Modelling mechanisms of change in crop populations

Computer -based simulation models of changes occurring within crop populations when subjected to agents of phenotypic change, have been developed for use on commonly available personal computer equipment. As an underlying developmental principle, the models have been designed as general -case, mechanistic, stochastic models, in contrast to the predominantly empirically- derived, system -specific, deterministic (predictive) models currently available. A modelling methodology has evolved, to develop portable simulation models, written in high - level, general purpose code, allowing for use, modification and continued development by biologists with little requirement for computer programming expertise.The initial subject of these modelling activities was the simulation of the effects of selection and other agents of genetic change in crop populations, resulting in the computer model, PSELECT. Output from PSELECT, specifically phenotypic and genotypic response to phenotypic truncation selection, conformed to expectation, as defined by results from established analogue modelling work. Validation of the model by comparison of output with the results from an experimental -scale plant breeding exercise was less conclusive, and, owing to the fact that the genetic basis of the phenotypic characters used in the selection programme was insufficiently defined, the validation exercise provided only broad qualitative agreement with the model output. By virtue of the predominantly subjective nature of plant breeding programmes, the development of PSELECT resulted in a model of theoretical interest, but with little current practical application.Modelling techniques from the development of the PSELECT model were applied to the simulation of plant disease epidemics, where the modelled system is well characterised, and simulation modelling is an area of active research. The model SATSUMA, simulating the spatial and temporal development of diseases within crop populations, was developed. The model generates output which conforms to current epidemiological theory, and is compatible with contemporary methods of temporal and spatial analysis of crop disease epidemics. Temporal disease progress in the simulations was accurately described by variations of a generalised logistic model. Analysis of the spatial pattern of simulated epidemics by frequency distribution fitting or distance class methods was found to give good qualitative agreement with observed biological systems.The mechanistic nature of SATSUMA and its deliberate design as a general case model make it especially suitable for the investigation of component processes in a generalised plant disease epidemic, and valuable as an educational tool. Subject to validation against observational data, such models can be utilised as predictive tools by the incorporation of information (concerning crop species, pathogen etc.) specifically relevant to the modelled system. In addition to its educational use, SATSUMA has been used as research tool for the examination of the effect of spatial pattern of disease and disease incidence on the efficiency of sampling protocols and in parameterising a general theoretical model for describing the spatio -temporal development of plant diseases

Computer Simulation of Cellular Patterning Within the Drosophila Pupal Eye

We present a computer simulation and associated experimental validation of assembly of glial-like support cells into the interweaving hexagonal lattice that spans the Drosophila pupal eye. This process of cell movements organizes the ommatidial array into a functional pattern. Unlike earlier simulations that focused on the arrangements of cells within individual ommatidia, here we examine the local movements that lead to large-scale organization of the emerging eye field. Simulations based on our experimental observations of cell adhesion, cell death, and cell movement successfully patterned a tracing of an emerging wild-type pupal eye. Surprisingly, altering cell adhesion had only a mild effect on patterning, contradicting our previous hypothesis that the patterning was primarily the result of preferential adhesion between IRM-class surface proteins. Instead, our simulations highlighted the importance of programmed cell death (PCD) as well as a previously unappreciated variable: the expansion of cells' apical surface areas, which promoted rearrangement of neighboring cells. We tested this prediction experimentally by preventing expansion in the apical area of individual cells: patterning was disrupted in a manner predicted by our simulations. Our work demonstrates the value of combining computer simulation with in vivo experiments to uncover novel mechanisms that are perpetuated throughout the eye field. It also demonstrates the utility of the Glazier–Graner–Hogeweg model (GGH) for modeling the links between local cellular interactions and emergent properties of developing epithelia as well as predicting unanticipated results in vivo

Guidelines for assessing pedestrian evacuation software applications

This paper serves to clearly identify and explain criteria to consider when evaluating the suitability of a pedestrian evacuation software application to assess the evacuation process of a building. Guidelines in the form of nine topic areas identify different modelling approaches adopted, as well as features / functionality provided by applications designed specifically for simulating the egress of pedestrians from inside a building. The paper concludes with a synopsis of these guidelines, identifying key questions (by topic area) to found an evaluation

Pedestrian Flow Simulation Validation and Verification Techniques

For the verification and validation of microscopic simulation models of pedestrian flow, we have performed experiments for different kind of facilities and sites where most conflicts and congestion happens e.g. corridors, narrow passages, and crosswalks. The validity of the model should compare the experimental conditions and simulation results with video recording carried out in the same condition like in real life e.g. pedestrian flux and density distributions. The strategy in this technique is to achieve a certain amount of accuracy required in the simulation model. This method is good at detecting the critical points in the pedestrians walking areas. For the calibration of suitable models we use the results obtained from analyzing the video recordings in Hajj 2009 and these results can be used to check the design sections of pedestrian facilities and exits. As practical examples, we present the simulation of pilgrim streams on the Jamarat bridge. The objectives of this study are twofold: first, to show through verification and validation that simulation tools can be used to reproduce realistic scenarios, and second, gather data for accurate predictions for designers and decision makers.Comment: 19 pages, 10 figure

Key challenges in agent-based modelling for geo-spatial simulation

Agent-based modelling (ABM) is fast becoming the dominant paradigm in social simulation due primarily to a worldview that suggests that complex systems emerge from the bottom-up, are highly decentralised, and are composed of a multitude of heterogeneous objects called agents. These agents act with some purpose and their interaction, usually through time and space, generates emergent order, often at higher levels than those at which such agents operate. ABM however raises as many challenges as it seeks to resolve. It is the purpose of this paper to catalogue these challenges and to illustrate them using three somewhat different agent-based models applied to city systems. The seven challenges we pose involve: the purpose for which the model is built, the extent to which the model is rooted in independent theory, the extent to which the model can be replicated, the ways the model might be verified, calibrated and validated, the way model dynamics are represented in terms of agent interactions, the extent to which the model is operational, and the way the model can be communicated and shared with others. Once catalogued, we then illustrate these challenges with a pedestrian model for emergency evacuation in central London, a hypothetical model of residential segregation tuned to London data which elaborates the standard Schelling (1971) model, and an agent-based residential location built according to spatial interactions principles, calibrated to trip data for Greater London. The ambiguities posed by this new style of modelling are drawn out as conclusions

Validation of numerical codes for impact and explosion cratering: Impacts on strengthless and metal targets

Over the last few decades, rapid improvement of computer capabilities has allowed impact cratering to be modeled with increasing complexity and realism, and has paved the way for a new era of numerical modeling of the impact process, including full, three-dimensional (3D) simulations. When properly benchmarked and validated against observation, computer models offer a powerful tool for understanding the mechanics of impact crater formation. This work presents results from the first phase of a project to benchmark and validate shock codes. A variety of 2D and 3D codes were used in this study, from commercial products like AUTODYN, to codes developed within the scientific community like SOVA, SPH, ZEUS-MP, iSALE, and codes developed at U.S. National Laboratories like CTH, SAGE/RAGE, and ALE3D. Benchmark calculations of shock wave propagation in aluminum-on-aluminum impacts were performed to examine the agreement between codes for simple idealized problems. The benchmark simulations show that variability in code results is to be expected due to differences in the underlying solution algorithm of each code, artificial stability parameters, spatial and temporal resolution, and material models. Overall, the inter-code variability in peak shock pressure as a function of distance is around 10 to 20%. In general, if the impactor is resolved by at least 20 cells across its radius, the underestimation of peak shock pressure due to spatial resolution is less than 10%. In addition to the benchmark tests, three validation tests were performed to examine the ability of the codes to reproduce the time evolution of crater radius and depth observed in vertical laboratory impacts in water and two well-characterized aluminum alloys. Results from these calculations are in good agreement with experiments. There appears to be a general tendency of shock physics codes to underestimate the radius of the forming crater. Overall, the discrepancy between the model and experiment results is between 10 and 20%, similar to the inter-code variability.The Meteoritics & Planetary Science archives are made available by the Meteoritical Society and the University of Arizona Libraries. Contact [email protected] for further information.Migrated from OJS platform February 202