Modelling and quantifying the effect of heterogeneity in soil physical conditions on fungal growth

Despite the importance of fungi in soil ecosystem services, a theoretical framework that links soil management strategies with fungal ecology is still lacking. One of the key challenges is to understand how the complex geometrical shape of pores in soil affects fungal spread and species interaction. Progress in this area has long been hampered by a lack of experimental techniques for quantification. In this paper we use X-ray computed tomography to quantify and characterize the pore geometry at microscopic scales (30 μm) that are relevant for fungal spread in soil. We analysed the pore geometry for replicated samples with bulk-densities ranging from 1.2–1.6 g/cm3. The bulk-density of soils significantly affected the total volume, mean pore diameter and connectivity of the pore volume. A previously described fungal growth model comprising a minimal set of physiological processes required to produce a range of phenotypic responses was used to analyse the effect of these geometric descriptors on fungal invasion, and we showed that the degree and rate of fungal invasion was affected mainly by pore volume and pore connectivity. The presented experimental and theoretical framework is a significant first step towards understanding how environmental change and soil management impact on fungal diversity in soils

The Motor System: The Whole and its Parts

Our knowledge of components of the human motor system has been growing steadily, but our understanding of its integration into a system is lagging behind. It is suggested that a combination of measurements of forces and movements of the motor system in a functionally meaningful environment in conjunction with computer simulations of the motor system may help us in understanding motor system properties. Neurotrauma can be seen as a natural deviation, with recovery as a slow path to yet another deviant state of the motor system. In that form they may be useful in explaining the close interaction between form and function of the human motor system

Multi-Joint Dynamics and the Development of Movement Control

The movement control of articulated limbs in humans has been explained in terms of equilibrium points and moving equilibrium points or virtual trajectories. One hypothesis is that the nervous system controls multi-segment limbs by simply planning in terms of these equilibrium points and trajectories. The present paper describes a planar computer simulation of an articulated three-segment limb, controlled by pairs of muscles. The shape of the virtual trajectory is analyzed when the limb is required to make fast movements with endpoint movements along a straight line with bell-shaped velocity profiles. Apparently, the faster the movement, the more the virtual trajectory deviates from the real trajectory and becomes up to eight times longer. The complexity of the shape of the virtual trajectories and its length in these fast movements makes it unlikely that the nervous system plans using these trajectories. it seems simpler to set up the required bursts of muscle activation, coupled in the nervous system to the direction of movement, the s peed, and the place in workspace. Finally, it is argued that the two types of explanation do not contradict each other: when a relation is established in the nervous system between muscle activation and movements, equilibrium points and virtual trajectories are necessarily part of that relation

Hardware acceleration of reaction-diffusion systems:a guide to optimisation of pattern formation algorithms using OpenACC

Reaction Diffusion Systems (RDS) have widespread applications in computational ecology, biology, computer graphics and the visual arts. For the former applications a major barrier to the development of effective simulation models is their computational complexity - it takes a great deal of processing power to simulate enough replicates such that reliable conclusions can be drawn. Optimizing the computation is thus highly desirable in order to obtain more results with less resources. Existing optimizations of RDS tend to be low-level and GPGPU based. Here we apply the higher-level OpenACC framework to two case studies: a simple RDS to learn the ‘workings’ of OpenACC and a more realistic and complex example. Our results show that simple parallelization directives and minimal data transfer can produce a useful performance improvement. The relative simplicity of porting OpenACC code between heterogeneous hardware is a key benefit to the scientific computing community in terms of speed-up and portability

Determination of the standard free energy of formation of Zr₃S₂

The Knudsen effusion method was used to find the equilibrium magnesium pressure for the reaction 3 Zr (s) + 2 MgS (s) = \u27Zr3S2\u27 (s) + 2 Mg (v) By using known standard free energy data for the formation of magnesium sulfide and by using the equilibrium magnesium pressure, the standard free energy of formation of Zr3S2 was calculated and could be expressed by the equation Δ F° = -139,800 + 49.13 T cal/mole in the temperature range 900 to 1100°C. It was also found that Zr3S2 was the zirconium sulfide of lowest sulfur content --Abstract, page ii

Emergent behavior of soil fungal dynamics:influence of soil architecture and water distribution

Macroscopic measurements and observations in two-dimensional soil-thin sections indicate that fungal hyphae invade preferentially the larger, air-filled pores in soils. This suggests that the architecture of soils and the microscale distribution of water are likely to influence significantly the dynamics of fungal growth. Unfortunately, techniques are lacking at present to verify this hypothesis experimentally, and as a result, factors that control fungal growth in soils remain poorly understood. Nevertheless, to design appropriate experiments later on, it is useful to indirectly obtain estimates of the effects involved. Such estimates can be obtained via simulation, based on detailed micron-scale X-ray computed tomography information about the soil pore geometry. In this context, this article reports on a series of simulations resulting from the combination of an individual-based fungal growth model, describing in detail the physiological processes involved in fungal growth, and of a Lattice Boltzmann model used to predict the distribution of air-liquid interfaces in soils. Three soil samples with contrasting properties were used as test cases. Several quantitative parameters, including Minkowski functionals, were used to characterize the geometry of pores, air-water interfaces, and fungal hyphae. Simulation results show that the water distribution in the soils is affected more by the pore size distribution than by the porosity of the soils. The presence of water decreased the colonization efficiency of the fungi, as evinced by a decline in the magnitude of all fungal biomass functional measures, in all three samples. The architecture of the soils and water distribution had an effect on the general morphology of the hyphal network, with a "looped" configuration in one soil, due to growing around water droplets. These morphologic differences are satisfactorily discriminated by the Minkowski functionals, applied to the fungal biomass

Modelling fungal growth in heterogeneous soil:analyses of the effect of soil physical structure on water distribution and fungal colonisation

Fungi play a pivital role in soil ecosystems contributing to plant productivity. The underlying soil physical and biological processes responsible for fungal colonistaion are interrelated and, at present, poorly understood. If these complex processes can be understood then this knowledge can be managed with an aim to providing more sustainable agriculture. Our understanding of microbial dynamics in soil has long been hampered by a lack of a theoretical framework and difficulties in observation and quantification. We will demonstrate how the spatial and temporal dynamics of fungi in soil can be understood by linking mathematical modelling with novel techniques that visualise the complex structure of the soil. The combination of these techniques and mathematical models opens up new possibilities to understand how the physical structure of soil affects water distribution which subsequently impacts on fungal colony dynamics. We will quantify, using X ray tomography, soil structure for a range of artificially prepared microcosms. We characterise the soil structures using soil metrics such as porosity, pore size distribution, and the connectivity of the pore volume. We use Lattice Boltzmann methods to predict the distribution of water in these soil microcosms. Furthermore we will use the individual based fungal colony growth model of Falconer et al. 2005, which is based on the physiological processes of fungi, to assess the effect of soil structure on water dynamics and microbial dynamics by qualifying biomass distributions. We demonstrate how soil structure can critically affect fungal colony growth and species interactions and how the distribution of water also effects this with consequences for biological control and fungal biodiversity

Combining X-ray CT and 3D printing technology to produce microcosms with replicable, complex pore geometries

Measurements in soils have been traditionally used to demonstrate that soil architecture is one of the key drivers of soil processes. Major advances in the use of X-ray Computed Tomography (CT) afford significant insight into the pore geometry of soils, but until recently no experimental techniques were available to reproduce this complexity in microcosms. This article describes a 3D additive manufacturing technology that can print physical structures with pore geometries reflecting those of soils. The process enables printing of replicated structures, and the printing materials are suitable to study fungal growth. This technology is argued to open up a wealth of opportunities for soil biological studies

Simulating microbial degradation of organic matter in a simple porous system using the 3-D diffusion-based model MOSAIC

This paper deals with the simulation of microbial degradation of organic matter in soil within the pore space at a microscopic scale. Pore space was analysed with micro-computed tomography and described using a sphere network coming from a geometrical modelling algorithm. The biological model was improved regarding previous work in order to include the transformation of dissolved organic compounds and diffusion processes. We tested our model using experimental results of a simple substrate decomposition experiment (fructose) within a simple medium (sand) in the presence of different bacterial strains. Separate incubations were carried out in microcosms using five different bacterial communities at two different water potentials of −10 and −100 cm of water. We calibrated the biological parameters by means of experimental data obtained at high water content, and we tested the model without changing any parameters at low water content. Same as for the experimental data, our simulation results showed that the decrease in water content caused a decrease of mineralization rate. The model was able to simulate the decrease of connectivity between substrate and microorganism due the decrease of water content