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).

Graze to grain - measuring and modelling the effects of grazed pasture leys on soil nitrogen and sorghum yield on a Vertosol soil in the Australian subtropics

Highly productive sown pasture systems can result in high growth rates of beef cattle and lead to increases in soil nitrogen and the production of subsequent crops. The nitrogen dynamics and growth of grain sorghum following grazed annual legume leys or a grass pasture were investigated in a no-till system in the South Burnett district of Queensland. Two years of the tropical legumes Macrotyloma daltonii and Vigna trilobata (both self regenerating annual legumes) and Lablab purpureus (a resown annual legume) resulted in soil nitrate N (0-0.9 m depth), at sorghum sowing, ranging from 35 to 86 kg/ha compared with 4 kg/ha after pure grass pastures. Average grain sorghum production in the 4 cropping seasons following the grazed legume leys ranged from 2651 to 4012 kg/ha. Following the grass pasture, grain sorghum production in the first and second year was < 1900 kg/ha and by the third year grain yield was comparable to the legume systems. Simulation studies utilising the farming systems model APSIM indicated that the soil N and water dynamics following 2-year ley phases could be closely represented over 4 years and the prediction of sorghum growth during this time was reasonable. In simulated unfertilised sorghum crops grown from 1954 to 2004, grain yield did not exceed 1500 kg/ha in 50% of seasons following a grass pasture, while following 2-year legume leys, grain exceeded 3000 kg/ha in 80% of seasons. It was concluded that mixed farming systems that utilise short term legume-based pastures for beef production in rotation with crop production enterprises can be highly productive.

Assessing the sustainability of wheat-based cropping systems using simulation modelling: sustainability

Concepts of agricultural sustainability and possible roles of simulation modelling for characterising sustainability were explored by conducting, and reflecting on, a sustainability assessment of rain-fed wheat-based systems in the Middle East and North Africa region. We designed a goal-oriented, model-based framework using the cropping systems model Agricultural Production Systems sIMulator (APSIM). For the assessment, valid (rather than true or false) sustainability goals and indicators were identified for the target system. System-specific vagueness was depicted in sustainability polygons-a system property derived from highly quantitative data-and denoted using descriptive quantifiers. Diagnostic evaluations of alternative tillage practices demonstrated the utility of the framework to quantify key bio-physical and chemical constraints to sustainability. Here, we argue that sustainability is a vague, emergent system property of often wicked complexity that arises out of more fundamental elements and processes. A 'wicked concept of sustainability' acknowledges the breadth of the human experience of sustainability, which cannot be internalised in a model. To achieve socially desirable sustainability goals, our model-based approach can inform reflective evaluation processes that connect with the needs and values of agricultural decision-makers. Hence, it can help to frame meaningful discussions, from which actions might emerge.

Heat stress effects on grain sorghum productivity-biology and modelling

Heat stress can cause sterility in sorghum and the anticipated increased frequency of high temperature events implies increasing risk to sorghum productivity in Australia. Here we summarise our research on specific varietal attributes associated with heat stress tolerance in sorghum and evaluate how they might affect yield outcomes in production environments by a crop simulation analysis. We have recently conducted a range of controlled environment and field experiments to study the physiology and genetics of high temperature effects on growth and development of sorghum. Sorghum seed set was reduced by high temperature effects (>36-38oC) on pollen germination around flowering, but genotypes differed in their tolerance to high temperature stress. Effects were quantified in a manner that enabled their incorporation into the APSIM sorghum crop model. Simulation analysis indicated that risk of high temperature damage and yield loss depended on sowing date, and variety. While climate trends will exacerbate high temperature effects, avoidance by crop management and genetic tolerance seems possible.

Systems analysis for planning of air fleets and maintenance facilities

The high cost and extraordinary demands made on sophisticated air defence systems, pose hard challenges to the managers and engineers who plan the operation and maintenance of such systems. This paper presents a study aimed at developing simulation and systems analysis techniques for the effective planning and efficient operation of small fleets of aircraft, typical of the air force of a developing country. We consider an important aspect of fleet management: the problem of resource allocation for achieving prescribed operational effectiveness of the fleet. At this stage, we consider a single flying-base, where the operationally ready aircraft are stationed, and a repair-depot, where the planes are overhauled. An important measure of operational effectiveness is ‘ availability ’, which may be defined as the expected fraction of the fleet fit for use at a given instant. The tour of aircraft in a flying-base, repair-depot system through a cycle of ‘ operationally ready ’ and ‘ scheduled overhaul ’ phases is represented first by a deterministic flow process and then by a cyclic queuing process. Initially the steady-state availability at the flying-base is computed under the assumptions of Poisson arrivals, exponential service times and an equivalent singleserver repair-depot. This analysis also brings out the effect of fleet size on availability. It defines a ‘ small ’ fleet essentially in terms of the important ‘ traffic ’ parameter of service rate/maximum arrival rate.A simulation model of the system has been developed using GPSS to study sensitivity to distributional assumptions, to validate the principal assumptions of the analytical model such as the single-server assumption and to obtain confidence intervals for the statistical parameters of interest.

Bridging East and West : The Establishment of the International Institute for Applied Systems Analysis (IIASA) in the United States Foreign Policy of Bridge Building, 1964-1972.

The dissertation examines the foreign policies of the United States through the prism of science and technology. In the focal point of scrutiny is the policy establishing the International Institute for Applied Systems Analysis (IIASA) and the development of the multilateral part of bridge building in American foreign policy during the 1960s and early 1970s. After a long and arduous negotiation process, the institute was finally established by twelve national member organizations from the following countries: Bulgaria, Canada, Czechoslovakia, Federal Republic of Germany (FRG), France, German Democratic Republic (GDR), Great Britain, Italy, Japan, Poland, Soviet Union and United States; a few years later Sweden, Finland and the Netherlands also joined. It is said that the goal of the institute was to bring together researchers from East and West to solve pertinent problems caused by the modernization process experienced in industrialized world. It originates from President Lyndon B. Johnson s bridge building policies that were launched in 1964, and was set in a well-contested and crowded domain of other international organizations of environmental and social planning. Since the distinct need for yet another organization was not evident, the process of negotiations in this multinational environment enlightens the foreign policy ambitions of the United States on the road to the Cold War détente. The study places this project within its political era, and juxtaposes it with other international organizations, especially that of the OECD, ECE and NATO. Conventionally, Lyndon Johnson s bridge building policies have been seen as a means to normalize its international relations bilaterally with different East European countries, and the multilateral dimension of the policy has been ignored. This is why IIASA s establishment process in this multilateral environment brings forth new information on US foreign policy goals, the means to achieve these goals, as well as its relations to other advanced industrialized societies before the time of détente, during the 1960s and early 1970s. Furthermore, the substance of the institute applied systems analysis illuminates the differences between European and American methodological thinking in social planning. Systems analysis is closely associated with (American) science and technology policies of the 1960s, especially in its military administrative applications, thus analysis within the foreign policy environment of the United States proved particularly fruitful. In the 1960s the institutional structures of European continent with faltering, and the growing tendencies of integration were in flux. One example of this was the long, drawn-out process of British membership in the EEC, another is de Gaulle s withdrawal from NATO s military-political cooperation. On the other hand, however, economic cooperation in Europe between East and West, and especially with the Soviet Union was expanding rapidly. This American initiative to form a new institutional actor has to be seen in that structural context, showing that bridge building was needed not only to the East, but also to the West. The narrative amounts to an analysis of how the United States managed both cooperation and conflict in its hegemonic aspirations in the emerging modern world, and how it used its special relationship with the United Kingdom to achieve its goals. The research is based on the archives of the United States, Great Britain, Sweden, Finland, and IIASA. The primary sources have been complemented with both contemporary and present day research literature, periodicals, and interviews.

EESM-Based Link Adaptation in Point-to-Point and Multi-Cell OFDM Systems: Modeling and Analysis

In contemporary wideband orthogonal frequency division multiplexing (OFDM) systems, such as Long Term Evolution (LTE) and WiMAX, different subcarriers over which a codeword is transmitted may experience different signal-to-noise-ratios (SNRs). Thus, adaptive modulation and coding (AMC) in these systems is driven by a vector of subcarrier SNRs experienced by the codeword, and is more involved. Exponential effective SNR mapping (EESM) simplifies the problem by mapping this vector into a single equivalent fiat-fading SNR. Analysis of AMC using EESM is challenging owing to its non-linear nature and its dependence on the modulation and coding scheme. We first propose a novel statistical model for the EESM, which is based on the Beta distribution. It is motivated by the central limit approximation for random variables with a finite support. It is simpler and as accurate as the more involved ad hoc models proposed earlier. Using it, we develop novel expressions for the throughput of a point-to-point OFDM link with multi-antenna diversity that uses EESM for AMC. We then analyze a general, multi-cell OFDM deployment with co-channel interference for various frequency-domain schedulers. Extensive results based on LTE and WiMAX are presented to verify the model and analysis, and gain new insights.

Dispersion analysis and compensation of collinear optical parametric chirped pulse amplification systems

In an optical parametric chirped pulse amplification (OPCPA) laser system, residual phase dispersion should be compensated as much as possible to shorten the amplified pulses and improve the pulse contrast ratio. Expressions of orders of the induced phases in collinear optical parametric amplification (OPA) processes are presented at the central signal wavelength to depict a clear physics picture and to simplify the design of phase compensation. As examples, we simulate two OPCPA systems to compensate for the phases up to the partial fourth-order terms, and obtain flat phase spectra of 200-nm bandwidth at 1064 nm and 90-nm at 800 nm.

Testable models of aquatic systems: A NERC special topic for integrating experiments and modelling

A major part of the support for fundamental research on aquatic ecosystems continues to be provided by the Natural Environment Research Council (NERC). Funds are released for ”thematic” studies in a selected special topic or programme. ”Testable Models of Aquatic Ecosystems” was a Special Topic of the NERC, initiated in 1995, the aim of which was to promote ecological modelling by making new links between experimental aquatic biologists and state-of-the-art modellers. The Topic covered both marine and freshwater systems. This paper summarises projects on aspects of the responses of individual organisms to the effects of environmental variability, on the assembly, permanence and resilience of communities, and on aspects of spatial models. The authors conclude that the NERC Special Topic has been highly successful in promoting the development and application of models, most particularly through the interplay between experimental ecologists and formal modellers.