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The development of deep-ocean anoxia in a comprehensive ocean phosphorus model. GEM : INTERNATIONAL JOURNAL ON GEOMATHEMATICS 2023; 14:12. [PMID: 37265756 PMCID: PMC10229728 DOI: 10.1007/s13137-023-00221-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 04/21/2023] [Indexed: 06/03/2023]
Abstract
We analyse a model of the phosphorus cycle in the ocean given by Slomp and Van Cappellen (Biogeosciences 4:155-171, 2007. 10.5194/bg-4-155-2007). This model contains four distinct oceanic boxes and includes relevant parts of the water, carbon and oxygen cycles. We show that the model can essentially be solved analytically, and its behaviour completely understood without recourse to numerical methods. In particular, we show that, in the model, the carbon and phosphorus concentrations in the different ocean reservoirs are all slaved to the concentration of soluble reactive phosphorus in the deep ocean, which relaxes to an equilibrium on a time scale of 180,000 y, and we show that the deep ocean is either oxic or anoxic, depending on a critical parameter which we can determine explicitly. Finally, we examine how the value of this critical parameter depends on the physical parameters contained in the model. The presented methodology is based on tools from applied mathematics and can be used to reduce the complexity of other large, biogeochemical models. Supplementary Information The online version contains supplementary material available at 10.1007/s13137-023-00221-0.
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Abstract
This paper addresses the problem of extinction in continuous models of population dynamics associated with small numbers of individuals. We begin with an extended discussion of extinction in the particular case of a stochastic logistic model, and how it relates to the corresponding continuous model. Two examples of ‘small number dynamics’ are then considered. The first is what Mollison calls the ‘atto-fox’ problem (in a model of fox rabies), referring to the problematic theoretical occurrence of a predicted rabid fox density of \documentclass[12pt]{minimal}
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\begin{document}$$10^{-18}$$\end{document}10-18 (atto-) per square kilometre. The second is how the production of large numbers of eggs by an individual can reliably lead to the eventual survival of a handful of adults, as it would seem that extinction then becomes a likely possibility. We describe the occurrence of the atto-fox problem in other contexts, such as the microbial ‘yocto-cell’ problem, and we suggest that the modelling resolution is to allow for the existence of a reservoir for the extinctively challenged individuals. This is functionally similar to the concept of a ‘refuge’ in predator–prey systems and represents a state for the individuals in which they are immune from destruction. For what I call the ‘frogspawn’ problem, where only a few individuals survive to adulthood from a large number of eggs, we provide a simple explanation based on a Holling type 3 response and elaborate it by means of a suitable nonlinear age-structured model.
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3
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Quasi-steady uptake and bacterial community assembly in a mathematical model of soil-phosphorus mobility. J Theor Biol 2020; 509:110530. [PMID: 33129953 DOI: 10.1016/j.jtbi.2020.110530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/14/2020] [Accepted: 10/21/2020] [Indexed: 11/28/2022]
Abstract
We mathematically model the uptake of phosphorus by a soil community consisting of a plant and two bacterial groups: copiotrophs and oligotrophs. Four equilibrium states emerge, one for each of the species monopolising the resource and dominating the community and one with coexistence of all species. We show that the dynamics are controlled by the ratio of chemical adsorption to bacterial death permitting either oscillatory states or quasi-steady uptake. We show how a steady state can emerge which has soil and plant nutrient content unresponsive to increased fertilization. However, the additional fertilization supports the copiotrophs leading to community reassembly. Our results demonstrate the importance of time-series measurements in nutrient uptake experiments.
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4
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Regularization of the Ostwald supersaturation model for Liesegang bands. Proc Math Phys Eng Sci 2019; 475:20190154. [PMID: 31534422 DOI: 10.1098/rspa.2019.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Accepted: 06/18/2019] [Indexed: 11/12/2022] Open
Abstract
In a previous paper, we analysed the Keller-Rubinow formulation of Ostwald's supersaturation theory for the formation of Liesegang rings or Liesegang bands, and found that the model is ill-posed, in the sense that after the termination of the first crystal front growth, secondary bands form, as in the experiment, but these are numerically found to be a single grid space wide, and thus an artefact of the numerical method. This ill-posedness is due to the discontinuity in the crystal growth rate, which itself reflects the supersaturation threshold inherent in the theory. Here we show that the ill-posedness can be resolved by the inclusion of a relaxation mechanism describing an impurity coverage fraction, which physically enables the transition in heterogeneous nucleation from precipitate-free impurity to precipitate-covered impurity.
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5
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Phase Transition in the Boltzmann-Vlasov Equation. JOURNAL OF STATISTICAL PHYSICS 2019; 174:1011-1026. [PMID: 30930484 PMCID: PMC6407734 DOI: 10.1007/s10955-019-02222-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 01/08/2019] [Indexed: 06/09/2023]
Abstract
In this paper we revisit the problem of explaining phase transition by a study of a form of the Boltzmann equation, where inter-molecular attraction is included by means of a Vlasov term in the evolution equation for the one particle distribution function. We are able to show that for typical gas densities, a uniform state is unstable if the inter-molecular attraction is large enough. Our analysis relies strongly on the assumption, essential to the derivation of the Boltzmann equation, that ν ≪ 1 , where ν = d / l is the ratio of the molecular diameter to the mean inter-particle distance; in this case, for fluctuations on the scale of the molecular spacing, the collision term is small, and an explicit approximate solution is possible. We give reasons why we think the resulting approximation is valid, and in conclusion offer some possibilities for extension of the results to finite amplitude.
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6
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Correction to: The Dynamics of Ascaris lumbricoides Infections. Bull Math Biol 2018; 80:2787. [DOI: 10.1007/s11538-018-0470-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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8
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Microbial dormancy and boom-and-bust population dynamics under starvation stress. Theor Popul Biol 2018; 120:114-120. [PMID: 29447840 DOI: 10.1016/j.tpb.2018.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 01/20/2018] [Accepted: 02/05/2018] [Indexed: 11/16/2022]
Abstract
We propose a model for the growth of microbial populations in the presence of a rate-limiting nutrient which accounts for the switching of cells to a dormant phase at low densities in response to decreasing concentration of a putative biochemical signal. We then show that in conditions of nutrient starvation, self-sustained oscillations can occur, thus providing a natural explanation for such phenomena as plankton blooms. However, unlike results of previous studies, the microbial population minima do not become unrealistically small, being buffered during minima by an increased dormant phase population. We also show that this allows microbes to survive in extreme environments for very long periods, consistent with observation. The mechanism provides a natural vehicle for other such sporadic outbreaks, such as viral epidemics.
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9
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Numerical simulations of drumlin formation. Proc Math Phys Eng Sci 2017; 473:20170220. [PMID: 28878560 DOI: 10.1098/rspa.2017.0220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 07/27/2017] [Indexed: 11/12/2022] Open
Abstract
We summarize the present form of the instability theory for drumlin formation, which describes the coupled subglacial flow of ice, water and sediment. This model has evolved over the last 20 years, and is now at the point where it can predict instabilities corresponding to ribbed moraine, drumlins and mega-scale glacial lineations, but efforts to provide numerical solutions of the model have been limited. The present summary adds some slight nuances to previously published versions of the theory, notably concerning the constitutive description of the subglacial water film and its flow. A new numerical method is devised to solve the model, and we show that it can be solved for realistic values of most of the parameters, with the exception of that corresponding to the water film thickness. We show that evolved bedforms can be three-dimensional and of the correct sizes, and we explore to some extent the variation of the solutions with the model's parameters.
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10
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On the Keller-Rubinow model for Liesegang ring formation. Proc Math Phys Eng Sci 2017; 473:20170128. [PMID: 28989302 DOI: 10.1098/rspa.2017.0128] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 08/21/2017] [Indexed: 11/12/2022] Open
Abstract
We study the model of Keller & Rubinow (Keller & Rubinow 1981 J. Chem. Phys74, 5000-5007. (doi:10.1063/1.441752)) describing the formation of Liesegang rings due to Ostwald's supersaturation mechanism. Keller and Rubinow provided an approximate solution both for the growth and equilibration of the first band, and also for the formation of secondary bands, based on a presumed asymptotic limit. However, they did not provide a parametric basis for the assumptions in their solution, nor did they provide any numerical corroboration, particularly of the secondary band formation. Here, we provide a different asymptotic solution, based on a specific parametric limit, and we show that the growth and subsequent cessation of the first band can be explained. We also show that the model is unable to explain the formation of finite width secondary bands, and we confirm this result by numerical computation. We conclude that the model is not fully posed, lacking a transition variable which can describe the hysteretic switch across the nucleation threshold.
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11
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A theoretical explanation of grain size distributions in explosive rock fragmentation. Proc Math Phys Eng Sci 2016; 472:20150843. [PMID: 27436962 DOI: 10.1098/rspa.2015.0843] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We have measured grain size distributions of the results of laboratory decompression explosions of volcanic rock. The resulting distributions can be approximately represented by gamma distributions of weight per cent as a function of [Formula: see text], where d is the grain size in millimetres measured by sieving, with a superimposed long tail associated with the production of fines. We provide a description of the observations based on sequential fragmentation theory, which we develop for the particular case of 'self-similar' fragmentation kernels, and we show that the corresponding evolution equation for the distribution can be explicitly solved, yielding the long-time lognormal distribution associated with Kolmogorov's fragmentation theory. Particular features of the experimental data, notably time evolution, advection, truncation and fines production, are described and predicted within the constraints of a generalized, 'reductive' fragmentation model, and it is shown that the gamma distribution of coarse particles is a natural consequence of an assumed uniform fragmentation kernel. We further show that an explicit model for fines production during fracturing can lead to a second gamma distribution, and that the sum of the two provides a good fit to the observed data.
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12
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Abstract
We extend the one-dimensional polymer solution theory of bacterial biofilm growth described by Winstanley et al. (2011 Proc. R. Soc. A467, 1449-1467 (doi:10.1098/rspa.2010.0327)) to deal with the problem of the growth of a patch of biofilm in more than one lateral dimension. The extension is non-trivial, as it requires consideration of the rheology of the polymer phase. We use a novel asymptotic technique to reduce the model to a free-boundary problem governed by the equations of Stokes flow with non-standard boundary conditions. We then consider the stability of laterally uniform biofilm growth, and show that the model predicts spatial instability; this is confirmed by a direct numerical solution of the governing equations. The instability results in cusp formation at the biofilm surface and provides an explanation for the common observation of patterned biofilm architectures.
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13
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An instability theory for the formation of ribbed moraine, drumlins and mega-scale glacial lineations. Proc Math Phys Eng Sci 2014; 470:20140185. [PMID: 25383019 DOI: 10.1098/rspa.2014.0185] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 08/08/2014] [Indexed: 11/12/2022] Open
Abstract
We present a theory for the coupled flow of ice, subglacial water and subglacial sediment, which is designed to represent the processes which occur at the bed of an ice sheet. The ice is assumed to flow as a Newtonian viscous fluid, the water can flow between the till and the ice as a thin film, which may thicken to form streams or cavities, and the till is assumed to be transported, either through shearing by the ice, squeezing by pressure gradients in the till, or by fluvial sediment transport processes in streams or cavities. In previous studies, it was shown that the dependence of ice sliding velocity on effective pressure provided a mechanism for the generation of bedforms resembling ribbed moraine, while the dependence of fluvial sediment transport on water film depth provides a mechanism for the generation of bedforms resembling mega-scale glacial lineations. Here, we combine these two processes in a single model, and show that, depending largely on the granulometry of the till, instability can occur in a range of types which range from ribbed moraine through three-dimensional drumlins to mega-scale glacial lineations.
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14
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Abstract
The existence of both water and sediment at the bed of ice streams is well documented, but there is a lack of fundamental understanding about the mechanisms of ice, water and sediment interaction. We pose a model to describe subglacial water flow below ice sheets, in the presence of a deformable sediment layer. Water flows in a rough-bedded film; the ice is supported by larger clasts, but there is a millimetric water layer submerging the smaller particles. Partial differential equations describing the water film are derived from a description of the dynamics of ice, water and mobile sediment. We assume that sediment transport is possible, either as fluvial bedload, but more significantly by ice-driven shearing and by internal squeezing. This provides an instability mechanism for rivulet formation; in the model, downstream sediment transport is compensated by lateral squeezing of till towards the incipient streams. We show that the model predicts the formation of shallow, swamp-like streams, with a typical depth of the order of centimetres. The swamps are stable features, typically with a width of the order of tens to hundreds of metres.
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15
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Subglacial hydrology and the formation of ice streams. Proc Math Phys Eng Sci 2014; 470:20130494. [PMID: 24399921 PMCID: PMC3857858 DOI: 10.1098/rspa.2013.0494] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Accepted: 10/09/2013] [Indexed: 11/28/2022] Open
Abstract
Antarctic ice streams are associated with pressurized subglacial meltwater but the role this water plays in the dynamics of the streams is not known. To address this, we present a model of subglacial water flow below ice sheets, and particularly below ice streams. The base-level flow is fed by subglacial melting and is presumed to take the form of a rough-bedded film, in which the ice is supported by larger clasts, but there is a millimetric water film which submerges the smaller particles. A model for the film is given by two coupled partial differential equations, representing mass conservation of water and ice closure. We assume that there is no sediment transport and solve for water film depth and effective pressure. This is coupled to a vertically integrated, higher order model for ice-sheet dynamics. If there is a sufficiently small amount of meltwater produced (e.g. if ice flux is low), the distributed film and ice sheet are stable, whereas for larger amounts of melt the ice–water system can become unstable, and ice streams form spontaneously as a consequence. We show that this can be explained in terms of a multi-valued sliding law, which arises from a simplified, one-dimensional analysis of the coupled model.
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17
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A simple model for multicomponent etching. J Colloid Interface Sci 2011; 354:421-3. [PMID: 21106203 DOI: 10.1016/j.jcis.2010.10.056] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 09/28/2010] [Accepted: 10/25/2010] [Indexed: 11/18/2022]
Abstract
We consider the situation where a multicomponent solid is etched using one or more acids. Of fundamental interest is the rate of surface etching but when this involves multicomponent surface reactions, it becomes unclear how the overall rate can be estimated. In this paper, we sketch a simple model designed to determine the effective etching rate by means of an atomic scale model of the etching process.
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Abstract
We provide and analyse a model for the growth of bacterial biofilms based on the concept of an extracellular polymeric substance as a polymer solution, whose viscoelastic rheology is described by the classical Flory–Huggins theory. We show that one-dimensional solutions exist, which take the form at large times of travelling waves, and we characterize their form and speed in terms of the describing parameters of the problem. Numerical solutions of the time-dependent problem converge to the travelling wave solutions.
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19
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Abstract
The instability theory of drumlin formation has been very successful in predicting the existence of ribbed moraine, as well as its amplitude and wavelength. However, the theory as it stands has not yet been shown to have the capability of predicting the existence of three-dimensional bedforms—drumlins—or their more extreme cousins, mega-scale glacial lineations. We extend the instability theory to include a dynamic description of the local subglacial drainage system, and in particular, we show that a uniform water-film flow between ice and deformable subglacial till is unstable, and that as a consequence, lineations will form. Predictions of the transverse wavelengths are consistent with observations.
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20
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The instability theory of drumlin formation applied to Newtonian viscous ice of finite depth. Proc Math Phys Eng Sci 2010. [DOI: 10.1098/rspa.2010.0017] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The Hindmarsh instability theory of drumlin formation is applied to the study of interfacial instabilities, which may arise when ice flows viscously over deformable sediments. Here, the analytic form of this theory is extended to the case where the ice is Newtonian viscous and of finite depth, and where the basal till can be both sheared by the ice and squeezed by basal effective pressure gradients: previous authors assumed infinitely deep ice, based on the assumption that the developing waveforms had wavelength much less than ice depth.
The previous infinite depth theory only allowed transverse instabilities to occur, and these have been associated with the formation of ribbed moraine; one of the purposes of extending the analysis to finite depth is to see whether three-dimensional instabilities, which might be associated with the formation of drumlins or mega-scale glacial lineations, can occur: we find that they do not. A second purpose is to calculate under what circumstances the infinite depth theory provides accurate prediction of bedform development in ice of finite depth
d
i
. We find that this is the case if the waveforms have a wavelength less than approximately 1.2
d
i
. Finally, the finite depth theory allows us to compute, for the first time, the response of the ice surface to the developing unstable bedforms. We find that this response is rapid, and we give explicit recipes for the surface perturbation transfer functions in terms of the perturbations to the basal stress and the basal topography.
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21
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Temperature-dependent shear flow and the absence of thermal runaway in valley glaciers. Proc Math Phys Eng Sci 2010. [DOI: 10.1098/rspa.2009.0335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We propose a two-dimensional model of a valley glacier in order to reconsider the question of whether thermal runaway could be a viable mechanism for the onset of creep instability in surging glaciers. We do this by providing an approximate solution for the temperature field based on the idea that shear is concentrated at the glacier bed. With this assumption, we show that a closed-form evolution equation for the glacier profile exists. While this is well known for isoviscous flows, it has not been previously derived for variable viscosity flows. During the process of deriving this equation, we show that thermal runaway does not occur. We provide numerical solutions of the model, and are led to infer that enhanced basal heating owing to refreezing of surface meltwater is an essential constituent in raising the bed temperature to the melting point.
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22
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A dynamic model of annual foliage growth and carbon uptake in trees. J R Soc Interface 2009; 6:1087-96. [PMID: 19324668 PMCID: PMC2827446 DOI: 10.1098/rsif.2009.0010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 02/10/2009] [Indexed: 11/12/2022] Open
Abstract
The growth of trees and other plants occurs through the interactive combination of photosynthesis and carbon (and other nutrient) assimilation. Photosynthesis enables the production of carbohydrate that can then be used in growing foliage, whereby photosynthesis is enabled. We construct a mathematical model of carbon uptake and storage, which allows the prediction of the growth dynamics of trees. We find that the simplest model allows uncontrolled foliage production through the positive feedback outlined above, but that leaf shading provides an automatic saturation to carbon assimilation, and hence to foliage production. The model explains the necessity for finite leaf area production at outbreak, and it explains why foliage density reaches a constant value during a growing season, while also non-leaf tissue also continues to grow. It also explains why trees will die when their carbon stores are depleted below a certain threshold, because the cost of foliage growth and maintenance exceeds the dynamic supply of carbon by photosynthesis.
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23
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Abstract
Recent experimental work has shown that, when a vertical column of rock under large pressure is suddenly depressurized, the column can ‘explode’ in a structured and repeatable way. The observations show that a sequence of horizontal fractures forms from the top down, and the resulting blocks are lifted off and ejected. The blocks can suffer secondary internal fractures. This experiment provides a framework for understanding the way in which catastrophic explosion can occur, and is motivated by the corresponding phenomenon of magmatic explosion during Vulcanian eruptions. We build a theoretical model to describe these results, and show that it is capable of describing both the primary sequence of fracturing and the secondary intrablock fracturing. The model allows us to suggest a practical criterion for when such explosions occur: firstly, the initial confining pressure must exceed the yield stress of the rock, and, secondly, the diffusion of the gas by porous flow must be sufficiently slow that a large excess pore pressure is built up. This will be the case if the rock permeability is small enough.
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24
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Instability modelling of drumlin formation incorporating lee-side cavity growth. Proc Math Phys Eng Sci 2009. [DOI: 10.1098/rspa.2008.0490] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
It is proposed that the formation of the subglacial bedforms known as drumlins occurs through an instability associated with the flow of ice over a wet deformable till. We pose a mathematical model that describes this instability, and we solve a simplified version of the model numerically in order to establish the form of finite-amplitude two-dimensional waveforms. A feature of the solutions is that cavities frequently form downstream of the bedforms; we allow the model to cater for this possibility and we provide an efficient numerical method to solve the resulting free boundary problem.
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25
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The segmentation clock in mice: Interaction between the Wnt and Notch signalling pathways. J Theor Biol 2007; 248:37-47. [PMID: 17570404 DOI: 10.1016/j.jtbi.2007.05.003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2006] [Revised: 05/02/2007] [Accepted: 05/04/2007] [Indexed: 10/23/2022]
Abstract
In the last few years, the efforts to elucidate the mechanisms underlying the segmentation clock in various vertebrate species have multiplied. Early evidence suggested that oscillations are caused by one of the genes under the Notch signalling pathway (like those of the her or Hes families). Recently, Aulehla et al. [Wnt3a plays a major role in the segmentation clock controlling somitogenesis. Dev. Cell 4, 395-406] discovered that Axin2 (a gene under the Wnt3a signalling pathway) also oscillates in the presomitic mesoderm (PSM) of mice embryos and proposed some mechanisms through which the Notch and Wnt3a pathways may interact. They further suggested that a decreasing concentration of Wnt3a along the PSM may be the gradient the segmentation clock interacts with to form somites. These results were reviewed by Rida et al. [A notch feeling of somite segmentation and beyond. Dev. Biol. 265, 2-22], who introduced a complex clockwork comprising genes Hes1, Lfng (under the Notch pathway), and Axin2, as well as their multiple interactions. In the present work we develop a mathematical model based on the Rida et al. review and use it to tackle some of the questions raided by the Aulehla et al. paper: can the Axin2 feedback loop constitute a clock? Could a decreasing Wnt3a signaling constitute the wavefront, where phase is recorded and the spatial pattern laid down? What is the master oscillator?
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26
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High frequency spikes in long period blood cell oscillations. J Math Biol 2006; 53:499-519. [PMID: 16897014 DOI: 10.1007/s00285-006-0027-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2005] [Revised: 05/05/2006] [Indexed: 10/24/2022]
Abstract
Several hematological diseases are characterised by oscillations of various blood cell populations. Two of these are a variant of chronic myelogenous leukemia (CML) and cyclical neutropenia (CN). These oscillations typically have long periods ranging from 20 to 60 days, despite the fact that the stem cell cycling time is thought to be of the order of 2-3 days. Clinical data from humans and laboratory data from the grey collie animal model of CN is suggestive of the idea that these long period oscillations may also contain higher frequency spiky oscillations. We show how such oscillations can be understood in the context of slow periodic stem cell oscillations, by analysing a two component differential-delay equation model of stem cell and neutrophil populations.
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27
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Subglacial floods beneath ice sheets. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2006; 364:1769-94. [PMID: 16782609 DOI: 10.1098/rsta.2006.1798] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Subglacial floods (jökulhlaups) are well documented as occurring beneath present day glaciers and ice caps. In addition, it is known that massive floods have occurred from ice-dammed lakes proximal to the Laurentide ice sheet during the last ice age, and it has been suggested that at least one such flood below the waning ice sheet was responsible for a dramatic cooling event some 8000 years ago. We propose that drainage of lakes from beneath ice sheets will generally occur in a time-periodic fashion, and that such floods can be of severe magnitude. Such hydraulic eruptions are likely to have caused severe climatic disturbances in the past, and may well do so in the future.
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28
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A delay recruitment model of the cardiovascular control system. J Math Biol 2005; 51:508-26. [PMID: 16012798 DOI: 10.1007/s00285-005-0339-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2004] [Revised: 04/12/2005] [Indexed: 10/25/2022]
Abstract
We develop a nonlinear delay-differential equation for the human cardiovascular control system, and use it to explore blood pressure and heart rate variability under short-term baroreflex control. The model incorporates an intrinsically stable heart rate in the absence of nervous control, and allows us to compare the baroreflex influence on heart rate and peripheral resistance. Analytical simplifications of the model allow a general investigation of the rôles played by gain and delay, and the effects of ageing.
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29
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A mathematical model for water and nutrient uptake by plant root systems. J Theor Biol 2004; 228:173-84. [PMID: 15094013 DOI: 10.1016/j.jtbi.2003.12.013] [Citation(s) in RCA: 75] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 11/25/2003] [Accepted: 12/09/2003] [Indexed: 11/20/2022]
Abstract
This article deals with modelling the simultaneous uptake of water and highly buffered nutrient, such as phosphate, by root branching structures from partially saturated soil. We use the simultaneous water and nutrient uptake model to investigate the effect that water movement has on nutrient uptake. With the aid of this model we are also able to show that the previous models by Barber and Tinker and Nye systematically underestimated the phosphate uptake, due to the oversimplified approach in dealing with root branching structure. In this article we show how this discrepancy can be remedied and the root branching structure included in the models of plant nutrient uptake. We will also discuss the differences in the results for continuous and spot fertilization combined with variable rainfall.
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A model for water uptake by plant roots. J Theor Biol 2004; 228:155-71. [PMID: 15094012 DOI: 10.1016/j.jtbi.2003.12.012] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2003] [Revised: 11/25/2003] [Accepted: 12/09/2003] [Indexed: 11/23/2022]
Abstract
We present a model for water uptake by plant roots from unsaturated soil. The model includes the simultaneous flow of water inside the root network and in the soil. It is constructed by considering first the water uptake by a single root, and then using the parameterized results thereby obtained to build a model for water uptake by the developing root network. We focus our model on annual plants, in particular the model will be applicable to commercial monocultures like maize, wheat, etc. The model is solved numerically, and the results are compared with approximate analytic solutions. The model predicts that as a result of water uptake by plant roots, dry and wet zones will develop in the soil. The wet zone is located near the surface of the soil and the depth of it is determined by a balance between rainfall and the rate of water uptake. The dry zone develops directly beneath the wet zone because the influence of the rainfall at the soil surface does not reach this region, due to the nonlinear nature of the water flow in the partially saturated soil. We develop approximate analytic expressions for the depth of the wet zone and discuss briefly its ecological significance for the plant. Using this model we also address the question of where water uptake sites are concentrated in the root system. The model indicates that the regions near the base of the root system (i.e. close to the ground surface) and near the root tips will take up more water than the middle region of the root system, again due to the highly nonlinear nature of water flow in the soil.
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Periodic breathing at high altitude. MATHEMATICAL MEDICINE AND BIOLOGY-A JOURNAL OF THE IMA 2002. [DOI: 10.1093/imammb/19.4.293] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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Abstract
The classical model of plant root nutrient uptake due to Nye. Tinker and Barber is developed and extended. We provide an explicit closed formula for the uptake by a single cylindrical root for all cases of practical interest by solving the absorption-diffusion equation for the soil nutrient concentration asymptotically in the limit of large time. We then use this single root model as a building block to construct a model which allows for root size distribution in a more realistic plant root system, and we include the effects of root branching and growth. The results are compared with previous theoretical and experimental studies.
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The effect of incubation time distribution on the extinction characteristics of a rabies epizootic. Bull Math Biol 2000; 62:633-55. [PMID: 10938626 DOI: 10.1006/bulm.1999.0170] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The continuous model of Anderson et al. (1981), Nature 289, 765-771, is successful in describing certain characteristics of rabies epizootics, in particular, the secondary recurrences which follow the initial outbreak; however, it also predicts the occurrence of exponentially small minima in the infected population, which would realistically imply extinction of the virus. Here we show that inclusion of a more realistic distribution of incubation times in the model can explain why extinction will not occur, and we give explicit parametric estimates for the minimum infected fox density which will occur in the model, in terms of the incubation time distribution.
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The role of the central chemoreceptor in causing periodic breathing. IMA JOURNAL OF MATHEMATICS APPLIED IN MEDICINE AND BIOLOGY 2000; 17:147-67. [PMID: 10994511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
In a previous publication (Fowler et al., 1993), we reduced the classical cardiorespiratory control model of (Grodins et al., 1967) to a much simpler form, which we then used to study the phenomenon of periodic breathing. In particular, cardiac output was assumed constant, and a single (constant) delay representing arterial blood transport time between lung and brain was included in the model. In this paper we extend this earlier work, both by allowing for the variability in transport delays, due to the dependence of cardiac output on blood gas concentrations, and also by including further delays in the system. In addition, we extensively discuss the physiological implications of parameter variations in the model; several novel mechanisms for periodic breathing in clinical situations are proposed. The results are discussed in the light of recent observational studies.
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Abstract
Irregularities in observed population densities have traditionally been attributed to discretization of the underlying dynamics. We propose an alternative explanation by demonstrating the evolution of spatiotemporal chaos in reaction-diffusion models for predator-prey interactions. The chaos is generated naturally in the wake of invasive waves of predators. We discuss in detail the mechanism by which the chaos is generated. By considering a mathematical caricature of the predator-prey models, we go on to explain the dynamical origin of the irregular behavior and to justify our assertion that the behavior we present is a genuine example of spatiotemporal chaos.
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Abstract
We present a method based on dynamical systems theory which can be used to filter time series in a way which is superior to classical Fourier decomposition. This method is applied to three data-sets, taken from respiratory measurements of two children in quiet and REM sleep. Our purpose is to filter the several different oscillatory mechanisms which operate, in order to provide clearer signals on which further analysis and diagnosis can be based.
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A mathematical analysis of the Grodins model of respiratory control. IMA JOURNAL OF MATHEMATICS APPLIED IN MEDICINE AND BIOLOGY 1993; 10:249-80. [PMID: 8133130 DOI: 10.1093/imammb/10.4.249] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The classical Grodins model of chemical respiratory control is analysed. Scaling and asymptotic analysis are used to reduce the model drastically to a much simplified form. In essence, the model consists of two separate controllers due to oxygen and carbon dioxide. The authors focus on the carbon dioxide controller, and show that it can be considered as two coupled delay recruitment equations. While, in normal circumstances, steady ventilation is stable, it is shown that, by varying controlling parameters, periodic and chaotic solutions may be obtained.
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A mathematical model of exoprotein production in bacteria. IMA JOURNAL OF MATHEMATICS APPLIED IN MEDICINE AND BIOLOGY 1984; 1:77-94. [PMID: 6600093 DOI: 10.1093/imammb/1.1.77] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
We present a simple mathematical model for the synthesis of extracellular proteins by a class of bacteria which secrete significant quantities of this exoprotein in late-exponential and stationary phases. This model is the simplest generalization of Michaelis-Menten kinetics (the Monod model) and agrees well with laboratory experiments in batch culture. The model may serve as a simple prototype for the analysis of certain virulent bacterial infections in vivo, particularly that of Pseudomonas aeruginosa in burn wounds.
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Abstract
A model of the humoral immune response, proposed by Dibrov, Livshits and Volkenstein (1977b), in which the antibody production by a constant target cell population depends on the antigenic stimulation at earlier times, is considered from an analytic standpoint. A method of approximation based on a consideration of the asymptotic limit of "large" delay in the antibody response is shown to be applicable, and to give results similar to those obtained numerically by the above authors. The relevance of this type of approximation to other systems exhibiting "outbreak" phenomena is discussed.
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