenic niche. In this study, we model neurogenesis as a multicompartmental system of ordinary differential equations based on experimental data. To analyse the results of KO experiments, we investigate how changes of cell properties, reflected by model parameters, influence the dynamics of cell counts and of the experimentally observed counts of cells labelled by the cell division marker bromodeoxyuridine (BrdU). We find that changing cell proliferation rates or the fraction of self-renewal, reflecting the balance between symmetric and asymmetric cell divisions, may result in multiple time phases in the response of the system, such as an initial increase in cell counts followed by a decrease. Furthermore, these phases may be qualitatively different in cells at different differentiation stages and even between mitotically labelled cells and all cells existing in the system.

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Liberman, Asaf, Matan Mussel, Danny Kario, David Sprinzak, and Uri Nevo. "Modelling cell surface dynamics and cell–cell interactions using Cell Studio: a three-dimensional visualization tool based on gaming technology." Journal of The Royal Society Interface 16, no. 160 (November 2019): 20190264. http://dx.doi.org/10.1098/rsif.2019.0264.

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Predictive modelling of complex biological systems and biophysical interactions requires the inclusion of multiple nano- and micro-scale events. In many scenarios, however, numerical solutions alone do not necessarily enhance the understanding of the system. Instead, this work explores the use of an agent-based model with visualization capabilities to elucidate interactions between single cells. We present a model of juxtacrine signalling, using Cell Studio, an agent-based modelling system, based on gaming and three-dimensional visualization tools. The main advantages of the system are its ability to apply any cell geometry and to dynamically visualize the diffusion and interactions of the molecules within the cells in real time. These provide an excellent tool for obtaining insight about different biological scenarios, as the user may view the dynamics of a system and observe its emergent behaviour as it unfolds. The agent-based model was validated against the results of a mean-field model of Notch receptors and ligands in two neighbouring cells. The conversion to an agent-based model is described in detail. To demonstrate the advantages of the model, we further created a filopodium-mediated signalling model. Our model revealed that diffusion and endocytosis alone are insufficient to produce significant signalling in a filopodia scenario. This is due to the bottleneck at the cell–filopodium contact region and the long distance to the end of the filopodium. However, allowing active transport of ligands into filopodia enhances the signalling significantly compared with a face-to-face scenario. We conclude that the agent-based approach can provide insights into mechanisms underlying cell signalling. The open-source model can be found in the Internet hosting service GitHub.

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Gleeson, Padraig, David Lung, Radu Grosu, Ramin Hasani, and Stephen D. Larson. "c302: a multiscale framework for modelling the nervous system of Caenorhabditis elegans." Philosophical Transactions of the Royal Society B: Biological Sciences 373, no. 1758 (September 10, 2018): 20170379. http://dx.doi.org/10.1098/rstb.2017.0379.

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The OpenWorm project has the ambitious goal of producing a highly detailed in silico model of the nematode Caenorhabditis elegans . A crucial part of this work will be a model of the nervous system encompassing all known cell types and connections. The appropriate level of biophysical detail required in the neuronal model to reproduce observed high-level behaviours in the worm has yet to be determined. For this reason, we have developed a framework, c302, that allows different instances of neuronal networks to be generated incorporating varying levels of anatomical and physiological detail, which can be investigated and refined independently or linked to other tools developed in the OpenWorm modelling toolchain. This article is part of a discussion meeting issue ‘Connectome to behaviour: modelling C. elegans at cellular resolution’.

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Sharifi Asl, S. M., S. Rowshanzamir, and M. H. Eikani. "Modelling and simulation of the steady-state and dynamic behaviour of a PEM fuel cell." Energy 35, no. 4 (April 2010): 1633–46. http://dx.doi.org/10.1016/j.energy.2009.12.010.

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Mefti, Nacim, Bernard Haussy, and Jean François Ganghoffer. "Modelling of the behaviour of the cell–wall interface during the rolling of a single cell: a probabilistic approach." Comptes Rendus Mécanique 334, no. 4 (April 2006): 230–37. http://dx.doi.org/10.1016/j.crme.2006.02.008.

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Gao, Xiaoping, and Liping Wang. "Finite Element Modelling for Tensile Behaviour of Thermally Bonded Nonwoven Fabric." Autex Research Journal 15, no. 1 (March 1, 2015): 48–53. http://dx.doi.org/10.2478/aut-2014-0035.

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Abstract A nonwoven fabric has been widely used in geotextile engineering in recent years; its tensile strength is an important behaviour. Since the fibre distributions in nonwoven fabrics are random and discontinuous, the unit-cell model of a nonwoven fabric cannot be developed to simulate its tensile behaviour. This article presents our research on using finite element method (FEM) to study the tensile behaviour of a nonwoven fabric in macro-scale based on the classical laminate composite theory. The laminate orientation was considered with orientation distribution function of fibres, which has been obtained by analysing the data acquired from scanning electron microscopy with Hough Transform. The FE model of a nonwoven fabric was developed using ABAQUS software; the required engineering constants of a nonwoven fabric were obtained from experimental data. Finally, the nonwoven specimens were stretched along with machine direction and cross direction. The experimental stress-strain curves were compared with the results of FE simulations. The approximate agreement proves the validity of an FE model, which could be used to precisely simulate the stress relaxation, strain creep, bending and shear property of a nonwoven fabric.

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Benary, Uwe, Elmar Wolf, and Jana Wolf. "Mathematical modelling of promoter occupancies in MYC-dependent gene regulation." Genomics and Computational Biology 3, no. 2 (January 12, 2017): 54. http://dx.doi.org/10.18547/gcb.2017.vol3.iss2.e54.

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The human MYC proto-oncogene protein (MYC) is a transcription factor that plays a major role in the regulation of cell proliferation. Deregulation of MYC expression is often found in cancer. In the last years, several hypotheses have been proposed to explain cell type specific MYC target gene expression patterns despite genome wide DNA binding of MYC. In a recent publication, a mathematical modelling approach in combination with experimental data demonstrated that differences in MYC-DNA-binding affinity are sufficient to explain distinct promoter occupancies and allow stratification of distinct MYC-regulated biological processes at different MYC concentrations. Here, we extend the analysis of the published mathematical model of DNA-binding behaviour of MYC to demonstrate that the insights gained in the investigation of the human osteosarcoma cell line U2OS can be generalized to other human cell types.

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Wiedmaier, Jing, Ulrich Weber, and Siegfried Schmauder. "Simulation of the Mechanical Behavior of Nanodispersed Elastomer Particle-Modified Polyamide 6." Advanced Materials Research 746 (August 2013): 250–55. http://dx.doi.org/10.4028/www.scientific.net/amr.746.250.

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In this work the nanodispersed elastomer copolymer particle-modified polyamide 6 (PA 6) is investigated. Micromechanical modelling is proposed to predict the mechanical behaviour of this material up to failure. A three-dimensional self-consistent embedded unit cell model is chosen which has been well applied for simulating the elastoplasticdeformation of this PA 6-composite [1,. This model will be here modified with the consideration of debonding between the elastomer particles and the PA 6-matrix. The predictions are in very good agreement with the experimental results. In terms of crash behavior, e.g. in the automotive industry the material behaviour under dynamic loading is also of particular interest. Impact strength is one of the most important parameters for describing this material behaviour. A full three-dimensional dynamic simulation of V-notched Charpy impact test is performed in ABAQUS/Explicit. The calculated impact strength coincides plausibly well with the experimental determination.

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Trinh, Mi Kieu, Matthew T. Wayland, and Sudhakaran Prabakaran. "Behavioural analysis of single-cell aneural ciliate, Stentor roeseli, using machine learning approaches." Journal of The Royal Society Interface 16, no. 161 (December 2019): 20190410. http://dx.doi.org/10.1098/rsif.2019.0410.

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There is still a significant gap between our understanding of neural circuits and the behaviours they compute—i.e. the computations performed by these neural networks (Carandini 2012 Nat. Neurosci. 15 , 507–509. ( doi:10.1038/nn.3043 )). Cellular decision-making processes, learning, behaviour and memory formation—all that have been only associated with animals with neural systems—have also been observed in many unicellular aneural organisms, namely Physarum , Paramecium and Stentor (Tang & Marshall2018 Curr. Biol. 28 , R1180–R1184. ( doi:10.1016/j.cub.2018.09.015 )). As these are fully functioning organisms, yet being unicellular, there is a much better chance to elucidate the detailed mechanisms underlying these learning processes in these organisms without the complications of highly interconnected neural circuits. An intriguing learning behaviour observed in Stentor roeseli (Jennings 1902 Am. J. Physiol. Legacy Content 8 , 23–60. ( doi:10.1152/ajplegacy.1902.8.1.23 )) when stimulated with carmine has left scientists puzzled for more than a century. So far, none of the existing learning paradigm can fully encapsulate this particular series of five characteristic avoidance reactions. Although we were able to observe all responses described in the literature and in a previous study (Dexter et al . 2019), they do not conform to any particular learning model. We then investigated whether models inferred from machine learning approaches, including decision tree, random forest and feed-forward artificial neural networks could infer and predict the behaviour of S. roeseli . Our results showed that an artificial neural network with multiple ‘computational’ neurons is inefficient at modelling the single-celled ciliate's avoidance reactions. This has highlighted the complexity of behaviours in aneural organisms. Additionally, this report will also discuss the significance of elucidating molecular details underlying learning and decision-making processes in these unicellular organisms, which could offer valuable insights that are applicable to higher animals.

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Journal articles on the topic 'Cell behaviour modelling'

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