Alternative harvest strategies to alleviate predation bottlenecks: a bioeconomic modeling approach to inform adaptive management

Thesis (Ph.D.)--University of Washington, 2016-06

On systems thinking, systems biology and the in Silico Plant

The recent summary report of a Department of Energy Workshop on Plant Systems Biology (P.V. Minorsky [2003] Plant Physiol 132: 404-409) offered a welcomed advocacy for systems analysis as essential in understanding plant development, growth, and production. The goal of the Workshop was to consider methods for relating the results of molecular research to real-world challenges in plant production for increased food supplies, alternative energy sources, and environmental improvement. The rather surprising feature of this report, however, was that the Workshop largely overlooked the rich history of plant systems analysis extending over nearly 40 years (Sinclair and Seligman, 1996) that has considered exactly those challenges targeted by the Workshop. Past systems research has explored and incorporated biochemical and physiological knowledge into plant simulation models from a number of perspectives. The research has resulted in considerable understanding and insight about how to simulate plant systems and the relative contribution of various factors in influencing plant production. These past activities have contributed directly to research focused on solving the problems of increasing biomass production and crop yields. These modeling approaches are also now providing an avenue to enhance integration of molecular genetic technologies in plant improvement (Hammer et al., 2002).

Modeling the development of acquired clinical immunity to Plasmodium falciparum malaria

Individuals living in regions where malaria is endemic develop an acquired immunity to malaria which enables them to remain asymptomatic while still carrying parasites. Field studies indicate that cumulative exposure to a variety of diverse Plasmodium parasites is required for the transition from symptomatic to asymptomatic malaria. This study used a simulation model of the within-host dynamics of P. falciparum to investigate the development of acquired clinical immunity under different transmission conditions and levels of parasite diversity. Antibodies developed to P. falciparum erythrocyte membrane protein 1 (PfEMP1), a clonally variant molecule, were assumed to be a key human immunological response to P. falciparum infection, along with responses to clonally conserved but polymorphic antigens. The time to the development of clinical immunity was found to be proportional to parasite diversity and inversely proportional to transmission intensity. The effect of early termination of symptomatic infections by chemotherapy was investigated and found not to inhibit the host's ability to develop acquired immunity. However, the time required to achieve this state was approximately double that compared to when no treatment was administered. This study demonstrates that an immune response primarily targeted against PfEMP1 has the ability to reduce clinical symptoms of infections irrespective of whether treatment is administered, supporting its role in the development of acquired clinical immunity. The results also illustrate a novel use for simulation models of P. falciparum infections, investigation of the influence of intervention strategies on the development of naturally acquired clinical immunity.

Modelling, nitrogen dynamics in sugarcane systems: Recent advances and applications

Substantial amounts of nitrogen (N) fertiliser are necessary for commercial sugarcane production because of the large biomass produced by sugarcane crops. Since this fertiliser is a substantial input cost and has implications if N is lost to the environment, there are pressing needs to optimise the supply of N to the crops' requirements. The complexity of the N cycle and the strong influence of climate, through its moderation of N transformation processes in the soil and its impact on N uptake by crops, make simulation-based approaches to this N management problem attractive. In this paper we describe the processes to be captured in modelling soil and plant N dynamics in sugarcane systems, and review the capability for modelling these processes. We then illustrate insights gained into improved management of N through simulation-based studies for the issues of crop residue management, irrigation management and greenhouse gas emissions. We conclude by identifying processes not currently represented in the models used for simulating N cycling in sugarcane production systems, and illustrate ways in which these can be partially overcome in the short term. (c) 2005 Elsevier B.V. All rights reserved.

Parthenium weed: a potential major weed for agro-ecosystems in Pakistan

Parthenium weed (Parthenium hysterophorus L.) is a new and potentially major weed in Pakistan. This weed, originating from central America, is now a major weed in many regions of the world including Eastern Africa, India, parts of South East Asia and Australia. Presumably its recent arrival in Pakistan has been due to its movement from India, but this has yet to be established. In Australia it has been present for about 50 years, in which time it has spread from isolated infestations to establish core populations in central Queensland with scattered and isolated plants occurring south into New South Wales and north-west into the Northern Territory. Its spread in Pakistan is likely to be much more rapid, but lessons learnt in Australia will be of great value for weed managers in Pakistan. This annual herb has the potential to spread to all medium rainfall rangeland, dairy and summer cropping areas in Pakistan. In Australia its main effect is upon livestock production, but it is also causing health concerns in regional communities. However, in India it has also had a significant impact in cropping systems. To help coordinate actions on its management in Australia, a National Weeds Program has created a Parthenium Weed Management Group (PWMG) and under this group a Parthenium Weed Research Group (PWRG) has been formed. Funding coming from this national program and other sources has supported the PWRG to undertake a collaborative and technology exchange research program in two main areas: 1) biology and ecology and 2) management; while the PWMG has focused on community awareness and the production of various extension and management packages. Research in the area of biology and ecology has included studies on the evaluation of competitive plants to displace parthenium weed, the use of process-based simulation models to monitor and predict future spread and abundance under present and future climate conditions, the effect of the weed on human health and the ecology of its seed bank. Management research has focussed on the development of biological control approaches using plant-feeding insects and pathogens. The effectiveness of biological control is also being monitored through long term studies on seed bank size and dynamics. The use of fire as another potential management tool is also being evaluated. In addition to this important research, an effort has also been made to spread the most important findings and management outcomes to the wider community through an extension and education program driven by the PWMG. These developments within Australia, in parthenium weed management, will be of great help to P

Organisational learning - a critical systems thinking discipline

Original Paper European Journal of Information Systems (2001) 10, 135–146; doi:10.1057/palgrave.ejis.3000394 Organisational learning—a critical systems thinking discipline P Panagiotidis1,3 and J S Edwards2,4 1Deloitte and Touche, Athens, Greece 2Aston Business School, Aston University, Aston Triangle, Birmingham, B4 7ET, UK Correspondence: Dr J S Edwards, Aston Business School, Aston University, Aston Triangle, Birmingham, B4 7ET, UK. E-mail: j.s.edwards@aston.ac.uk 3Petros Panagiotidis is Manager responsible for the Process and Systems Integrity Services of Deloitte and Touche in Athens, Greece. He has a BSc in Business Administration and an MSc in Management Information Systems from Western International University, Phoenix, Arizona, USA; an MSc in Business Systems Analysis and Design from City University, London, UK; and a PhD degree from Aston University, Birmingham, UK. His doctorate was in Business Systems Analysis and Design. His principal interests now are in the ERP/DSS field, where he serves as project leader and project risk managment leader in the implementation of SAP and JD Edwards/Cognos in various major clients in the telecommunications and manufacturing sectors. In addition, he is responsible for the development and application of knowledge management systems and activity-based costing systems. 4John S Edwards is Senior Lecturer in Operational Research and Systems at Aston Business School, Birmingham, UK. He holds MA and PhD degrees (in mathematics and operational research respectively) from Cambridge University. His principal research interests are in knowledge management and decision support, especially methods and processes for system development. He has written more than 30 research papers on these topics, and two books, Building Knowledge-based Systems and Decision Making with Computers, both published by Pitman. Current research work includes the effect of scale of operations on knowledge management, interfacing expert systems with simulation models, process modelling in law and legal services, and a study of the use of artifical intelligence techniques in management accounting. Top of pageAbstract This paper deals with the application of critical systems thinking in the domain of organisational learning and knowledge management. Its viewpoint is that deep organisational learning only takes place when the business systems' stakeholders reflect on their actions and thus inquire about their purpose(s) in relation to the business system and the other stakeholders they perceive to exist. This is done by reflecting both on the sources of motivation and/or deception that are contained in their purpose, and also on the sources of collective motivation and/or deception that are contained in the business system's purpose. The development of an organisational information system that captures, manages and institutionalises meaningful information—a knowledge management system—cannot be separated from organisational learning practices, since it should be the result of these very practices. Although Senge's five disciplines provide a useful starting-point in looking at organisational learning, we argue for a critical systems approach, instead of an uncritical Systems Dynamics one that concentrates only on the organisational learning practices. We proceed to outline a methodology called Business Systems Purpose Analysis (BSPA) that offers a participatory structure for team and organisational learning, upon which the stakeholders can take legitimate action that is based on the force of the better argument. In addition, the organisational learning process in BSPA leads to the development of an intrinsically motivated information organisational system that allows for the institutionalisation of the learning process itself in the form of an organisational knowledge management system. This could be a specific application, or something as wide-ranging as an Enterprise Resource Planning (ERP) implementation. Examples of the use of BSPA in two ERP implementations are presented.

Cost and performance analysis of new wood-fuelled power plant concepts

The objective of the thesis was to analyse several process configurations for the production of electricity from biomass. Process simulation models using AspenPlus aimed at calculating the industrial performance of power plant concepts were built, tested, and used for analysis. The criteria used in analysis were performance and cost. All of the advanced systems appear to have higher efficiencies than the commercial reference, the Rankine cycle. However, advanced systems typically have a higher cost of electricity (COE) than the Rankine power plant. High efficiencies do not reduce fuel costs enough to compensate for the high capital costs of advanced concepts. The successful reduction of capital costs would appear to be the key to the introduction of the new systems. Capital costs account for a considerable, often dominant, part of the cost of electricity in these concepts. All of the systems have higher specific investment costs than the conventional industrial alternative, i.e. the Rankine power plant; Combined beat and power production (CUP) is currently the only industrial area of application in which bio-power costs can be considerably reduced to make them competitive. Based on the results of this work, AsperiPlus is an appropriate simulation platform. How-ever, the usefulness of the models could be improved if a number of unit operations were modelled in greater detail. The dryer, gasifier, fast pyrolysis, gas engine and gas turbine models could be improved.

A study of the dynamic behaviour of a pulsed column solvent extraction plant

A study has been made of the dynamic behaviour of a nuclear fuel reprocessing plant utilising pulsed solvent extraction columns. A flowsheet is presented and the choice of an extraction device is discussed. The plant is described by a series of modules each module representing an item of equipment. Each module consists of a series of differential equations describing the dynamic behaviour of the equipment. The model is written in PMSP, a language developed for dynamic simulation models. The differential equations are solved to predict plant behaviour with time. The dynamic response of the plant to a range of disturbances has been assessed. The interactions between pulsed columns have been demonstrated and illustrated. The importance of auxillary items of equipment to plant performance is demonstrated. Control of the reprocessing plant is considered and the effect of control parameters on performance assessed.

Aspects of design for a spare parts provisioning system

This thesis describes an investigation by the author into the spares operation of compare BroomWade Ltd. Whilst the complete system, including the warehousing and distribution functions, was investigated, the thesis concentrates on the provisioning aspect of the spares supply problem. Analysis of the historical data showed the presence of significant fluctuations in all the measures of system performance. Two Industrial Dynamics simulation models were developed to study this phenomena. The models showed that any fluctuation in end customer demand would be amplified as it passed through the distributor and warehouse stock control systems. The evidence from the historical data available supported this view of the system's operation. The models were utilised to determine which parts of the total system could be expected to exert a critical influence on its performance. The lead time parameters of the supply sector were found to be critical and further study showed that the manner in which the lead time changed with work in progress levels was also an important factor. The problem therefore resolved into the design of a spares manufacturing system. Which exhibited the appropriate dynamic performance characteristics. The gross level of entity presentation, inherent in the Industrial Dynamics methodology, was found to limit the value of these models in the development of detail design proposals. Accordingly, an interacting job shop simulation package was developed to allow detailed evaluation of organisational factors on the performance characteristics of a manufacturing system. The package was used to develop a design for a pilot spares production unit. The need for a manufacturing system to perform successfully under conditions of fluctuating demand is not limited to the spares field. Thus, although the spares exercise provides an example of the approach, the concepts and techniques developed can be considered to have broad application throughout batch manufacturing industry.

H264 data partitioned video streaming

Motivated by the increasing demand and challenges of video streaming in this thesis, we investigate methods by which the quality of the video can be improved. We utilise overlay networks that have been created by implemented relay nodes to produce path diversity, and show through analytical and simulation models for which environments path diversity can improve the packet loss probability. We take the simulation and analytical models further by implementing a real overlay network on top of Planetlab, and show that when the network conditions remain constant the video quality received by the client can be improved. In addition, we show that in the environments where path diversity improves the video quality forward error correction can be used to further enhance the quality. We then investigate the effect of IEEE 802.11e Wireless LAN standard with quality of service enabled on the video quality received by a wireless client. We find that assigning all the video to a single class outperforms a cross class assignment scheme proposed by other researchers. The issue of virtual contention at the access point is also examined. We increase the intelligence of our relay nodes and enable them to cache video, in order to maximise the usefulness of these caches. For this purpose, we introduce a measure, called the PSNR profit, and present an optimal caching method for achieving the maximum PSNR profit at the relay nodes where partitioned video contents are stored and provide an enhanced quality for the client. We also show that the optimised cache the degradation in the video quality received by the client becomes more graceful than the non-optimised system when the network experiences packet loss or is congested.

The feasibility of hybrid solar-biomass power plants in India

We assess the feasibility of hybrid solar-biomass power plants for use in India in various applications including tri-generation, electricity generation and process heat. To cover this breadth of scenarios we analyse, with the help of simulation models, case studies with peak thermal capacities ranging from 2 to 10 MW. Evaluations are made against technical, financial and environmental criteria. Suitable solar multiples, based on the trade-offs among the various criteria, range from 1 to 2.5. Compared to conventional energy sources, levelised energy costs are high - but competitive in comparison to other renewables such as photovoltaic and wind. Long payback periods for hybrid plants mean that they cannot compete directly with biomass-only systems. However, a 1.2-3.2 times increase in feedstock price will result in hybrid systems becoming cost competitive. Furthermore, in comparison to biomass-only, hybrid operation saves up to 29% biomass and land with an 8.3-24.8 $/GJ/a and 1.8-5.2 ¢/kWh increase in cost per exergy loss and levelised energy cost. Hybrid plants will become an increasingly attractive option as the cost of solar thermal falls and feedstock, fossil fuel and land prices continue to rise. In the foreseeable future, solar will continue to rely on subsidies and it is recommended to subsidise preferentially tri-generation plants. © 2012 Elsevier Ltd.

Desalination of brackish water by a batch reverse osmosis desalink system for use with solar thermal energy

For remote, semi-arid areas, brackish groundwater (BW) desalination powered by solar energy may serve as the most technically and economically viable means to alleviate the water stresses. For such systems, high recovery ratio is desired because of the technical and economical difficulties of concentrate management. It has been demonstrated that the current, conventional solar reverse osmosis (RO) desalination can be improved by 40–200 times by eliminating unnecessary energy losses. In this work, a batch-RO system that can be powered by a thermal Rankine cycle has been developed. By directly recycling high pressure concentrates and by using a linkage connection to provide increasing feed pressures, the batch-RO has been shown to achieve a 70% saving in energy consumption compared to a continuous single-stage RO system. Theoretical investigations on the mass transfer phenomena, including dispersion and concentration polarization, have been carried out to complement and to guide experimental efforts. The performance evaluation of the batch-RO system, named DesaLink, has been based on extensive experimental tests performed upon it. Operating DesaLink using compressed air as power supply under laboratory conditions, a freshwater production of approximately 300 litres per day was recorded with a concentration of around 350 ppm, whilst the feed water had a concentration range of 2500–4500 ppm; the corresponding linkage efficiency was around 40%. In the computational aspect, simulation models have been developed and validated for each of the subsystems of DesaLink, upon which an integrated model has been realised for the whole system. The models, both the subsystem ones and the integrated one, have been demonstrated to predict accurately the system performance under specific operational conditions. A simulation case study has been performed using the developed model. Simulation results indicate that the system can be expected to achieve a water production of 200 m3 per year by using a widely available evacuated tube solar collector having an area of only 2 m2. This freshwater production would satisfy the drinking water needs of 163 habitants in the Rajasthan region, the area for which the case study was performed.

Complex Adaptive On-line Learning System “Theory of Automatic Control"

The controlled from distance teaching (DT) in the system of technical education has a row of features: complication of informative content, necessity of development of simulation models and trainers for conducting of practical and laboratory employments, conducting of knowledge diagnostics on the basis of mathematical-based algorithms, organization of execution collective projects of the applied setting. For development of the process of teaching bases of fundamental discipline control system Theory of automatic control (TAC) the combined approach of optimum combination of existent programmatic instruments of support was chosen DT and own developments. The system DT TAC included: controlled from distance course (DC) of TAC, site of virtual laboratory practical works in LAB.TAC and students knowledge remote diagnostic system d-tester.

Monte Carlo Random Walk Simulations Based on Distributed Order Differential Equations with Applications to Cell Biology

Mathematics Subject Classification: 65C05, 60G50, 39A10, 92C37

An automatic tuning strategy for local fuzzy logic ramp metering algorithm using Particle Swarm Optimization (PSO)

Freeway systems are becoming more congested each day. One contribution to freeway traffic congestion comprises platoons of on-ramp traffic merging into freeway mainlines. As a relatively low-cost countermeasure to the problem, ramp meters are being deployed in both directions of an 11-mile section of I-95 in Miami-Dade County, Florida. The local Fuzzy Logic (FL) ramp metering algorithm implemented in Seattle, Washington, has been selected for deployment. The FL ramp metering algorithm is powered by the Fuzzy Logic Controller (FLC). The FLC depends on a series of parameters that can significantly alter the behavior of the controller, thus affecting the performance of ramp meters. However, the most suitable values for these parameters are often difficult to determine, as they vary with current traffic conditions. Thus, for optimum performance, the parameter values must be fine-tuned. This research presents a new method of fine tuning the FLC parameters using Particle Swarm Optimization (PSO). PSO attempts to optimize several important parameters of the FLC. The objective function of the optimization model incorporates the METANET macroscopic traffic flow model to minimize delay time, subject to the constraints of reasonable ranges of ramp metering rates and FLC parameters. To further improve the performance, a short-term traffic forecasting module using a discrete Kalman filter was incorporated to predict the downstream freeway mainline occupancy. This helps to detect the presence of downstream bottlenecks. The CORSIM microscopic simulation model was selected as the platform to evaluate the performance of the proposed PSO tuning strategy. The ramp-metering algorithm incorporating the tuning strategy was implemented using CORSIM's run-time extension (RTE) and was tested on the aforementioned I-95 corridor. The performance of the FLC with PSO tuning was compared with the performance of the existing FLC without PSO tuning. The results show that the FLC with PSO tuning outperforms the existing FL metering, fixed-time metering, and existing conditions without metering in terms of total travel time savings, average speed, and system-wide throughput.