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

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

Plants that differ in height investment can coexist if they are distributed non-uniformly within an area.

In nature, there is a large variability in the intrinsic height of plants living within an area. The question arises whether these height differences affect the plants' ability to coexist and thus is an adaptive trait. Using a biologically mechanistic model, we explored the possibilities for coexistence of plant types that differ in their pattern of allocation between stem (i.e. height growth) and other organs. We simulated the competition for light between growing individual plants. The study was game theoretical in the sense that each individual plant at any time affected the light availability for all plants in a locality, making conditions variable throughout the growing season and between seasons when the composition of competing plants changed. It was found that plant types that differed in their allocation to height growth could coexist over the course of years when these plants distributed their seeds non-uniformly in space, creating local differences in plant density. At each different density, one type with a specific investment in height performed better (i.e. achieved a greater seed production) than the rest of the types, thus preventing the exclusion of that type over the years. The resulting model community was self-assembling; local densities and competitive pressures originated as traits from the model plants themselves and were not the result of imposed external factors acting upon the model community. This mechanistic modelling approach shows that a condition as simple as a non-uniform distribution of seeds can generate the conditions for plants of various height growth strategies to live together over multiple generations. This study suggests that differences in plant height can be an emerging property of dispersing populations.</p