Transdisciplinary food systems research aims to merge insights from multiple fields, often revealing confounding, complex interactions. Computational modeling offers a means to discover patterns and formulate novel solutions to such systems-level problems. The best models serve as hubs—or boundary objects—which ground and unify a collaborative, iterative, and transdisciplinary process of stakeholder engagement. This dissertation demonstrates the application of agent-based modeling, network analytics, and evolutionary computational optimization to the pressing food systems problem areas of livestock epidemiology and global food security. It is comprised of a methodological introduction, an executive summary, three journal-article formatted chapters, and an overarching discussion section. Chapter One employs an agent-based computer model (RUSH-PNBM v.1.1) developed to study the potential impact of the trend toward increased producer specialization on resilience to catastrophic epidemics within livestock production chains. In each run, an infection is introduced and may spread according to probabilities associated with the various modes of contact between hog producer, feed mill, and slaughter plant agents. Experimental data reveal that more-specialized systems are vulnerable to outbreaks at lower spatial densities, have more abrupt percolation transitions, and are characterized by less-predictable outcomes; suggesting that reworking network structures may represent a viable means to increase biosecurity. Chapter Two uses a calibrated, spatially-explicit version of RUSH-PNBM (v.1.2) to model the hog production chains within three U.S. states. Key metrics are calculated after each run, some of which pertain to overall network structures, while others describe each actor’s positionality within the network. A genetic programming algorithm is then employed to search for mathematical relationships between multiple individual indicators that effectively predict each node’s vulnerability. This “meta-metric” approach could be applied to aid livestock epidemiologists in the targeting of biosecurity interventions and may also be useful to study a wide range of complex network phenomena. Chapter Three focuses on food insecurity resulting from the projected gap between global food supply and demand over the coming decades. While no single solution has been identified, scholars suggest that investments into multiple interventions may stack together to solve the problem. However, formulating an effective plan of action requires knowledge about the level of change resulting from a given investment into each wedge, the time before that effect unfolds, the expected baseline change, and the maximum possible level of change. This chapter details an evolutionary-computational algorithm to optimize investment schedules according to the twin goals of maximizing global food security and minimizing cost. Future work will involve parameterizing the model through an expert informant advisory process to develop the existing framework into a practicable food policy decision-support tool.

Physically based space planning is a means for automating the conceptual design process by applying the physics of motion to space plan elements. This methodology provides for a responsive design process, allowing a designer to easily make decisions whose consequences propagate throughout the design. It combines the speed of automated design methods with the flexibility of manual design methods, while adding a highly interactive quality and a sense of collaboration with the design. The primary assumption is that a digital design tool based on a physics paradigm can facilitate the architectural space planning process. The hypotheses are that Newtonian dynamics can be used 1) to define mechanical metaphors to represent the elements in an architectural space plan, 2) to compute architectural space planning solutions, and 3) to interact with architectural space plans. I show that space plan elements can be represented as physical masses, that design objectives can be represented using mechanical metaphors such as springs, repulsion fields, and screw clamps, that a layout solution can be computed by using these elements in a dynamical simulation, and that the user can interact with that solution by applying forces that are also models of the same mechanical objects. I present a prototype software application that successfully implements this approach. A subjective evaluation of this prototype reveals that it demonstrates a feasible process for producing space plans, and that it can potentially improve the design process because of the quality of the manipulation and the enhanced opportunities for design exploration it provides to the designer. I found that an important characteristic of this approach is that representation, computation, and interaction are all defined using the same paradigm. This contrasts with most approaches to automated space planning, where these three characteristics are usually defined in completely different ways. Also emerging from this work is a new cognitive theory of design titled 'dynamical design imagery,' which proposes that the elements in a designer's mental imagery during the act of design are dynamic in nature and act as a dynamical system, rather than as static images that are modified in a piecewise algorithmic manner.

Fire prone Mediterranean-type vegetation systems like those in the Mediterranean Basin and South-Western Australia are global hot spots for plant species diversity. To ensure management programs act to maintain these highly diverse plant communities, it is necessary to get a profound understanding of the crucial mechanisms of coexistence. In the current literature several mechanisms are discussed. The objective of my thesis is to systematically explore the importance of potential mechanisms for maintaining multi-species, fire prone vegetation by modelling. The model I developed is spatially-explicit, stochastic, rule- and individual-based. It is parameterised on data of population dynamics collected over 18 years in the Mediterranean-type shrublands of Eneabba, Western Australia. From 156 woody species of the area seven plant traits have been identified to be relevant for this study: regeneration mode, annual maximum seed production, seed size, maximum crown diameter, drought tolerance, dispersal mode and seed bank type. Trait sets are used for the definition of plant functional types (PFTs). The PFT dynamics are simulated annual by iterating life history processes. In the first part of my thesis I investigate the importance of trade-offs for the maintenance of high diversity in multi-species systems with 288 virtual PFTs. Simulation results show that the trade-off concept can be helpful to identify non-viable combinations of plant traits. However, the Shannon Diversity Index of modelled communities can be high despite of the presence of ‘supertypes’. I conclude, that trade-offs between two traits are less important to explain multi-species coexistence and high diversity than it is predicted by more conceptual models. Several studies show, that seed immigration from the regional seed pool is essential for maintaining local species diversity. However, systematical studies on the seed rain composition to multi-species communities are missing. The results of the simulation experiments, as presented in part two of this thesis, show clearly, that without seed immigration the local species community found in Eneabba drifts towards a state with few coexisting PFTs. With increasing immigration rates the number of simulated coexisting PFTs and Shannon diversity quickly approaches values as also observed in the field. Including the regional seed input in the model is suited to explain more aggregated measures of the local plant community structure such as species richness and diversity. Hence, the seed rain composition should be implemented in future studies. In the third part of my thesis I test the sensitivity of Eneabba PFTs to four different climate change scenarios, considering their impact on both local and regional processes. The results show that climate change clearly has the potential to alter the number of dispersed seeds for most of the Eneabba PFTs and therefore the source of the ‘immigrants’ at the community level. A classification tree analysis shows that, in general, the response to climate change was PFT-specific. In the Eneabba sand plains sensitivity of a PFT to climate change depends on its specific trait combination and on the scenario of environmental change i.e. development of the amount of rainfall and the fire frequency. This result emphasizes that PFT-specific responses and regional process seed immigration should not be ignored in studies dealing with the impact of climate change on future species distribution. The results of the three chapters are finally analysed in a general discussion. The model is discussed and improvements and suggestions are made for future research. My work leads to the following conclusions: i) It is necessary to support modelling with empirical work to explain coexistence in species-rich plant communities. ii) The chosen modelling approach allows considering the complexity of coexistence and improves the understanding of coexistence mechanisms. iii) Field research based assumptions in terms of environmental conditions and plant life histories can relativise the importance of more hypothetic coexistence theories in species-rich systems. In consequence, trade-offs can play a lower role than predicted by conceptual models. iv) Seed immigration is a key process for local coexistence. Its alteration because of climate change should be considered for prognosis of coexistence. Field studies should be carried out to get data on seed rain composition. / Feuer geprägte, mediterrane Vegetationstypen, wie sie im Mittelmeerraum und Süd-West Australien zu finden sind, gelten als globale „hotspots“ für Pflanzendiversität. Um sicher zu stellen, dass Managementprogramme zum Erhalt dieser hoch diversen Pflanzengesellschaften zielgerichtet beitragen, ist ein profundes Verständnis der wesentlichen Koexistenzmechanismen notwendig. In der aktuellen Literatur werden verschiedene Mechanismen diskutiert. Das Ziel meiner Doktorarbeit ist es, die Bedeutung der Mechanismen für den Erhalt der artenreichen, feuergeprägten Vegetation anhand eines Modells systematisch zu untersuchen. Das von mir dafür entwickelte Modell ist räumlich-explizit, stochastisch und regel- und individuenbasiert. Es ist unter Zuhilfenahme von Daten zu Populationsdynamiken parametrisiert, die über 18 Jahre im Mediterranen Buschland von Eneabba Westaustraliens gesammelt wurden. Anhand von 156 Arten sind sieben für meine Studie relevante Pflanzeneigenschaften identifiziert wurden: Regenerationsart, jährlich maximale Samenproduktion, Samengröße, maximaler Durchmesser, Trockentoleranz, Ausbreitungsart und Samenbanktyp. Kombinationen der Eigenschaften bilden funktionelle Pflanzentypen (PFTs), deren jährliche Dynamik über Lebenszyklusprozesse im Modell simuliert wird. Der erste Teil meiner Arbeit präsentiert die Studie zur Bedeutung von „trade-offs“ für den Erhalt der hohen Diversität in artenreichen Systemen. Die Simulationsergebnisse mit 288 virtuellen PFTs zeigen, dass das „trade-offs“-Konzept für die Identifizierung nicht-lebensfähiger Kombinationen von Pflanzeneigenschaften hilfreich sein kann. Allerdings kann der Shannon-Diversitäts-Index der modellierten Pflanzengesellschaft trotz der Anwesenheit von „Supertypen“ hoch sein. Ich schlussfolgere, dass „trade-off“ zwischen zwei Eigenschaften weniger wichtig für die Erklärung der Koexistenz von vielen Arten und hoher Diversität sind, als es durch konzeptionelle Modelle vorhergesagt wird. Viele Studien zeigen, dass Sameneintrag aus dem regionalen Samenpool essenziell für den Erhalt lokaler Artendiversität ist. Es gibt allerdings noch keine systematischen Studien zur Zusammensetzung des Samenregens artenreichen Systemen. Die Ergebnisse der Simulationsexperimente im zweiten Teil meiner Arbeit machen deutlich, dass ohne Sameneintrag die lokale Pflanzengesellschaft Eneabbas sich in eine Richtung entwickelt, in der nur wenige PFTs koexistieren. Mit steigender Samenimmigrationsrate erreicht die Anzahl an koexistierenden PFTs und die Shannon-Diversität schnell die Werte, die auch im Feld gefunden werden. Der regionale Sameneintrag kann also als Erklärung zur Struktur lokaler Pflanzengesellschaften dienen. Seine Zusammensetzung sollte jedoch in zukünftigen Studien berücksichtigt werden. Im dritten Teil meiner Doktorarbeit präsentiere ich Analysen zur Sensibilität der PFTs von Eneabba vorhergesagte Klimaszenarien und der Auswirkungen auf die Samenimmigration. Die Ergebnisse zeigen deutlich, dass Klimaänderungen das Potential haben, die Anzahl an ausgebreiteten Samen der meisten Eneabba PFTs zu verändern. Die Entscheidungsbaum-Analyse veranschaulicht, dass die Reaktion auf Klimaänderung PFT-spezifisch ist. In den Eneabba hängt die Sensitivität der PFTs gegenüber klimatischen Veränderungen von den PFT-spezifischen Eigenschaftskombinationen und vom Klimaszenarium ab, d.h. von der Entwicklung der Regenfallmenge und der Feuerfrequenz. Dieses Ergebnis betont, dass PFT-spezifische Reaktionen und die klimabedingten Änderungen in der Samenimmigration in Studien zum Einfluss von Klimaänderungen auf die zukünftige Artenverteilung berücksichtigt werden sollten. Die Ergebnisse aus den drei Kapiteln werden in der allgemeinen Diskussion zusammengeführt und analysiert. Das Modell wird diskutiert und Verbesserungen und Vorschläge für weitere Forschung aufgezeigt. Meine Arbeit führt zu folgenden Schlussfolgerungen: i) Es ist notwendig, empirische Arbeit und Modellierung zu kombinieren, um Koexistenz in artenreichen Systemen zu erklären. ii) Durch den gewählten Modellansatz kann die Komplexität von Koexistenz erfasst und das Verständnis vertieft werden. iii) Auf Felddaten basierende Annahmen bezüglich Umweltbedingungen und Lebenzyklus können zur Relativierung der Bedeutsamkeit von Mechanismen führen. So können Trade-offs eine geringere Rolle spielen, als konzeptionelle Modelle nahe legen. iv) Samenimmigration ist ein Schlüsselprozess für lokale Koexistenz. Deren Änderung aufgrund von Klimawandel sollte für Prognosen zu Artenvorkommen berücksichtigt werden. Feldstudien sollten durchgeführt werden, um die Datenlücken zur Samenregenzusammensetzung zu füllen.

The whole in a complex system is the sum of its parts, plus the interactions between the parts. Understanding social, biological, and economic systems therefore often depends on understanding their patterns of interactions---their networks. In this thesis, the approach is to understand complex systems by making simple network models with nodes and links. It is first of all an attempt to investigate how the communication over the network affects the network structure and, vice versa, how the network structure affects the conditions for communication. To explore the local mechanism behind network organization, we used simplified social systems and modeled the response to communication. Low communication levels resulted in random networks, whereas higher communication levels led to structured networks with most nodes having very few links and a few nodes having very many links. We also explored various models where nodes merge into bigger units, to reduce communication costs, and showed that these merging models give rise to the same kind of structured networks. In addition to this modeling of communication networks, we developed new ways to measure and characterize real-world networks. For example, we found that they in general favor communication on short distance, two-three steps away in the network, within what we call the information horizon. / Helheten i ett komplext system är mer än summan av dess delar, då den även inbegriper interaktionerna mellan dem. Att studera sociala, biologiska och ekonomiska system blir därför ofta en fråga om att förstå deras interaktionsmönster, d.v.s. deras nätverk av noder och länkar. Med utgångspunkt i enkla nätverksmodeller undersöker avhandlingen i huvudsak hur kommunikation i nätverk påverkar nätverksstrukturen och, vice versa, hur nätverksstrukturen påverkar villkoren för kommunikation. Vi utforskade mekanismerna bakom hur nätverk är organiserade genom att modellera effekten av kommunikation i förenklade sociala system. En låg kommunikationsnivå visade sig ge upphov till kaotiska nätverk där ingen nod i princip hade fler länkar än någon annan. En hög kommunikationsnivå resulterade däremot i strukturerade nätverk, med några få centrala noder med många länkar, medan flertalet noder var perifera med enbart några få länkar. Det visade sig också att alla aktörer i nätverket gynnades av kommunikation, även när den var ojämnt fördelad. Kvaliteten på kommunikationen, d.v.s. informationens giltighet, var också avgörande för vilka positioner som gynnades i ett nätverk, vilket vi visade genom att studera aktörer som spred falsk information. Eftersom effektiv kommunikation är en viktig del i många nätverk betraktar vi utvecklingen av dem som en optimeringsprocess. Varje kommunikationshandling mellan noderna tar tid och genom att slå sig samman till större enheter begränsas dessa kostnader och gör nätverket effektivare. Dessa s.k. sammanslagningsmodeller gav upphov till samma typ av strukturerade nätverk som ovan. Genom att utveckla olika sätt att mäta nätverksstrukturer visade vi bland annat att många verkliga system främjar kommunikation över korta avstånd, två-tre steg bort i nätverket, innanför det vi kallar informationshorisonten. Vi uppskattade också den mängd information som krävs för att orientera sig i städer, och fann att det är lättare att hitta i moderna, planerade städer än i äldre städer som utvecklats under lång tid.

Biofilms are communities of sessile microorganisms attached to a surface and imbeddedin a matrix of extracellular polysaccharide substances. These communities can be foundin diverse aquatic environments, such as in industrial pipes and in humans. By formingmicrocolony structures, which are highly resistant to adverse physical conditions as wellas antimicrobial agents, biofilms are very problematic when associated with e.g.persistent infections. In order to find new ways of controlling biofilm growth, theprocesses involved in biofilm development must be investigated further. The maininterest of this study is the occurrence of void formation inside biofilms. Thisphenomenon has been observed in several studies and has been correlated to cell deathinside the microcolonies. The occurrence of cell death has recently been associated withthe presence of nitric oxide in the biofilm. In this study, the implications of nitric oxideaccumulation on biofilm development were investigated using an individual-basedmodel. Specifically, the role of nitric oxide in void formation was considered. A largenumber of simulations were run using different parameter settings in order to determine ifnitric oxide could account for the occurrence of void formation observed experimentally.The general predictions made by the model system showed agreement to someexperimental data, but not to others. Sloughing, the detachment of chunks of cells fromthe biofilm, was observed in the majority of simulations. In some cases, the model alsopredicted the presence of live cells inside the voids, which has been observedexperimentally.

This dissertation investigates selected empirical and theoretical aspects of land-use and land-cover change (LUCC) in exurban areas. Two challenges – observation and monitoring of LUCC, and spatially explicit modeling, are addressed using three main approaches – measuring, reviewing and agent-based modeling (ABM). All of these approaches focus on LUCC at the individual household level, investigating how micro-scale elements interact to influence macro-scale functional patterns—bottom-up analysis. First, the temporal change of the quantity and pattern of land-cover types within exurban residential parcels in three townships in the southeastern Michigan is examined using landscape metrics and local indicators of spatial association at the parcel and parcel-neighborhood level respectively. The results demonstrate that the number and area of exurban residential parcels increased steadily from 1960 to 2000, and different land-cover types have distinctive temporal changes over time. The results also indicate that there is a convergence process at the neighborhood level through which the quantity and pattern of land cover in parcels conform with the neighborhood appearance. Second, 51 urban residential choice models based on ABM are reviewed. The results divide these models into three categories (i.e. models based on classical theories, models focusing on different stages of urbanization process; and integrated ABM and microsimulation models). This review also compares the differences among these models in their representations of three essential features brought by the technique of ABM: agent heterogeneity, the land market and output measurement. Challenges in incorporating these features, such as the trade-off between the simplicity and abstraction of model and the complexity of urban residential system, interactions of multiple features and demands for data at individual level, are also discussed. Third, the effects of agent heterogeneity on spatial and socioeconomic outcomes under different levels of land-market representations are explored through three experiments using a stylized agent-based land-market model. The results reveal that budget heterogeneity has prominent effects on socioeconomic outcomes, while preference heterogeneity is highly pertinent to spatial outcomes. The relationship between agent heterogeneity and macro-measures becomes more complex as more land-market mechanisms are represented. The results also imply that land-market representation (e.g., competitive bidding) is indispensable to reproduce the results of classical urban land market models (e.g., monocentric city model) in a spatial ABM when agents are heterogeneous.

Agriculture is undergoing extreme change. The introduction of new generation agricultural products has generated an increased need for efficient and accurate product segregation across a number of Canadian agricultural sectors. In particular, monitoring, controlling and preventing commingling of various wheat grades is critical to continued agri-food safety and quality assurance in the Canadian grain handling system. The Canadian grain handling industry is a vast regional supply chain with many participants. Grading of grain for blending had historically been accomplished by the method of Kernel Visual Distinguishability (KVD). KVD allowed a trained grain grader to distinguish the class of a registered variety of wheat solely by visual inspection. While KVD enabled rapid, dependable, and low-cost segregation of wheat into functionally different classes or quality types, it also put constraints on the development of novel traits in wheat. To facilitate the introduction of new classes of wheat to enable additional export sales in new markets, the federal government announced that KVD was to be eliminated from all primary classes of wheat as of August 1, 2008. As an alternative, the Canadian Grain Commission has implemented a system called Variety Eligibility Declaration (VED) to replace KVD. As a system based on self-declaration, the VED system may create moral hazard for misrepresentation. This system is problematic in that incentives exist for farmers to misrepresent their grain. Similarly, primary elevators have an incentive to commingle wheat classes in a profitable manner. Clearly, the VED system will only work as desired for the grain industry when supported by a credible monitoring system. That is, to ensure the security of the wheat supply chain, sampling and testing at some specific critical points along the supply chain is needed. While the current technology allows the identification of visually indistinguishable grain varieties with enough precision for most modern segregation requirements, this technology is relatively slow and expensive. With the potential costs of monitoring VED through the current wheat supply chain, there is a fundamental tradeoff confronting grain handlers, and effective handling strategies will be needed to maintain historical wheat uniformity and consistency while keeping monitoring costs down. There are important operational issues to efficiently testing grain within the supply chain, including the choice of the optimal location to test and how intensively to test. The testing protocols for grain deliveries as well as maintaining effective responsiveness to information feedback among farmers will certainly become a strategic emphasis for wheat handlers in the future. In light of this, my research attempts to identify the risks, incentives and costs associated with a functional declaration system. This research tests a series of incentives designed to generate truthful behavior within the new policy environment. In this manner, I examine potential and easy to implement testing strategies designed to maintain integrity and efficiency in this agricultural supply chain. This study is developed in the first instance by using an analytic model to explore the economic incentives for motivating farmer’s risk control efforts and handlers’ optimal handling strategies with respect to testing cost, penalty level, contamination risks and risk control efforts. We solve for optimal behavior in the supply chain assuming cost minimization among the participants, under several simplifying assumptions. In reality, the Canadian grain supply chain is composed of heterogeneous, boundedly rational and dynamically interacting individuals, and none of these characteristics fit the standard optimization framework used to solve these problems. Given this complex agent behavior, the grain supply chain is characterized by a set of non-linear relationships between individual participants, coupled with out of equilibrium dynamics, meaning that analytic solutions will not always identify or validate the set of optimized strategies that would evolve in the real world. To account for this inherent complexity, I develop an agent-based (farmers and elevators) model to simulate behaviour in a more realistic but virtual grain supply chain. After characterizing the basic analytics of the problem, the grain supply chain participants are represented as autonomous economic agents with a certain level of programmed behavioral heterogeneity. The agents interact via a set of heuristics governing their actions and decisions. The operation of a major portion of the Canadian grain handling system is simulated in this manner, moving from the individual farm up through to the country elevator level. My simulation results suggest testing strategies to alleviate misrepresentation (moral hazard) in this supply chain are more efficient for society when they are flexible and can be easily adjusted to react to situational change within the supply chain. While the idea of using software agents for modeling and understanding the dynamics of the supply chain under consideration is somewhat novel, I consider this exercise a first step to a broader modeling representation of modern agricultural supply chains. The agent-based simulation methodology developed in my dissertation can be extended to other economic systems or chains in order to examine risk management and control costs. These include food safety and quality assurance network systems as well as natural-resource management systems. Furthermore, to my knowledge there are no existing studies that develop and compare both analytic and agent-based simulation approaches for this type of complex economic situation. In the dissertation, I conduct explicit comparisons between the analytic and agent-based simulation solutions where applicable. While the two approaches generated somewhat different solutions, in many respects they led to similar overall conclusions regarding this particular agricultural policy issue.

The rapid advancement of information technology and its integration with the manufacturing technology increased the necessity of consistent and coherent data flow in the chain of Computer Aided Design (CAD)-Computer aided Manufacturing (CAM)-Computer Numerical Control (CNC). To achieve this, ISO 10303 standard (STEP), developed by ISO, is seen as a solution since STEP is independent of the environment on which design data, manufacturing data or machining data produced. In this thesis, efficiency of NC-code generation, with the inclusion of process planning data, from a STEP based CAD data is investigated. For the investigation purposes, software responsible for both building the STEP based CAD data and generating related NC-code automatically is developed. Using this software, several parts are designed / generated NC-codes are verified via CNC simulators and some test parts are produced. STEP AP224 based feature modeler, developed specifically for 2- axis rotational part design, includes / feature library, feature modeler employing SW2007 via API for visualization and preprocessor responsible for generation of STEP file in neutral format, called STEP Part 21. The NC-code generator includes / postprocessor responsible for STEP Part 21 interpretation, CNC machine tool and cutting tool database and preprocessor responsible for NC-code generation.

We present a method for representing seams in clothing animation, and its application in simulation level of detail. Specifically we consider cloth represented as a regular grid of particles connected by spring-dampers, and a seam specified by a closed set of parametric trim curves in the cloth domain. Conventional cloth animation requires the tessellation of seams so that they are handled uniformly by the dynamics process. Our goal is a seam definition which does not constrain the attached clothing panels to be of the same resolution, or even constant resolution, while not being a hindrance to the dynamics process. We also apply our seams to cloth defined on a regular grid, as opposed to the irregular meshes commonly used with seams. The determination of particles interior to the cloth panel can be done using wellknown graphics operations such as scan-conversion. Due to the particle-based nature of the simulation, the dynamics approach combines easily with existing implicit and explicit methods. Finally, because the seams are resolution independent, the particle density per clothing panel can be adjusted as desired. This gives rise to a simple application of the given seams approach illustrating how it may be used for simulation level of detail.

<p>Biofilms are communities of sessile microorganisms attached to a surface and imbeddedin a matrix of extracellular polysaccharide substances. These communities can be foundin diverse aquatic environments, such as in industrial pipes and in humans. By formingmicrocolony structures, which are highly resistant to adverse physical conditions as wellas antimicrobial agents, biofilms are very problematic when associated with e.g.persistent infections. In order to find new ways of controlling biofilm growth, theprocesses involved in biofilm development must be investigated further. The maininterest of this study is the occurrence of void formation inside biofilms. Thisphenomenon has been observed in several studies and has been correlated to cell deathinside the microcolonies. The occurrence of cell death has recently been associated withthe presence of nitric oxide in the biofilm. In this study, the implications of nitric oxideaccumulation on biofilm development were investigated using an individual-basedmodel. Specifically, the role of nitric oxide in void formation was considered. A largenumber of simulations were run using different parameter settings in order to determine ifnitric oxide could account for the occurrence of void formation observed experimentally.The general predictions made by the model system showed agreement to someexperimental data, but not to others. Sloughing, the detachment of chunks of cells fromthe biofilm, was observed in the majority of simulations. In some cases, the model alsopredicted the presence of live cells inside the voids, which has been observedexperimentally.</p>