42 research outputs found
The role of plant traits in the regulation of diversity : a modelling study
According to the principle of competitive exclusion, the number of resources determines the number of different plant types that are able to coexist. In this thesis, it is investigated whether plant types can maintain themselves in a homogeneous environment that has only one limiting resource, simply by possessing different traits.
To investigate growth and competitive interactions of plants that possess different traits, a model was developed. Light availability was presumed as the only limiting resource. The plant growth was mechanistic in the way that growth of plant organs was not superimposed on the plant, but was at any time determined by the allocation to organs and the costs and benefits this brought about in relation to neighbouring plants. Only one trait at a time was varied in value. This provided a good way to isolate the role of particular traits and assess the adaptiveness of different values of the trait. A closer look was taken on the role of investment in height growth, crown architecture, seed production and dispersal as determinants for growth, competition, and coexistence between plants. Additionally, the effects of density and frequency dependency were investigated with help of game theory.
In the different simulations reported in this thesis, several factors promoting coexistence under light limitation were found. Interestingly, the role of any plant trait in itself for generating coexistence was limited. These plant traits, however, were the basis for less tangible factors that did affect coexistence. It was the interplay of plant traits with frequency and density dependent processes and the inclusion of space that generated possibilities for plants to live together. By the different susceptibility of plants with different traits to frequency, density and space, situations were created where each of the types could be successful. It is noted explicitly here that the investment patterns of plants and the emerging traits were the actual mechanism through which all other processes worked.
By including mechanisms at the plant and organ scale in the simulations of processes at population or community scale, self-assembling communities were achieved without inserting community-level specifications. The community structures obtained were truly a result of underlying mechanisms. Some general statements could be formulated on the influence of plants’ investment patterns on competition, population development and coexistence, independent of variation in external factors for growth
Multiple verification in computational modeling of bone pathologies
We introduce a model checking approach to diagnose the emerging of bone
pathologies. The implementation of a new model of bone remodeling in PRISM has
led to an interesting characterization of osteoporosis as a defective bone
remodeling dynamics with respect to other bone pathologies. Our approach allows
to derive three types of model checking-based diagnostic estimators. The first
diagnostic measure focuses on the level of bone mineral density, which is
currently used in medical practice. In addition, we have introduced a novel
diagnostic estimator which uses the full patient clinical record, here
simulated using the modeling framework. This estimator detects rapid (months)
negative changes in bone mineral density. Independently of the actual bone
mineral density, when the decrease occurs rapidly it is important to alarm the
patient and monitor him/her more closely to detect insurgence of other bone
co-morbidities. A third estimator takes into account the variance of the bone
density, which could address the investigation of metabolic syndromes, diabetes
and cancer. Our implementation could make use of different logical combinations
of these statistical estimators and could incorporate other biomarkers for
other systemic co-morbidities (for example diabetes and thalassemia). We are
delighted to report that the combination of stochastic modeling with formal
methods motivate new diagnostic framework for complex pathologies. In
particular our approach takes into consideration important properties of
biosystems such as multiscale and self-adaptiveness. The multi-diagnosis could
be further expanded, inching towards the complexity of human diseases. Finally,
we briefly introduce self-adaptiveness in formal methods which is a key
property in the regulative mechanisms of biological systems and well known in
other mathematical and engineering areas.Comment: In Proceedings CompMod 2011, arXiv:1109.104
Exploring the zebrafish embryo as an alternative model for the evaluation of liver toxicity by histopathology and expression profiling. Arch.Toxicol. 87, no. 5:807-823
Drug Delivery Technolog
Diversity by temporal oscillations in plant communities with a differential timing of reproduction
Background and Aims: Species can coexist at non-equilibrium circumstances, for
instance by oscillations in population densities or chaos, caused by non-linear responses of
species to their environment. We analyzed whether plant genotypes that vary in their timing of
reproduction can coexist under equilibrium or non-equilibrium circumstances when
competing for light.
Methods: We used a game theoretical approach, based on a biologically mechanistic
model of plant growth.
Key Results: In our model, the genotype switching to reproduction slightly later than its
competitor attained a higher fitness. This caused a succession from early switching genotypes
to those switching later to reproductive investment. However, there were cyclic opportunities
for extinct genotypes that switch early to reproduction to re-establish and grow into the
community. The cause was that genotypes that switched very late produced relatively very
little seed because of an overinvestment in vegetative growth; especially when competing
against individuals of the same genotype. Because the very early switch genotypes could
establish, circumstances were such that other extinct switch genotypes could re-enter the
vegetation as well. In this way the diversity of genotypes was maintained over time by
temporal oscillations of genotype abundances.
Conclusions: We show that within a model, an externally undisturbed plant community
can produce its own temporal cyclic or chaotic disturbances to promote diversity, rather than converge to a stable equilibrium when competing for light. Cyclic fluctuations in species
composition can occur in a model community of plants sharing the same growing season and
that are limited just by light as a single resource
Towards design space exploration for biological systems
For both embedded systems and biological cell systems, design is a feature that defines their identity. The assembly of different components in designs of both systems can vary widely. Given the similarities between computers and cellular systems, methods and models of computation from the domain of computer systems engineering could be applied to model cellular systems. Our aim is to construct a framework that focuses on understanding the design options and consequences within a cell, taking an in-silico (forward-) engineering approach rather than the reverse-engineering approach now used by default in this domain. We take our ideas from the domain of embedded computer systems. The most important features of our approach, as taken from this domain, are a variable abstraction level of model components that allows for inclusion of components of which detailed information is lacking, and a separation of concerns between function and performance by components in the design. This allows for efficient and flexible modeling. Also, there is a strict separation between computation within and communication between components, thus reducing complexity. As a proof-of-principle, we show that we can make a statement regarding the design of the gene expression machinery of a cell to produce a protein, using such a method