| 1. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Increasing effciency in the EBT algorithm
- 2019
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Ingår i: Proceedings of 18th Applied Stochastic Models and Data Analysis International Conference with the Demographics 2019 Workshop, Florence, Italy: 11-14 June, 2019. - : ISAST: International Society for the Advancement of Science and Technology. - 9786185180331 ; , s. 179-205
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Konferensbidrag (refereegranskat)abstract
- The Escalator Boxcar Train (EBT) is a commonly used method for solving physiologically structured population models. The main goal of this paper is to overcome computational disadvantages of the EBT method. We prove convergence, for a general class of EBT models in which we modify the original EBT formulation, allowing merging of cohorts. We show that this modified EBT method induces a bounded number of cohorts, independent of the number of time steps. This in turn, improve the numerical algorithm from polynomial to linear time. An EBT simulation of the Daphnia model is used as an illustration of these findings.
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| 2. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Increasing Efficiency in the EBT Algorithm
- 2020
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Ingår i: Demography of Population Health, Aging and Health Expenditures. - Cham : Springer. - 9783030446956 - 9783030446956 ; , s. 289-317
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Bokkapitel (refereegranskat)abstract
- The Escalator Boxcar Train (EBT) is a commonly used method for solving physiologically structured population models. The main goal of this paper is to overcome computational disadvantages of the EBT method. We prove convergence, for a general class of EBT models in which we modify the original EBT formulation, allowing merging of cohorts. We show that this modified EBT method induces a bounded number of cohorts, independent of the number of time steps. This in turn, improves the numerical algorithm from polynomial to linear time. An EBT simulation of the Daphnia model is used as an illustration of these findings.
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| 3. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Method development for emergent properties in stage-structured population models with stochastic resource growth.
- 2022
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Ingår i: <em>Springer Proceedings in Mathematics and Statistics</em>. - Cham : Springer International Publishing. ; , s. 33-58
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Konferensbidrag (refereegranskat)abstract
- Modelling population dynamics in ecological systems reveals properties that are difficult to find by empirical means, such as the probability that a population will go extinct when it is exposed to harvesting. In this article, we use an aquatic ecological system containing one fish species and an underlying resource as our model. In particular, we study a class of stage-structured population systems, in both the deterministic and the stochastic settings, including stochasticity in such a way such that we allow the underlying resource to have a random growth rate. In these models, we study how properties connected to the fish species depend on different harvesting rates. To investigate models in the stochastic setting, we use Monte Carlo simulations to capture several of the emergent properties of the population. These properties have previously been studied in the deterministic case. In the stochastic setting, we get estimates for the expected outcome of population properties in our model, but we also get measures of dispersion. There are properties that emerge when introducing randomness in the model that cannot be studied in the deterministic cases, such as the probability of extinction. In this paper, we develop a method to derive this property. We also construct a method to determine the recovery potential of a species by introducing it in a virgin environment.
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| 4. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Numerical stability of the escalator boxcar train under reducing system of ordinary differential equations.
- 2017
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Konferensbidrag (refereegranskat)abstract
- The Escalator Boxcar Train (EBT) is one of the most popular numericalmethods used to study the dynamics of physiologically structured population models.The original EBT model accumulates an increasing system of ODEs to solve for eachtime step. In this project, we propose a merging procedure to overcome computationaldisadvantageous of the EBT method, the merging is done as an automatic feature.In particular we apply the model including merging to a colony of Daphnia Pulex.
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| 5. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Pipe Model Theory for Prediction Tree Sapwood and Heartwood Profiles
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The classical pipe model theory introduced by Shinozaki, Yoda, Hozumi,and Kira (1964a,b) is used to estimate tree sapwood area. It rests on theconceptual idea that leaves are supported by pipes, serving as vascularpassages. The simple pipe model of plant form does not predict the heartwood area and is thus not suitable for stem diameter estimates below thetree crown. For this reason, Shinozaki, Yoda, Hozumi, and Kira (1964a)verbally described an extended pipe model theory of tree form that inprinciple accounts for the accumulation of disused pipes from discardedbranches and leaves. However, this pipe model theory of tree form is difficultto apply in practice as lost branches and leaves are rarely known. Here, we synthesize the pipe model theory of plant form with a recentlydeveloped theory of branch thinning that quantify discarded branches andleaves. This allows us to develop a new stem model of tree profiles frombreast height up to the top of the tree. We test the stem model performance on empirical data from four tree species across three continents.We find that the stem model accurately describes heartwood and sapwoodprofiles of all tested tree species (calibration; R2: 84-99 %). Furthermore,once calibrated to a tree species, the stem model predicts heartwood andsapwood profiles of conspecific trees in similar growing environments basedonly on the age and height of a tree (cross-validation / prediction; R2:62-98 %).
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| 6. |
- Aye, Tin Nwe, 1989-
(författare)
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POPULATION DYNAMICS AND TREE GROWTH STRUCTURE IN MATHEMATICAL ECOLOGY
- 2021
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis is based on four papers related to mathematical biology, where three papers focus on population dynamics and one paper concerns tree growth and stem structure. The first two papers are mainly devoted to studying the dynamics of physiologically structured population models by using Escalator Boxcar Train (EBT) method. The third paper concerns a class of stage-structured population systems, in both deterministic and stochastic settings. The fourth paper explores how a branch thinning model can be utilized to describe the cross-sectional area of the stem of a tree, thus generalizing the classical pipe model.In Paper I, we present a merging procedure to reduce the increasing system of ordinary differential equations generated by the EBT method. In particular, we modify the EBT method to include merging of cohorts. The accuracy of this model is explored on a colony of Daphnia Pulex.In Paper II, we study the convergence rate of the modified EBT model, allowing a general class of non-linear merging procedures. We show that this modified EBT method induces a bounded number of cohorts, independent of the number of time steps. This in turn, improves the speed of the numerical algorithm for solving the population dynamics from polynomial time to linear time, that is, the time consumption to find the solution is proportional to the number of time steps.In Paper III, a class of non-linear two-stage structured population models is studied with different growth rates for the unstructured food resource under different harvesting rates in both deterministic and stochastic settings. In the stochastic setting, we develop methods to evaluate emergent properties equivalent to the properties investigated in the deterministic case. In addition, new emergent properties, e.g. probability of extinction, are also investigated.In Paper IV, we explore the stem model which is developed by combining the pipe model and the branch thinning model. The stem model provides estimates of the heartwood, sapwood and stem cross-sectional area at any height. We corroborate the accuracy of our model with empirical data and the cross validation of our results shows a very high goodness of fit for the stem model.
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| 7. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Prediction of tree sapwood and heartwood profiles using pipe model and branch thinning theory
- 2022
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Ingår i: Tree Physiology. - : Oxford University Press. - 0829-318X .- 1758-4469. ; 42:11, s. 2174-2185
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Tidskriftsartikel (refereegranskat)abstract
- Estimates of tree heartwood and sapwood profiles are important in the pulp industry and for dynamic vegetation models, in which they determine tree biomechanical stability and hydraulic conductivity. Several phenomenological models of stem profiles have been developed for this purpose, based on assumptions on how tree crown and foliage distributions change over time. Here, we derive estimates of tree profiles by synthesizing a simple pipe model theory of plant form with a recently developed theory of branch thinning that from simple assumptions quantifies discarded branches and leaves. This allows us to develop a new trunk model of tree profiles from breast height up to the top of the tree. We postulate that leaves that are currently on the tree are connected by sapwood pipes, while pipes that previously connected discarded leaves or branches form the heartwood. By assuming that a fixed fraction of all pipes remain on the trunk after a branching event, as the trunk is traversed from the root system to the tips, this allows us to quantify trunk heartwood and sapwood profiles. We test the trunk model performance on empirical data from five tree species across three continents. We find that the trunk model accurately describes heartwood and sapwood profiles of all tested tree species (calibration; R2: 84-99%). Furthermore, once calibrated to a tree species, the trunk model predicts heartwood and sapwood profiles of conspecific trees in similar growing environments based only on the age and height of a tree (cross-validation/prediction; R2: 68-98%). The fewer and often contrasting parameters needed for the trunk model make it a potentially useful complementary tool for biologists and foresters.
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| 8. |
- Aye, Tin Nwe, 1989-, et al.
(författare)
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Properties in Stage-Structured Population Models with Deterministic and Stochastic Resource Growth
- 2022
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Ingår i: Journal of Applied Mathematics. - : Hindawi Limited. - 1110-757X .- 1687-0042. ; 2022
-
Tidskriftsartikel (refereegranskat)abstract
- Modelling population dynamics in ecological systems reveals properties that are difficult to find by empirical means, such as the probability that a population will go extinct when it is exposed to harvesting. To study these properties, we use an aquatic ecological system containing one fish species and an underlying resource as our models. In particular, we study a class of stage-structured population systems with and without starvation. In these models, we study the resilience, the recovery potential, and the probability of extinction and show how these properties are affected by different harvesting rates, both in a deterministic and stochastic setting. In the stochastic setting, we develop methods for deriving estimates of these properties. We estimate the expected outcome of emergent population properties in our models, as well as measures of dispersion. In particular, two different approaches for estimating the probability of extinction are developed. We also construct a method to determine the recovery potential of a species that is introduced in a virgin environment.
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| 9. |
- Backlund, Ulf, et al.
(författare)
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Semi-Bloch functions in several complex variables
- 2013
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- Let $M$ be an $n$-dimensional complex manifold. A holomorphic function $f:M\to \mathbb C$ is said to be semi-Bloch if for every $\lambda\in \mathbb C$ the function $g_\lambda=\exp(\lambda f(z))$ is normal on $M$. We characterise Semi-Bloch functions on infinitesimally Kobayashi non-degenerate $M$ in geometric as well as analytic terms. Moreover, we show that on such manifolds, semi-Bloch functions are normal.
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| 10. |
- Brännström, Åke, 1975-, et al.
(författare)
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On the convergence of the Escalator Boxcar Train
- 2013
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Ingår i: SIAM Journal on Numerical Analysis. - : Society for Industrial & Applied Mathematics (SIAM). - 0036-1429 .- 1095-7170. ; 51:6, s. 3213-3231
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Tidskriftsartikel (refereegranskat)abstract
- The Escalator Boxcar Train (EBT) is a numerical method that is widely used in theoretical biology to investigate the dynamics of physiologically structured population models, i.e., models in which individuals differ by size or other physiological characteristics. The method was developed more than two decades ago, but has so far resisted attempts to give a formal proof of convergence. Using a modern framework of measure-valued solutions, we investigate the EBT method and show that the sequence of approximating solution measures generated by the EBT method converges weakly to the true solution measure under weak conditions on the growth rate, birth rate, and mortality rate. In rigorously establishing the convergence of the EBT method, our results pave the way for wider acceptance of the EBT method beyond theoretical biology and constitutes an important step towards integration with established numerical schemes.Read More: http://epubs.siam.org/doi/abs/10.1137/120893215
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| 11. |
- Canpwonyi, S., et al.
(författare)
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On the Approximation of Physiologically Structured Population Model with a Three Stage-Structured Population Model in a Grazing System
- 2022
-
Ingår i: Springer Proc. Math. Stat.. - Cham : Springer. - 9783031178207 ; , s. 753-771
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Konferensbidrag (refereegranskat)abstract
- A great deal of ecological theory is based on simple Lotka-Volterra-type of unstructured population models in the study of complex population dynamics and communities. The main reason is to obtain important information for predicting their future evolution. In these unstructured models, it is assumed that all individuals in the population are identical, with the same birth and death rates, and consume equally from shared resources in a homogeneous environment. In reality, these assumptions are not biologically true but still forms a basis for modeling population ecology. We apply this paradigm on the grazing system consisting of coupled ordinary differential equations describing the dynamics of forage resource and livestock population in a grassland ecosystem. We do this by investigating the dynamics of the individuals at different life-history stages of juvenile and adult livestock. The mathematical derivation of the model is carried out to show how the physiologically structured population model can be approximated using a three stage-structured population model. Thus the resulting system of ordinary differential equations can be solved to predict density-dependent properties of the population since it provides a somewhat close-to-reality description of the natural and traditional grazing system. This model therefore certainly contains the needed information in the modeling methodology and accommodates the necessary amount of biological details about the population.
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| 12. |
- Carlsson, Linus, 1972-, et al.
(författare)
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A note on B-envelope of holomorphy and B-extendable domains
- 2008
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Ingår i: Complex Variables and Elliptic Equations. - Abingdon, Oxon, UK : Taylor & Francis. - 1747-6933 .- 1747-6941. ; 53:4, s. 307-309
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Tidskriftsartikel (refereegranskat)abstract
- Let B subset of H(infinity)(X) be a Banach Algebra on a Riemann domain X over C(n). We show that under certain conditions on B and X, all functions in B can be extended to functions in B(E(B, X)) where E(B, X) is the B-envelope of holomorphy.
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| 13. |
- Carlsson, Linus, 1972-
(författare)
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An equivalence to the Gleason problem
- 2010
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Ingår i: Journal of Mathematical Analysis and Applications. - : Elsevier BV. - 0022-247X .- 1096-0813. ; 370:2, s. 373-378
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Tidskriftsartikel (refereegranskat)abstract
- In this article we study the Gleason problem locally. A new method for solving the Gleason A problem is presented. This is done by showing an equivalent statement to the Gleason A problem. In order to prove this statement, necessary and a sufficient conditions for a bounded domain to have the Gleason A property are found. Also an example of a bounded but not smoothly-bounded domain in C(n) is given, which satisfies the sufficient condition at the origin, and hence has the Gleason A property there.
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| 14. |
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| 15. |
- Carlsson, Linus, 1972-
(författare)
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Ideals and boundaries in Algebras of Holomorphic functions
- 2006
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- We investigate the spectrum of certain Banach algebras. Properties like generators of maximal ideals and generalized Shilov boundaries are studied. In particular we show that if the ∂-equation has solutions in the algebra of bounded functions or continuous functions up to the boundary of a domain D ⊂⊂ Cn then every maximal ideal over D is generated by the coordinate functions. This implies that the fibres over D in the spectrum are trivial and that the projection on Cn of the n − 1 order generalized Shilov boundary is contained in the boundary of D.For a domain D ⊂⊂ Cn where the boundary of the Nebenhülle coincide with the smooth strictly pseudoconvex boundary points of D we show that there always exist points p ∈ D such that D has the Gleason property at p.If the boundary of an open set U is smooth we show that there exist points in U such that the maximal ideals over those points are generated by the coordinate functions.An example is given of a Riemann domain, Ω, spread over Cn where the fibers over a point p ∈ Ω consist of m > n elements but the maximal ideal over p is generated by n functions.
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| 16. |
- Carlsson, Linus, 1972-
(författare)
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Nebenhülle and the Gleason problem
- 2010
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Ingår i: Proceedings of the American Mathematical Society. - : American Mathematical Society (AMS). - 0002-9939 .- 1088-6826. ; 138:1, s. 267-273
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Tidskriftsartikel (refereegranskat)
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| 17. |
- Carlsson, Linus, 1972-, et al.
(författare)
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Spectrum of certain Banach algebras and DBAR-problems
- 2007
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Ingår i: Annales Polonici Mathematici. - 0066-2216. ; 90:1, s. 51-58
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Tidskriftsartikel (refereegranskat)abstract
- We study the spectrum of certain Banach algebras of holomorphic functions defined on a domain Ω where ∂−-problems with certain estimates can be solved. We show that the projection of the spectrum onto Cn equals Ω−− and that the fibers over Ω are trivial. This is used to solve a corona problem in the special case where all but one generator are continuous up to the boundary.
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| 18. |
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| 19. |
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| 20. |
- Carlsson, Linus, 1972-
(författare)
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Trivial generators for nontrivial fibres
- 2008
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Ingår i: MATHEMATICA BOHEMICA. - 0862-7959. ; 133:2, s. 121-131
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Tidskriftsartikel (refereegranskat)abstract
- Pseudoconvex domains are exhausted in such a way that we keep a part of the boundary fixed in all the domains of the exhaustion. This is used to solve a problem concerning whether the generators for the ideal of either the holomorphic functions continuous up to the boundary or the bounded holomorphic functions, vanishing at a point in $\mathbb{C}^n$ where the fibre is nontrivial, has to exceed $n$. This is shown not to be the case.
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| 21. |
- Hellgren, Mikko, 1972-, et al.
(författare)
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Enrichment of ligands with molecular dockings and subsequent characterization for human alcohol dehydrogenase 3
- 2010
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Ingår i: CELLULAR AND MOLECULAR LIFE SCIENCES. - : Springer Science Business Media. - 1420-682X .- 1420-9071. ; 67:17, s. 3005-3015
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Tidskriftsartikel (refereegranskat)abstract
- Alcohol dehydrogenase 3 (ADH3) has been assigned a role in nitric oxide homeostasis due to its function as an S-nitrosoglutathione reductase. As altered S-nitrosoglutathione levels are often associated with disease, compounds that modulate ADH3 activity might be of therapeutic interest. We performed a virtual screening with molecular dockings of more than 40,000 compounds into the active site of human ADH3. A novel knowledge-based scoring method was used to rank compounds, and several compounds that were not known to interact with ADH3 were tested in vitro. Two of these showed substrate activity (9-decen-1-ol and dodecyltetraglycol), where calculated binding scoring energies correlated well with the logarithm of the k (cat)/K (m) values for the substrates. Two compounds showed inhibition capacity (deoxycholic acid and doxorubicin), and with these data three different lines for specific inhibitors for ADH3 are suggested: fatty acids, glutathione analogs, and cholic acids.
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| 22. |
- Hellström, Lars, 1974-, et al.
(författare)
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Branch Thinning and the Large-Scale, Self-Similar Structure of Trees
- 2018
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Ingår i: American Naturalist. - : UNIV CHICAGO PRESS. - 0003-0147 .- 1537-5323. ; 192:1, s. E37-E47
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Tidskriftsartikel (refereegranskat)abstract
- Branch formation in trees has an inherent tendency toward exponential growth, but exponential growth in the number of branches cannot continue indefinitely. It has been suggested that trees balance this tendency toward expansion by also losing branches grown in previous growth cycles. Here, we present a model for branch formation and branch loss during ontogeny that builds on the phenomenological assumption of a branch carrying capacity. The model allows us to derive approximate analytical expressions for the number of tips on a branch, the distribution of growth modules within a branch, and the rate and size distribution of tree wood litter produced. Although limited availability of data makes empirical corroboration challenging, we show that our model can fit field observations of red maple (Acer rubrum) and note that the age distribution of discarded branches predicted by our model is qualitatively similar to an empirically observed distribution of dead and abscised branches of balsam poplar (Populus balsamifera). By showing how a simple phenomenological assumptionthat the number of branches a tree can maintain is limitedleads directly to predictions on branching structure and the rate and size distribution of branch loss, these results potentially enable more explicit modeling of woody tissues in ecosystems worldwide, with implications for the buildup of flammable fuel, nutrient cycling, and understanding of plant growth.
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| 23. |
- Mishra, Rajesh, 1973-, et al.
(författare)
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A conformationally isoformic thermophilic protein with high kinetic unfolding barriers
- 2008
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Ingår i: Cellular and Molecular Life Sciences (CMLS). - : Springer Science and Business Media LLC. - 1420-682X .- 1420-9071. ; 65:5, s. 827-839
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Tidskriftsartikel (refereegranskat)abstract
- The basis for the stability of thermophilic proteins is of fundamental interest for extremophile biology. We investigated the folding and unfolding processes of the homotetrameric Thermoanaerobacter brockii alcohol dehydrogenase (TBADH). TBADH subunits were 4.8 kcal/mol less stable towards guanidinium chloride (GdmCl) unfolding compared to urea, indicating ionic modulation of TBADH stability. Strongly denaturing conditions promoted mono-exponential unfolding kinetics with linear dependence on denaturant concentration. Here TBADH unfolded >40-fold slower when extrapolated from urea as compared to GdmCl unfolding. A marked unfolding hysteresis was shown when comparing refolding and unfolding in urea. An unusual biphasic unfolding trajectory with an exceptionally slow phase at intermediate concentrations of GdmCl and urea was also observed. We advocate that TBADH forms two distinctly different tetrameric isoforms, and likely an ensemble of native states. This unusual supramolecular folding behavior has been shown responsible for formation of amyloidotic yeast prion strains and can have functional importance for TBADH. © 2008 Birkhaueser.
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| 24. |
- Nankinga, L., et al.
(författare)
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A Mathematical Model for Harvesting in a Stage-Structured Cannibalistic System
- 2022
-
Ingår i: Springer Proc. Math. Stat.. - Cham : Springer. - 9783031178207 ; , s. 735-751
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Konferensbidrag (refereegranskat)abstract
- To increase the production of proteins in East Africa, aquaculture gained increased attention recently. In this paper, we study the interactions of a consumer-resource system with harvesting, in which African Catfish (Gl ar i as gar i epi nus) consume a food resource. The cannibalistic behavior of African Catfish is captured by using a four stage-structured system. The dynamics of food resource and African Catfish result in a system of ordinary differential equations called a stage-structured fish population model. Existence and stability of steady states are analyzed quantitatively. We have investigated eight different harvesting scenarios which account for yield of the fish stock. Results from the simulations revealed that harvesting large juveniles and small adults under equal harvesting rates gives the highest maximum sustainable yield compared to other harvesting scenarios. In contrast to non-cannibalistic models, we find an increase of the proportion of the adult individuals under harvesting.
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| 25. |
- Nankinga, L., et al.
(författare)
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A Stage-Structured Fishery Model for African Catfish and Nile Tilapia Feeding on Two Food Resources with Harvesting
- 2022
-
Ingår i: Journal of Applied Mathematics. - : Hindawi Publishing Corporation. - 1110-757X .- 1687-0042.
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Tidskriftsartikel (refereegranskat)abstract
- In this paper, a fishery model for African catfish and Nile tilapia is formulated. This model is used to compare financial profit and biomass outtakes in a two-species system versus single species systems. We consider a stage-structured fish population model consisting of the aforementioned fish species together with two food resources. The model dynamics include cannibalism, predator-prey, feeding, reproduction, maturation, development, mortality, and harvesting. We prove consistency of the model in the sense that the solutions will stay bounded and nonnegative over time. Conditions for local stability of fish-free equilibrium point are established. The simulation results reveal asymptotically stable solutions with coexistence of African catfish, Nile tilapia, and two food resources. The major conclusion from our findings is that fisheries should culture both species to maximize the biomass outtake and financial profit.
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