Dynamic simulation of cyclic batch anaerobic digestion of cattle manure

Cyclic batch reactors with periodical feeds and extractions, are often used in cattle manure anaerobic digestion. The dynamic behavior of this type of reactor was simulated in this study. The kinetic model developed by I. Angelidaki et al. [Biotechnol. Bioeng. 42 (1993) 159], together with microbial growth kinetics, conventional material balances for an ideally cyclic batch reactor, liquid-gas interactions, and liquid phase equilibrium chemistry were used in this study. The model showed good agreement with the experimental data of R.I. Mackie and M.P. Bryant [Appl. Microbiol. Biotechnol. 43 (1995) 346], and R. Borja et al. [Chem. Eng. J. 54 (1994) B9]. The effects of hydraulic retention time (HRT), organic loading rate, reactant concentrations, feeding interval, and initial conditions such as pH and ammonia concentration on process performance can be evaluated by the dynamic model. Also simulation results show that the equilibrium conditions can be considered for CO2 distribution between liquid and gas phases, especially for processes with long retention times.     

A rule-based model of barley morphogenesis, with special respect to shading and gibberellic acid signal transduction

BACKGROUND AND AIMS: Functional-structural plant models (FSPM) constitute a paradigm in plant modelling that combines 3D structural and graphical modelling with the simulation of plant processes. While structural aspects of plant development could so far be represented using rule-based formalisms such as Lindenmayer systems, process models were traditionally written using a procedural code. The faithful representation of structures interacting with functions across scales, however, requires a new modelling formalism. Therefore relational growth grammars (RGG) were developed on the basis of Lindenmayer systems. METHODS: In order to implement and test RGG, a new modelling language, the eXtended L-system language (XL) was created. Models using XL are interpreted by the interactive, Java-based modelling platform GroIMP. Three models, a semi-quantitative gibberellic acid (GA) signal transduction model, and a phytochrome-based shade detection and object avoidance model, both coupled to an existing morphogenetic structural model of barley (Hordeum vulgare L.), serve as examples to demonstrate the versatility and suitability of RGG and XL to represent the interaction of diverse biological processes across hierarchical scales. KEY RESULTS: The dynamics of the concentrations in the signal transduction network could be modelled qualitatively and the phenotypes of GA-response mutants faithfully reproduced. The light model used here was simple to use yet effective enough to carry out local measurement of red:far-red ratios. Suppression of tillering at low red:far-red ratios could be simulated. CONCLUSIONS: The RGG formalism is suitable for implementation of multi-scaled FSPM of plants interacting with their environment via hormonal control. However, their ensuing complexity requires careful design. On the positive side, such an FSPM displays knowledge gaps better thereby guiding future experimental design.     

Shaken helical track bioreactors: Providing oxygen to high-density cultures of mammalian cells at volumes up to 1000 L by surface aeration with air

A new scalable reactor was developed by applying a novel mixing principle that allows the large-scale cultivation of mammalian cells simply with surface aeration using air owing to increased liquid-gas transfer compared to standard stirred-tank bioreactors. In the cylindrical vessels (50 mL-1500 L) with a helical track attached to the inside wall, the liquid moved upward onto the track as the result of orbital shaking to increase the liquid-gas interface area significantly. This typically resulted in a 5-10-fold improvement in the volumetric mass transfer coefficient (k(L)a). In a 1500-L helical track vessel with a working volume of 1000 L, a k(L)a of 10h(-1) was obtained at a shaking speed of 39 rpm. Cultivations of CHO cells in a shaken 55-L helical track bioreactor resulted in improved cell growth profiles compared to control cultures in standard systems. These results demonstrated the possibility of using these new bioreactors at scales of 1000 L or more.     

Measuring collective behaviour of multicellular ensembles: role of space-time scales

Living systems are spectacular examples of spatiotemporally organized structures. During the development of complex organization there is dynamic equilibrium between the local and global processes acting at the intra-and intercellular levels in multiple space and time scales. Although in modelling studies such spatiotemporal systems can be described by different space-time scales and at many organizational levels, the experimental quantities measured and predictions useful for practical applications are at a macroscopic (coarser or averaged) level/scale; these are limited by the resolution of the measuring method and experimental protocol. In this work, we address whether the spatiotemporal collective dynamics exhibited by a multiscale system can discriminate between, or be borne out by, the coarse-grained and averaged measurements done at different spatial and temporal scales. Using a simple model of a ring of cells, we show that measurements of both spatial and spatiotemporal average behaviour in this multicellular ensemble can mask the variety of collective dynamics observed at other space-time scales, and exhibit completely different behaviours. Such outcomes of measurements can lead to incomplete and incorrect understanding of physiological functions and pathogenesis in multicell ensembles.     

Fish (Labeo rohita) Scales as Potential Low-Cost Biosorbent for Removal of Malachite Green from Aqueous Solutions

The feasibility of using fish (Labeo rohita) scales as low-cost biosorbent for the removal of hazardous Malachite Green (MG) dye from aqueous solutions was investigated. Employing a batch experimental setup, the effect of operational parameters such as biosorbent dose, initial solution pH, contact time, and temperature on the dye removal process was studied. The equilibrium biosorption data followed both Langmuir and Freundlich isotherm models, whereas the experimental kinetic data fitted well to the pseudo-second-order kinetic model. Thermodynamic study indicated spontaneous and endothermic nature of the biosorption process. The results suggest that fish scales could be used as an effective biosorbent for removal of MG dye from aqueous solutions.     

Mechanics of stabilized intercellular bridges

Numerous engineered and natural systems form through reinforcement and stabilization of a deformed configuration that was generated by a transient force. An important class of such structures arises during gametogenesis, when a dividing cell undergoes incomplete cytokinesis, giving rise to daughter cells that remain connected through a stabilized intercellular bridge (ICB). ICBs can form through arrest of the contractile cytokinetic furrow and its subsequent stabilization. Despite knowledge of the molecular components, the mechanics underlying robust ICB assembly and the interplay between ring contractility and stiffening are poorly understood. Here, we report joint experimental and theoretical work that explores the physics underlying robust ICB assembly. We develop a continuum mechanics model that reveals the minimal requirements for the formation of stable ICBs, and validate the model’s equilibrium predictions through a tabletop experimental analog. With insight into the equilibrium states, we turn to the dynamics: we demonstrate that contractility and stiffening are in dynamic competition and that the time intervals of their action must overlap to ensure assembly of ICBs of biologically observed proportions. Our results highlight a mechanism in which deformation and remodeling are tightly coordinated—one that is applicable to several mechanics-based applications and is a common theme in biological systems spanning several length scales.     

Predator–prey interactions in a ladybeetle–aphid system depend on spatial scale

The outcome of species interactions may manifest differently at different spatial scales; therefore, our interpretation of observed interactions will depend on the scale at which observations are made. For example, in ladybeetle–aphid systems, the results from small‐scale cage experiments usually cannot be extrapolated to landscape‐scale field observations. To understand how ladybeetle–aphid interactions change across spatial scales, we evaluated predator–prey interactions in an experimental system. The experimental habitat consisted of 81 potted plants and was manipulated to facilitate analysis across four spatial scales. We also simulated a spatially explicit metacommunity model parallel to the experiment. In the experiment, we found that the negative effect of ladybeetles on aphids decreased with increasing spatial scales. This pattern can be explained by ladybeetles strongly suppressing aphids at small scales, but not colonizing distant patches fast enough to suppress aphids at larger scales. In the experiment, the positive effects of aphids on ladybeetles were strongest at three‐plant scale. In a model scenario where predators did not have demographic dynamics, we found, consistent with the experiment, that both the effects of ladybeetles on aphids and the effects of aphids on ladybeetles decreased with increasing spatial scales. These patterns suggest that dispersal was the primary cause of ladybeetle population dynamics in our experiment: aphids increased ladybeetle numbers at smaller scales because ladybeetles stayed in a patch longer and performed area‐restricted searches after encountering aphids; these behaviors did not affect ladybeetle numbers at larger spatial scales. The parallel experimental and model results illustrate how predator–prey interactions can change across spatial scales, suggesting that our interpretation of observed predator–prey dynamics would differ if observations were made at different scales. This study demonstrates how studying ecological interactions at a range of scales can help link the results of small‐scale ecological experiments to landscape‐scale ecological problems.     

Multiscale computational models can guide experimentation and targeted measurements for crop improvement

Computational models of plants have identified gaps in our understanding of biological systems, and have revealed ways to optimize cellular processes or organ‐level architecture to increase productivity. Thus, computational models are learning tools that help direct experimentation and measurements. Models are simplifications of complex systems, and often simulate specific processes at single scales (e.g. temporal, spatial, organizational, etc.). Consequently, single‐scale models are unable to capture the critical cross‐scale interactions that result in emergent properties of the system. In this perspective article, we contend that to accurately predict how a plant will respond in an untested environment, it is necessary to integrate mathematical models across biological scales. Computationally mimicking the flow of biological information from the genome to the phenome is an important step in discovering new experimental strategies to improve crops. A key challenge is to connect models across biological, temporal and computational (e.g. CPU versus GPU) scales, and then to visualize and interpret integrated model outputs. We address this challenge by describing the efforts of the international Crops in silico consortium.     

Evaluation of ethanol evaporation losses in acetic acid fermentations

Three different operation systems have been employed at laboratory, pilot plant and industrial scales. Developed experimentation has demonstrated that quantified ethanol losses minimize significantly when operating at low temperatures with low aerations and when mainly working with the closed system.     

Thermodynamic modeling of the partitioning of biomolecules in aqueous two-phase systems using a modified Flory–Huggins equation

A modified Flory–Huggins equation accounting for the solvation of polymer molecules by water molecules was used to model the phase behavior of aqueous two-phase systems (ATPS) formed by poly(ethylene glycol) (PEG) and dextran. The parameters of the equation were obtained by fitting experimental equilibrium data either accounting for or disregarding dextran polidispersity. The modified equation was subsequently applied to calculate partition coefficients of biomolecules in these systems. It was found that accounting for polidispersity did not affect significantly the calculated phase equilibrium, but increased the agreement of calculated partition coefficients with experimental data. Further improvement was obtained by using a size dependent interaction parameter for dextran pseudo-components.     

Expanding on Watson's framework for classifying patches: when is an island not an island?

Aim The aims were: (1) evaluate the potential of Watson's framework for studying species composition in fragments and islands for a specific landscape type: cryptobiotic crust systems in the arid south‐western US; (2) expand Watson's original model to include ephemeral/non‐equilibrium systems by revising his categories of patch age and matrix contrast; and (3) examine the interplay between patch dynamics and species autecology, demonstrating the need for more work on ephemeral patchy systems. Location Cryptobiotic crust systems in two piñon‐juniper sites in Central New Mexico, western North America. Results Watson's patch age designation was not applicable to our system because of its ephemeral or non‐equilibrial nature. Based on this result, we constructed what we refer to as a ‘speed key’ that includes equilibrium and non‐equilibrium patches of all kinds. For this model we maintained one of Watson's original traits: patch origin, and amended two others to describe persistence and permeability across the matrix. Importantly, persistence and matrix permeability must be evaluated as functions of the organisms under consideration. Systems that may be in equilibrium for one taxon may well be non‐equilibrial (ephemeral) for another. A patch that appears to be in high contrast with its intervening matrix may actually be in low contrast, depending on the dispersal ability of the organism through that matrix. Main conclusions To improve substantially on our understanding of patchy systems (whether islands or fragments) it is important to account explicitly for relevant organismal life‐history traits in the designation of those systems. Too often, patches are defined by how the researcher views them from his/her own spatio‐temporal viewpoint. Once we move to an organism‐centred understanding of these patches we may find surprising and novel comparisons that allow us to move across scales and inform our view of ecological patterns and processes. By incorporating non‐equilibrium systems into a model of insularity, this work has general implications that go beyond the scope of cryptobiotic crusts to add to the current dialogue in biogeography.     

Studies of Water Uptake from Multiple Sources

Water uptake in systems consisting of a potted plant and twoembedded reservoirs, which had been fitted with microporousbottoms, were monitored daily over test intervals that rangedfrom 1 to 3 years. When both reservoirs contained aqueous solutionsof the same chemical composition, plants took water from thealternate sources without bias, but when one reservoir containedtap water and the other a strong aqueous nutrient solution,an initially fluctuating bias developed. Eventually the systemre-stabilized at an equilibrium state in which total uptakeof water (in 1 day^–1) to nutrient salt (in g day^–1)was about 16 to 1 independent of the concentration in the nutrientsolution. This equilibrium ratio was altered sharply wheneverthe plant was damaged severely, or whenever the quality of thewater in one of the reservoirs was impaired by addition of atoxicant. The equilibrium state was re-established within 6months following plant damage, and within a few weeks followingelimination of the toxicant. The above results demonstrate thatmultireservoir systems, which can be assembled easily from inexpensivecomponents, provide a reliable means for studying water uptakeby a single plant from two or more independent sources, andthat these systems are very sensitive to changes that affectthe physiology of the plant. water uptake, selective uptake, potometry, membranes, permeability, root growth, split-root growth, hydroponic     

Influence of ligand valency on ligand-influenced monomer-dimer equilibrium systems and biological control mechanisms

Two specific ligand-influenced monomer-dimer equilibrium systems are discussed. Each has a ligand-to-dimer subunit ratio of 0.5. Equilibrium characteristics of the system are described in terms of the effect of a bivalent ligand on both experimental and theoretical analysis. It is shown that Hill expressions need to be modified for multivalent ligand systems, and care is needed in equilibrium parameter determination. Some unique properties of these systems are retained, yet others are altered in the presence of a multivalent ligand. A suggestion as to the minimum amount of information needed to describe completely a ligand-influenced monomerdimer system is given. The estrogen-receptor system is presented as an attractive biological model for both theoretical and experimental study of ligand-influenced polymerizing systems and their role in cellular control requirements.     

Plant systems biology: network matters

Systems biology is all about networks. A recent trend has been to associate systems biology exclusively with the study of gene regulatory or protein-interaction networks. However, systems biology approaches can be applied at many other scales, from the subatomic to the ecosystem scales. In this review, we describe studies at the sub-cellular, tissue, whole plant and crop scales and highlight how these studies can be related to systems biology. We discuss the properties of system approaches at each scale as well as their current limits, and pinpoint in each case advances unique to the considered scale but representing potential for the other scales. We conclude by examining plant models bridging different scales and considering the future prospects of plant systems biology.     

A simulation study of the effects of architectural constraints and resource translocation on population structure and competition in clonal plants

(1) Spatially explicit simulation of clonal plant growth is used to determine how ramet-level traits affect ramet density, spatial pattern of ramets and competitive ability of a clonal plant. The simulation model used combines elements of (i) an individual-based model of plant interactions, (ii) an architectural model of clonal plant growth, and (iii) a model of resource translocation within a set of physiologically integrated plant individuals. (2) The effects of two groups of parameters were studied: growth and resource acquisition parameters (resource accumulation, density-dependence of resource accumulation, resource translocation between ramets) and architectural rules (branching angle and probability of branching, internode length). The model was parameterised by values approximating those of clonally growing grasses as closely as possible. The basic parameter values were chosen from a short-turf grassland. Sensitivity analysis was carried out on relevant parameters around three basic points in the parameter space. Both single-species and two-species systems were studied. (3) It is shown that increasing resource acquisition and growth parameters increase ramet density, genet number and competitive ability. Translocation parameters and architectural parameters modify the effects of resource acquisition and growth, but their effect in single-species stands was smaller. (4) The simulations of species with fixed ramet sizes showed that ramet density in single-species stands cannot be used for predicting competitive ability. Increase in resource acquisition and growth parameters was correlated with an increase in equilibrium ramet density and competitive ability. Increasing branching angle, branching probability or internode length lead to an increased competitive ability, but did not affect equilibrium ramet density. Change of architectural parameters could therefore affect competitive ability independently of their effect on the final ramet density. (5) Spatial pattern both in single-species and two-species stands was also highly parameter-dependent. Changes in architectural parameters and in translocation usually lead to pronounced change in the spatial pattern; change in growth and resource acquisition parameters generally had little effect on spatial pattern.     

All is not loss: plant biodiversity in the anthropocene

Anthropogenic global changes in biodiversity are generally portrayed in terms of massive native species losses or invasions caused by recent human disturbance. Yet these biodiversity changes and others caused directly by human populations and their use of land tend to co-occur as long-term biodiversity change processes in the Anthropocene. Here we explore contemporary anthropogenic global patterns in vascular plant species richness at regional landscape scales by combining spatially explicit models and estimates for native species loss together with gains in exotics caused by species invasions and the introduction of agricultural domesticates and ornamental exotic plants. The patterns thus derived confirm that while native losses are likely significant across at least half of Earth's ice-free land, model predictions indicate that plant species richness has increased overall in most regional landscapes, mostly because species invasions tend to exceed native losses. While global observing systems and models that integrate anthropogenic species loss, introduction and invasion at regional landscape scales remain at an early stage of development, integrating predictions from existing models within a single assessment confirms their vast global extent and significance while revealing novel patterns and their potential drivers. Effective global stewardship of plant biodiversity in the Anthropocene will require integrated frameworks for observing, modeling and forecasting the different forms of anthropogenic biodiversity change processes at regional landscape scales, towards conserving biodiversity within the novel plant communities created and sustained by human systems.     

Non-smooth plant disease models with economic thresholds

In order to control plant diseases and eventually maintain the number of infected plants below an economic threshold, a specific management strategy called the threshold policy is proposed, resulting in Filippov systems. These are a class of piecewise smooth systems of differential equations with a discontinuous right-hand side. The aim of this work is to investigate the global dynamic behavior including sliding dynamics of one Filippov plant disease model with cultural control strategy. We examine a Lotka–Volterra Filippov plant disease model with proportional planting rate, which is globally studied in terms of five types of equilibria. For one type of equilibrium, the global structure is discussed by the iterative equations for initial numbers of plants. For the other four types of equilibria, the bounded global attractor of each type is obtained by constructing appropriate Lyapunov functions. The ideas of constructing Lyapunov functions for Filippov systems, the methods of analyzing such systems and the main results presented here provide scientific support for completing control regimens on plant diseases in integrated disease management.