| 1. |
- Scott, Jacob G, et al.
(författare)
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A filter-flow perspective of haematogenous metastasis offers a non-genetic paradigm for personalised cancer therapy
- 2014
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Ingår i: European Journal of Cancer. - : Elsevier BV. - 0959-8049. ; 50:17, s. 3068-3075
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Tidskriftsartikel (refereegranskat)abstract
- Research into mechanisms of haematogenous metastasis has largely become genetic in focus, attempting to understand the molecular basis of ‘seed–soil’ relationships. Preceding this biological mechanism is the physical process of dissemination of circulating tumour cells (CTCs) in the circulation. Patterns of metastatic spread have been previously quantified using the metastatic efficiency index, a measure quantifying metastatic incidence for a given primary-target organ pair and the relative blood flow between them. We extend this concept to take into account the reduction in CTCs which occurs in organ capillary beds connected by a realistic vascular network topology. Application to a dataset of metastatic incidence reveals that metastatic patterns depend strongly on assumptions about the existence and location of micrometastatic disease which governs CTC dynamics on the network, something which has heretofore not been considered – an oversight which precludes our ability to predict metastatic patterns in individual patients.
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| 2. |
- Anderson, Alexander, et al.
(författare)
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Evolution, regulation and disruption of homeostasis and its role in carcinogenesis
- 2010
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Ingår i: Multiscale Cancer Modeling. - : CRC Press. - 9781439814406 ; , s. 1-30
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Homeostasis is a critical property of living beings that involves the ability to self-regulate in response to changes in the environment in order to maintain a certain dynamic balance aecting form and/or function. Homeostasis is of particular importance in multicellular organisms, where it is intertwined with development [2,3]. Organisms have evolved intricate control mechanisms that ensure developmental processes achieve their end points and stabilize (e.g., dierentiate) as well as allow for a degree of adaptability to a range of conditions (e.g., stress or damage induced by wounding). is allows for the emergence of a more robust system that can tolerate both external and internal perturbations [4]. However, there are limitations to this tolerance, and oen it is the rare events that cause the most disruption [5]; think of the extinction of dinosaurs for an example. From an evolutionary point of view, this is a viable trade-o between the energetic cost of homeostasis versus the tness benet it would provide. In practical terms, homeostasis of living multicellular organisms is constrained in terms of the amount of disruption they can cope with and in terms of the amount of time they will remain homeostatic.
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| 3. |
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| 4. |
- Bengmark, Samuel, 1965, et al.
(författare)
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Combining engineering and teacher education – ideas and experiences from Chalmers University of Technology
- 2021
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Ingår i: Bidrag från 8:e Utvecklingskonferensen för Sveriges ingenjörsutbildningar. - 9789178672714
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Konferensbidrag (refereegranskat)abstract
- In response to the lack of STEM teachers in Sweden, Chalmers University of Technology offers a double degree program in engineering and education. This article investigates which ideas behind the program’s design have been of particular value in implementing the program and their added value. The five main ideas are: involve skilled schoolteachers called master teachers in the education, having many entrances to the program but only one exit, using interviews as part of the admission process, using a competency model to ensure coherence in the education, focusing on concrete work skills at the beginning of the education and later move on to theory and further development. We invite other universities to consider double degree programs in engineering and education and be inspired by these five ideas in their implementation.
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| 5. |
- Bernhardsson, Sebastian, et al.
(författare)
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Structural correlations in bacterial metabolic networks
- 2011
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Ingår i: BMC Evolutionary Biology. - : Springer Science and Business Media LLC. - 1471-2148. ; 11:20
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Tidskriftsartikel (refereegranskat)abstract
- Background Evolution of metabolism occurs through the acquisition and loss of genes whose products acts as enzymes in metabolic reactions, and from a presumably simple primordial metabolism the organisms living today have evolved complex and highly variable metabolisms. We have studied this phenomenon by comparing the metabolic networks of 134 bacterial species with known phylogenetic relationships, and by studying a neutral model of metabolic network evolution. Results We consider the 'union-network' of 134 bacterial metabolisms, and also the union of two smaller subsets of closely related species. Each reaction-node is tagged with the number of organisms it belongs to, which we denote organism degree (OD), a key concept in our study. Network analysis shows that common reactions are found at the centre of the network and that the average OD decreases as we move to the periphery. Nodes of the same OD are also more likely to be connected to each other compared to a random OD relabelling based on their occurrence in the real data. This trend persists up to a distance of around five reactions. A simple growth model of metabolic networks is used to investigate the biochemical constraints put on metabolic-network evolution. Despite this seemingly drastic simplification, a 'union-network' of a collection of unrelated model networks, free of any selective pressure, still exhibit similar structural features as their bacterial counterpart. Conclusions The OD distribution quantifies topological properties of the evolutionary history of bacterial metabolic networks, and lends additional support to the importance of horizontal gene transfer during bacterial metabolic evolution where new reactions are attached at the periphery of the network. The neutral model of metabolic network growth can reproduce the main features of real networks, but we observe that the real networks contain a smaller common core, while they are more similar at the periphery of the network. This suggests that natural selection and biochemical correlations can act both to diversify and to narrow down metabolic evolution.
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| 6. |
- Borgqvist, Johannes, 1990, et al.
(författare)
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Cell polarisation in a bulk-surface model can be driven by both classic and non-classic Turing instability
- 2021
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Ingår i: Npj Systems Biology and Applications. - : Springer Science and Business Media LLC. - 2056-7189. ; 7:1
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Tidskriftsartikel (refereegranskat)abstract
- The GTPase Cdc42 is the master regulator of eukaryotic cell polarisation. During this process, the active form of Cdc42 is accumulated at a particular site on the cell membrane called the pole. It is believed that the accumulation of the active Cdc42 resulting in a pole is driven by a combination of activation-inactivation reactions and diffusion. It has been proposed using mathematical modelling that this is the result of diffusion-driven instability, originally proposed by Alan Turing. In this study, we developed, analysed and validated a 3D bulk-surface model of the dynamics of Cdc42. We show that the model can undergo both classic and non-classic Turing instability by deriving necessary conditions for which this occurs and conclude that the non-classic case can be viewed as a limit case of the classic case of diffusion-driven instability. Using three-dimensional Spatio-temporal simulation we predicted pole size and time to polarisation, suggesting that cell polarisation is mainly driven by the reaction strength parameter and that the size of the pole is determined by the relative diffusion.
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| 7. |
- Borgqvist, Johannes, 1990, et al.
(författare)
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Turing pattern formation on the sphere is robust to the removal of a hole
- 2024
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Ingår i: JOURNAL OF MATHEMATICAL BIOLOGY. - : Springer Science+Business Media B.V.. - 0303-6812 .- 1432-1416. ; 88:2
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Tidskriftsartikel (refereegranskat)abstract
- The formation of buds on the cell membrane of budding yeast cells is thought to be driven by reactions and diffusion involving the protein Cdc42. These processes can be described by a coupled system of partial differential equations known as the Schnakenberg system. The Schnakenberg system is known to exhibit diffusion-driven pattern formation, thus providing a mechanism for bud formation. However, it is not known how the accumulation of bud scars on the cell membrane affect the ability of the Schnakenberg system to form patterns. We have approached this problem by modelling a bud scar on the cell membrane with a hole on the sphere. We have studied how the spectrum of the Laplace-Beltrami operator, which determines the resulting pattern, is affected by the size of the hole, and by numerically solving the Schnakenberg system on a sphere with a hole using the finite element method. Both theoretical predictions and numerical solutions show that pattern formation is robust to the introduction of a bud scar of considerable size, which lends credence to the hypothesis that bud formation is driven by diffusion-driven instability.
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| 8. |
- Gerlee, Philip, 1980, et al.
(författare)
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Autocrine signaling can explain the emergence of Allee effects in cancer cell populations
- 2022
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Ingår i: Plos Computational Biology. - : Public Library of Science (PLoS). - 1553-734X .- 1553-7358. ; 18:3
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Tidskriftsartikel (refereegranskat)abstract
- In many human cancers, the rate of cell growth depends crucially on the size of the tumour cell population. Low, zero, or negative growth at low population densities is known as the Allee effect; this effect has been studied extensively in ecology, but so far lacks a good explanation in the cancer setting. Here, we formulate and analyze an individual-based model of cancer, in which cell division rates are increased by the local concentration of an autocrine growth factor produced by the cancer cells themselves. We show, analytically and by simulation, that autocrine signaling suffices to cause both strong and weak Allee effects. Whether low cell densities lead to negative (strong effect) or reduced (weak effect) growth rate depends directly on the ratio of cell death to proliferation, and indirectly on cellular dispersal. Our model is consistent with experimental observations from three patient-derived brain tumor cell lines grown at different densities. We propose that further studying and quantifying population-wide feedback, impacting cell growth, will be central for advancing our understanding of cancer dynamics and treatment, potentially exploiting Allee effects for therapy.
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| 9. |
- Gerlee, Philip, 1980, et al.
(författare)
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Bridging scales in cancer progression: Mapping genotype to phenotype using neural networks
- 2015
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Ingår i: Seminars in Cancer Biology. - : Elsevier BV. - 1096-3650 .- 1044-579X. ; 30, s. 30-41
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Tidskriftsartikel (refereegranskat)abstract
- In this review we summarise our recent efforts in trying to understand the role of heterogeneity in cancer progression by using neural networks to characterise different aspects of the mapping from a cancer cells genotype and environment to its phenotype. Our central premise is that cancer is an evolving system subject to mutation and selection, and the primary conduit for these processes to occur is the cancer cell whose behaviour is regulated on multiple biological scales. The selection pressure is mainly driven by the microenvironment that the tumour is growing in and this acts directly upon the cell phenotype. In turn, the phenotype is driven by the intracellular pathways that are regulated by the genotype. Integrating all of these processes is a massive undertaking and requires bridging many biological scales (i.e. genotype, pathway, phenotype and environment) that we will only scratch the surface of in this review. We will focus on models that use neural networks as a means of connecting these different biological scales, since they allow us to easily create heterogeneity for selection to act upon and importantly this heterogeneity can be implemented at different biological scales. More specifically, we consider three different neural networks that bridge different aspects of these scales and the dialogue with the micro-environment, (i) the impact of the micro-environment on evolutionary dynamics, (ii) the mapping from genotype to phenotype under drug-induced perturbations and (iii) pathway activity in both normal and cancer cells under different micro-environmental conditions.
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| 10. |
- Gerlee, Philip, 1980, et al.
(författare)
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Complexity and stability in growing cancer cell populations
- 2015
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : Proceedings of the National Academy of Sciences. - 0027-8424 .- 1091-6490. ; 112:21
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Evolutionary game theory (EGT) describes dynamics in populations in which individual fitness can change because of the interactions with others, called frequency-dependent selection (1). Interactions are driven by differences in phenotype. EGT has been proposed as a framework for evolutionary dynamics of tumors (2). An underlying assumption is that different cancer cell types within a tumor engage in different heritable behavior; thus, frequency-dependent selection acts. Until now there has been little direct empirical evidence for this. The study by Archetti et al. (3) demonstrates frequency-dependent growth rates of two phenotypically distinct cancer subclones. One clone produced the insulin-like growth factor (IGF)-II, the other did not. In a mix of producers and nonproducers, the growth rates of both clones varied with the frequency of producers. Because a similar effect was shown when varying the concentration of serum, the production of IGF-II could be viewed as a public goods game.
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| 11. |
- Gerlee, Philip, 1980, et al.
(författare)
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Computational models predicting the early development of the COVID-19 pandemic in Sweden: systematic review, data synthesis, and secondary validation of accuracy
- 2022
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Ingår i: Scientific Reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- Computational models for predicting the early course of the COVID-19 pandemic played a central role in policy-making at regional and national levels. We performed a systematic review, data synthesis, and secondary validation of studies that reported on prediction models addressing the early stages of the COVID-19 pandemic in Sweden. A literature search in January 2021 based on the search triangle model identified 1672 peer-reviewed articles, preprints and reports. After applying inclusion criteria 52 studies remained out of which 12 passed a Risk of Bias Opinion Tool. When comparing model predictions with actual outcomes only 4 studies exhibited an acceptable forecast (mean absolute percentage error, MAPE < 20%). Models that predicted disease incidence could not be assessed due to the lack of reliable data during 2020. Drawing conclusions about the accuracy of the models with acceptable methodological quality was challenging because some models were published before the time period for the prediction, while other models were published during the prediction period or even afterwards. We conclude that the forecasting models involving Sweden developed during the early stages of the COVID-19 pandemic in 2020 had limited accuracy. The knowledge attained in this study can be used to improve the preparedness for coming pandemics.
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| 12. |
- Gerlee, Philip, 1980
(författare)
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Derivation of a Generalised Replicator Equation in the Limit of Weak Selection
- 2023
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Ingår i: Springer Proceedings in Mathematics and Statistics. - 2194-1009 .- 2194-1017. ; 429, s. 249-260
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Konferensbidrag (refereegranskat)abstract
- The replicator equation is often applied for describing the change in frequency of competing subpopulations, but has only been formally derived under strong limitations on the dynamics of the total population size. We show that a generalised replicator equation can be derived from a wide class of population dynamical models that allow for a factorisation into density-dependent and frequency-dependent birth and death rates. The method relies on weak selection (i.e. small fitness differences) and the generalised replicator equation is obtained as the zeroth order approximation in a perturbation expansion. We apply our theoretical results to a specific model with linear frequency-dependence and logistic dynamics for the population size, and show that the error introduced by considering a zeroth order composite solution scales as the fitness difference.
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| 13. |
- Gerlee, Philip, 1980, et al.
(författare)
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Diffusion-limited tumour growth: Simulations and analysis.
- 2010
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Ingår i: Mathematical Biosciences and Engineering. - : American Institute of Mathematical Sciences (AIMS). - 1551-0018 .- 1547-1063. ; 7:2, s. 385-400
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Tidskriftsartikel (refereegranskat)abstract
- The morphology of solid tumours is known to be affected by the background oxygen concentration of the tissue in which the tumour grows, and both computational and experimental studies have suggested that branched tumour morphology in low oxygen concentration is caused by diffusion-limited growth. In this paper we present a simple hybrid cellular automaton model of solid tumour growth aimed at investigating this phenomenon. Simulation results show that for high consumption rates (or equivalently low oxygen concentrations) the tumours exhibit branched morphologies, but more importantly the simplicity of the model allows for an analytic approach to the problem. By applying a steady-state assumption we derive an approximate solution of the oxygen equation, which closely matches the simulation results. Further, we derive a dispersion relation which reveals that the average branch width in the tumour depends on the width of the active rim, and that a smaller active rim gives rise to thinner branches. Comparison between the prediction of the stability analysis and the results from the simulations shows good agreement between theory and simulation.
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| 14. |
- Gerlee, Philip, 1980, et al.
(författare)
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Effect of space in the game “war of attrition”
- 2012
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Ingår i: Physical Review E. - 1539-3755 .- 2470-0045 .- 2470-0053. ; 85:4
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Tidskriftsartikel (refereegranskat)abstract
- Spatial dynamics has in many cases been invoked as a mechanism that can promote the evolution of coexistence and cooperation, although the precise conditions for this to occur have not yet been characterised. In an effort to address this question we have analyzed an alternative version of the theoretical game “war of attrition,” which exhibits unusual behavior: The well-mixed system exhibits quasistationary coexistence and a relaxation time that scales exponentially with the system size, while the spatial system shows a relaxation time that is considerably smaller and scales with a power α≈1.4 of the system size. Further, the spatial system exhibits a first-order phase transition in the strategy distribution at a consolation prize of k≈1/3. Close to this point the relaxation time diverges with an exponent γ≈1.2. This analysis shows that the effect of space is highly dependent on the type of game considered.
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| 15. |
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| 16. |
- Gerlee, Philip, 1980, et al.
(författare)
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Evolving homeostatic tissue using genetic algorithms
- 2011
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Ingår i: Progress in Biophysics & Molecular Biology. - : Elsevier BV. - 0079-6107. ; 106:2, s. 414-425
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Tidskriftsartikel (refereegranskat)abstract
- Multicellular organisms maintain form and function through a multitude of homeostatic mechanisms. The details of these mechanisms are in many cases unknown, and so are their evolutionary origin and their link to development. In order to illuminate these issues we have investigated the evolution of structural homeostasis in the simplest of cases, a tissue formed by a mono-layer of cells. To this end, we made use of a 3-dimensional hybrid cellular automaton, an individual-based model in which the behaviour of each cell depends on its local environment. Using an evolutionary algorithm (EA) we evolved cell signalling networks, both with a fixed and an incremental fitness evaluation, which give rise to and maintain a mono-layer tissue structure. Analysis of the solutions provided by the EA shows that the two evaluation methods gives rise to different types of solutions to the problem of homeostasis. The fixed method leads to almost optimal solutions, where the tissue relies on a high rate of cell turnover, while the solutions from the incremental scheme behave in a more conservative manner, only dividing when necessary. In order to test the robustness of the solutions we subjected them to environmental stress, by wounding the tissue, and to genetic stress, by introducing mutations. The results show that the robustness very much depends on the mechanism responsible for maintaining homeostasis. The two evolved cell types analysed present contrasting mechanisms by which tissue homeostasis can be maintained. This compares well to different tissue types found in multicellular organisms. For example the epithelial cells lining the colon in humans are shed at a considerable rate, while in other tissue types, which are not as exposed, the conservative type of homeostatic mechanism is normally found. These results will hopefully shed light on how multicellular organisms have evolved homeostatic mechanisms and what might occur when these mechanisms fail, as in the case of cancer. (C) 2011 Published by Elsevier Ltd.
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| 17. |
- Gerlee, Philip, 1980, et al.
(författare)
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Extinction rates in tumour public goods games
- 2017
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Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 14:134
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Tidskriftsartikel (refereegranskat)abstract
- Cancer evolution and progression are shaped by cellular interactions and Darwinian selection. Evolutionary game theory incorporates both of these principles, and has been proposed as a framework to understand tumour cell population dynamics. A cornerstone of evolutionary dynamics is the replicator equation, which describes changes in the relative abundance of different cell types, and is able to predict evolutionary equilibria. Typically, the replicator equation focuses on differences in relative fitness. We here showthat this framework might not be sufficient under all circumstances, as it neglects important aspects of population growth. Standard replicator dynamics might miss critical differences in the time it takes to reach an equilibrium, as this time also depends on cellular turnover in growing but bounded populations. As the system reaches a stable manifold, the time to reach equilibrium depends on cellular death and birth rates. These rates shape the time scales, in particular, in coevolutionary dynamics of growth factor producers and free-riders. Replicator dynamics might be an appropriate framework only when birth and death rates are of similar magnitude. Otherwise, population growth effects cannot be neglected when predicting the time to reach an equilibrium, and cell-type-specific rates have to be accounted for explicitly.
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| 18. |
- Gerlee, Philip, 1980, et al.
(författare)
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Gene divergence and pathway duplication in the metabolic network of yeast and digital organisms
- 2009
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Ingår i: Journal of the Royal Society Interface. - : The Royal Society. - 1742-5689 .- 1742-5662. ; 6, s. 1233-1245
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Tidskriftsartikel (refereegranskat)abstract
- We have studied the metabolic gene–function network in yeast and digital organisms evolved in the artificial life platform Avida. The gene–function network is a bipartite network in which a link exists between a gene and a function (pathway) if that function depends on that gene, and can also be viewed as a decomposition of the more traditional functional gene networks, where two genes are linked if they share any function. We show that the gene–function network exhibits two distinct degree distributions: the gene degree distribution is scale-free while the pathway distribution is exponential. This is true for both yeast and digital organisms, which suggests that this is a general property of evolving systems, and we propose that the scale-free gene degree distribution is due to pathway duplication, i.e. the development of a new pathway where the original function is still retained. Pathway duplication would serve as preferential attachment for the genes, and the experiments with Avida revealed precisely this; genes involved in many pathways are more likely to increase their connectivity. Measuring the overlap between different pathways, in terms of the genes that constitute them, showed that pathway duplication also is a likely mechanism in yeast evolution. This analysis sheds new light on the evolution of genes and functionality, and suggests that function duplication could be an important mechanism in evolution.
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| 19. |
- Gerlee, Philip, 1980, et al.
(författare)
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Impact of anticipation in dynamical systems
- 2017
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Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 96:6
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Tidskriftsartikel (refereegranskat)abstract
- Many animals, including humans, have predictive capabilities and, presumably, base their behavioral decisions-at least partially-upon an anticipated state of their environment. We explore a minimal version of this idea in the context of particles that interact according to a pairwise potential. Anticipation enters the picture by calculating the interparticle forces from linear extrapolations of the particle positions some time tau in the future. Simulations show that for intermediate values of t, compared to a transient time scale defined by the potential and the initial conditions, the particles form rotating clusters in which the particles are arranged in a hexagonal pattern. Analysis of the system shows that anticipation induces energy dissipation and we show that the kinetic energy asymptotically decays as 1/t. Furthermore, we show that the angular momentum is not necessarily conserved for tau > 0, and that asymmetries in the initial condition therefore can cause rotational movement. These results suggest that anticipation could play an important role in collective behavior, since it may induce pattern formation and stabilizes the dynamics of the system.
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| 20. |
- Gerlee, Philip, 1980, et al.
(författare)
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Inferring rates of metastatic dissemination using stochastic network models
- 2019
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Ingår i: Plos Computational Biology. - : Public Library of Science (PLoS). - 1553-7358 .- 1553-734X. ; 15:4
-
Tidskriftsartikel (refereegranskat)abstract
- The formation of metastases is driven by the ability of cancer cells to disseminate from the site of the primary tumour to target organs. The process of dissemination is constrained by anatomical features such as the flow of blood and lymph in the circulatory system. We exploit this fact in a stochastic network model of metastasis formation, in which only anatomically feasible routes of dissemination are considered. By fitting this model to two different clinical datasets (tongue & ovarian cancer) we show that incidence data can be modelled using a small number of biologically meaningful parameters. The fitted models reveal site specific relative rates of dissemination and also allow for patient-specific predictions of metastatic involvement based on primary tumour location and stage. Applied to other data sets this type of model could yield insight about seed-soil effects, and could also be used in a clinical setting to provide personalised predictions about the extent of metastatic spread. Author summary For most cancer patients the occurrence of metastases equals incurable disease. Despite this fact our quantitative knowledge about the process of metastatic dissemination is limited. In this manuscript we improve on a previously published mathematical model by incorporating known biological facts about metastatic spread and also consider the temporal dimension of dissemination. The model is fit to two different cancer types with very different patterns of spread, which highlights the versatility of our framework. Properly parametrised this type of model can be used for making personalised predictions about metastatic burden.
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| 21. |
- Gerlee, Philip, 1980, et al.
(författare)
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Persistence of cooperation in diffusive public goods games
- 2019
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Ingår i: Physical Review E. - 2470-0045 .- 2470-0053. ; 99:6
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Tidskriftsartikel (refereegranskat)abstract
- Diffusive public goods (PG) games are difficult to analyze due to population assortment affecting growth rates of cooperators (producers) and free-riders. We study these growth rates using spectral decomposition of cellular densities and derive a finite cell-size correction of the growth rate advantage which exactly describes the dynamics of a randomly assorted population and approximates the dynamics under limited dispersal. The resulting effective benefit-to-cost ratio relates the physical parameters of PG dynamics to the persistence of cooperation, and our findings provide a powerful tool for the analysis of diffusive PG games, explaining commonly observed patterns of cooperation. © 2019 American Physical Society.
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| 22. |
- Gerlee, Philip, 1980, et al.
(författare)
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Predicting regional COVID-19 hospital admissions in Sweden using mobility data.
- 2021
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Ingår i: Scientific reports. - : Springer Science and Business Media LLC. - 2045-2322. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- The transmission of COVID-19 is dependent on social mixing, the basic rate of which varies with sociodemographic, cultural, and geographic factors. Alterations in social mixing and subsequent changes in transmission dynamics eventually affect hospital admissions. We employ these observations to model and predict regional hospital admissions in Sweden during the COVID-19 pandemic. We use an SEIR-model for each region in Sweden in which the social mixing is assumed to depend on mobility data from public transport utilisation and locations for mobile phone usage. The results show that the model could capture the timing of the first and beginning of the second wave of the pandemic 3weeks in advance without any additional assumptions about seasonality. Further, we show that for two major regions of Sweden, models with public transport data outperform models using mobile phone usage. We conclude that a model based on routinely collected mobility data makes it possible to predict future hospital admissions for COVID-19 3weeks in advance.
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| 23. |
- Gerlee, Philip, 1980, et al.
(författare)
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Productivity and diversity in a cross-feeding population of digital organisms
- 2010
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Ingår i: Evolution. - : Wiley. - 0014-3820 .- 1558-5646. ; 64:9, s. 2716-2730
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Tidskriftsartikel (refereegranskat)abstract
- Cross-feeding interactions are a common feature of many microbial systems, such as colonies of Escherichia coli grown on a single limiting resource, and microbial consortia cooperatively degrading complex compounds. We have studied this phenomenon from an abstract point of view by considering artificial organisms that metabolize binary strings from a shared environment. The organisms are represented as simple cellular automaton rules and the analog of energy in the system is an approximation of the Shannon entropy of the binary strings. Only organisms that increase the entropy of the transformed strings are allowed to replicate. This system exhibits a large degree of species diversity, which increases when the flow of binary strings into the system is reduced. Investigating the relation between ecosystem productivity and diversity we find that diversity is negatively correlated with biomass production and energy uptake, while it correlates positively with energy-uptake efficiency. By performing invasion experiments, we show that the source of diversity is negative frequency-dependent selection acting among the different species, and that some of these interactions are intransitive, another mechanism known to promote diversity.
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| 24. |
- Gerlee, Philip, 1980, et al.
(författare)
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Rock-scissor-paper dynamics in a digital ecology
- 2010
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Ingår i: 12th International Conference on the Synthesis and Simulation of Living Systems: Artificial Life XII, ALIFE 2010; Odense; Denmark; 19 August 2010 through 23 August 2010. - 9780262290753 ; , s. 285-295
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Konferensbidrag (refereegranskat)abstract
- In this paper we present an Alife-platform named Urdar aimed at investigating dynamics of ecosystems where species engage in cross-feeding, i.e. where metabolites are passed from one species to the next in a process of sequential degra- dation. This type of interactions are commonly found in microbial ecosystems such as bacterial consortia degrading complex compounds. We have studied this phenomenon from an abstract point of view by considering artificial organisms which metabolise binary strings from a shared environment. The organisms are represented as simple cellular automaton rules and the analogue of energy in the system is an approxi- mation of the Shannon entropy of the binary strings. Only or- ganisms which increase the entropy of the transformed strings are allowed to replicate. We find that the system exhibits a large degree of biodiversity and a non-stationary species dis- tribution, especially during low rates of energy inflow, and that the time spent in each species configuration exhibits a broad distribution. Investigating the interaction between dif- ferent species in the system by invasion experiments we ob- serve that co-existence is a common feature and that some triplets of species exhibit intransitive, i.e. rock-paper-scissors like, interactions.
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| 25. |
- Gerlee, Philip, 1980, et al.
(författare)
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Scientific Models : Red Atoms, White Lies and Black Boxes in a Yellow Book
- 2016
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Bok (övrigt vetenskapligt/konstnärligt)abstract
- A zebrafish, the hull of a miniature ship, a mathematical equation and a food chain - what do these things have in common? They are examples of models used by scientists to isolate and study particular aspects of the world around us. This book begins by introducing the concept of a scientific model from an intuitive perspective, drawing parallels to mental models and artistic representations. It then recounts the history of modelling from the 16th century up until the present day. The iterative process of model building is described and discussed in the context of complex models with high predictive accuracy versus simpler models that provide more of a conceptual understanding. To illustrate the diversity of opinions within the scientific community, we also present the results of an interview study, in which ten scientists from different disciplines describe their views on modelling and how models feature in their work. Lastly, it includes a number of worked examples that span different modelling approaches and techniques. It provides a comprehensive introduction to scientific models and shows how models are constructed and used in modern science. It also addresses the approach to, and the culture surrounding modelling in different scientific disciplines. It serves as an inspiration for model building and also facilitates interdisciplinary collaborations by showing how models are used in different scientific fields. The book is aimed primarily at students in the sciences and engineering, as well as students at teacher training colleges but will also appeal to interested readers wanting to get an overview of scientific modelling in general and different modelling approaches in particular.
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