Improving wheat simulation capabilities in Australia from a cropping systems perspective - II. Testing simulation capabilities of wheat growth

To simulate cropping systems, crop models must not only give reliable predictions of yield across a wide range of environmental conditions, they must also quantify water and nutrient use well, so that the status of the soil at maturity is a good representation of the starting conditions for the next cropping sequence. To assess the suitability for this task a range of crop models, currently used in Australia, were tested. The models differed in their design objectives, complexity and structure and were (i) tested on diverse, independent data sets from a wide range of environments and (ii) model components were further evaluated with one detailed data set from a semi-arid environment. All models were coded into the cropping systems shell APSIM, which provides a common soil water and nitrogen balance. Crop development was input, thus differences between simulations were caused entirely by difference in simulating crop growth. Under nitrogen non-limiting conditions between 73 and 85% of the observed kernel yield variation across environments was explained by the models. This ranged from 51 to 77% under varying nitrogen supply. Water and nitrogen effects on leaf area index were predicted poorly by all models resulting in erroneous predictions of dry matter accumulation and water use. When measured light interception was used as input, most models improved in their prediction of dry matter and yield. This test highlighted a range of compensating errors in all modelling approaches. Time course and final amount of water extraction was simulated well by two models, while others left up to 25% of potentially available soil water in the profile. Kernel nitrogen percentage was predicted poorly by all models due to its sensitivity to small dry matter changes. Yield and dry matter could be estimated adequately for a range of environmental conditions using the general concepts of radiation use efficiency and transpiration efficiency. However, leaf area and kernel nitrogen dynamics need to be improved to achieve better estimates of water and nitrogen use if such models are to be use to evaluate cropping systems. (C) 1998 Elsevier Science B.V.

Improving wheat simulation capabilities in Australia from a cropping systems perspective - III. The integrated wheat model (I_WHEAT)

Previous work has identified several short-comings in the ability of four spring wheat and one barley model to simulate crop processes and resource utilization. This can have important implications when such models are used within systems models where final soil water and nitrogen conditions of one crop define the starting conditions of the following crop. In an attempt to overcome these limitations and to reconcile a range of modelling approaches, existing model components that worked demonstrably well were combined with new components for aspects where existing capabilities were inadequate. This resulted in the Integrated Wheat Model (I_WHEAT), which was developed as a module of the cropping systems model APSIM. To increase predictive capability of the model, process detail was reduced, where possible, by replacing groups of processes with conservative, biologically meaningful parameters. I_WHEAT does not contain a soil water or soil nitrogen balance. These are present as other modules of APSIM. In I_WHEAT, yield is simulated using a linear increase in harvest index whereby nitrogen or water limitations can lead to early termination of grainfilling and hence cessation of harvest index increase. Dry matter increase is calculated either from the amount of intercepted radiation and radiation conversion efficiency or from the amount of water transpired and transpiration efficiency, depending on the most limiting resource. Leaf area and tiller formation are calculated from thermal time and a cultivar specific phyllochron interval. Nitrogen limitation first reduces leaf area and then affects radiation conversion efficiency as it becomes more severe. Water or nitrogen limitations result in reduced leaf expansion, accelerated leaf senescence or tiller death. This reduces the radiation load on the crop canopy (i.e. demand for water) and can make nitrogen available for translocation to other organs. Sensitive feedbacks between light interception and dry matter accumulation are avoided by having environmental effects acting directly on leaf area development, rather than via biomass production. This makes the model more stable across environments without losing the interactions between the different external influences. When comparing model output with models tested previously using data from a wide range of agro-climatic conditions, yield and biomass predictions were equal to the best of those models, but improvements could be demonstrated for simulating leaf area dynamics in response to water and nitrogen supply, kernel nitrogen content, and total water and nitrogen use. I_WHEAT does not require calibration for any of the environments tested. Further model improvement should concentrate on improving phenology simulations, a more thorough derivation of coefficients to describe leaf area development and a better quantification of some processes related to nitrogen dynamics. (C) 1998 Elsevier Science B.V.

Thermal diffusion in molecular dynamics simulations of thin film diamond deposition

Molecular dynamics simulations of carbon atom depositions are used to investigate energy diffusion from the impact zone. A modified Stillinger-Weber potential models the carbon interactions for both sp2 and sp3 bonding. Simulations were performed on 50 eV carbon atom depositions onto the (111) surface of a 3.8 x 3.4 x 1.0 nm diamond slab containing 2816 atoms in 11 layers of 256 atoms each. The bottom layer was thermostated to 300 K. At every 100th simulation time step (27 fs), the average local kinetic energy, and hence local temperature, is calculated. To do this the substrate is divided into a set of 15 concentric hemispherical zones, each of thickness one atomic diameter (0.14 nm) and centered on the impact point. A 50-eV incident atom heats the local impact zone above 10 000 K. After the initial large transient (200 fs) the impact zone has cooled below 3000 K, then near 1000 K by 1 ps. Thereafter the temperature profile decays approximately as described by diffusion theory, perturbed by atomic scale fluctuations. A continuum model of classical energy transfer is provided by the traditional thermal diffusion equation. The results show that continuum diffusion theory describes well energy diffusion in low energy atomic deposition processes, at distance and time scales larger than 1.5 nm and 1-2 ps, beyond which the energy decays essentially exponentially. (C) 1998 Published by Elsevier Science S.A. All rights reserved.

Flush air data system calibration using numerical simulation

The use of computational fluid dynamics simulations for calibrating a flush air data system is described, In particular, the flush air data system of the HYFLEX hypersonic vehicle is used as a case study. The HYFLEX air data system consists of nine pressure ports located flush with the vehicle nose surface, connected to onboard pressure transducers, After appropriate processing, surface pressure measurements can he converted into useful air data parameters. The processing algorithm requires an accurate pressure model, which relates air data parameters to the measured pressures. In the past, such pressure models have been calibrated using combinations of flight data, ground-based experimental results, and numerical simulation. We perform a calibration of the HYFLEX flush air data system using computational fluid dynamics simulations exclusively, The simulations are used to build an empirical pressure model that accurately describes the HYFLEX nose pressure distribution ol cr a range of flight conditions. We believe that computational fluid dynamics provides a quick and inexpensive way to calibrate the air data system and is applicable to a broad range of flight conditions, When tested with HYFLEX flight data, the calibrated system is found to work well. It predicts vehicle angle of attack and angle of sideslip to accuracy levels that generally satisfy flight control requirements. Dynamic pressure is predicted to within the resolution of the onboard inertial measurement unit. We find that wind-tunnel experiments and flight data are not necessary to accurately calibrate the HYFLEX flush air data system for hypersonic flight.

Two-dimensional nonlinear dynamics of evanescent-wave guided atoms in a hollow fiber

We describe the classical and quantum two-dimensional nonlinear dynamics of large blue-detuned evanescent-wave guiding cold atoms in hollow fiber. We show that chaotic dynamics exists for classic dynamics, when the intensity of the beam is periodically modulated. The two-dimensional distributions of atoms in (x,y) plane are simulated. We show that the atoms will accumulate on several annular regions when the system enters a regime of global chaos. Our simulation shows that, when the atomic flux is very small, a similar distribution will be obtained if we detect the atomic distribution once each the modulation period and integrate the signals. For quantum dynamics, quantum collapses, and revivals appear. For periodically modulated optical potential, the variance of atomic position will be suppressed compared to the no modulation case. The atomic angular momentum will influence the evolution of wave function in two-dimensional quantum system of hollow fiber.

Thermal Characteristics of Polybia scutellaris Nests (Hymenoptera: Vespidae) Using Computational Fluid Dynamics: A Possible Adaptation to Tropical Climates

Polybia scutellaris constructs huge nests characterized by numerous spinal projections on the surface. We investigated the thermal characteristics of P scutellaris nests in order to determine whether their nest temperature is homeothermically maintained and whether the spines play a role in the thermoregulation of the nests. In order to examine these hypotheses, we measured the nest temperature in a active nest and in an abandoned nest. The temperature in the active nest was almost stable at 27 degrees C, whereas that of the abandoned nest varied with changes in the ambient temperature, suggesting that nest temperature was maintained by the thermogenesis of colony individuals. In order to predict the thermal properties of the spines, a numerical simulation was employed. To construct a 3D-model of a P scutellaris nest, the nest architecture was simplified into an outer envelope and the surface spines, for both of which the initial temperature was set at 27 degrees C. The physical properties of the simulated nest were regarded to be those of wood since the nest of this species is constructed from plant materials. When the model was exposed to cool air (12 degrees C), the temperature was lower in the models with more spines. On the other hand, when the nest was heated (42 degrees C), the temperature increase was smaller in models with more spines. It is suggested that the spines act as a heat radiator, not as an insulator, against the changes in ambient temperature.

On the dynamics of mechanical milling in a vibratory mill

The dynamics of mechanical milling in a vibratory mill have been studied by means of mechanical vibration, shock measurements, computer simulation and microstructural evolution measurements. Two distinct modes of ball motion during milling, periodic and chaotic vibration, were observed. Mill operation in the regime of periodic vibration, in which each collision provides a constant energy input to milled powders, enabled a quantitative description of the effect of process parameters on system dynamics. An investigation of the effect of process parameters on microstructural development in an austenitic stainless steel showed that the impact force associated with collision events is an important process parameter for characterizing microstructural evolution. (C) 1997 Elsevier Science S.A.

Molecular Characterization, Distribution, and Dynamics of Hepatitis C Virus Genotypes in Blood Donors in Colombia

Hepatitis C virus (HCV) is a frequent cause of acute and chronic hepatitis and a leading cause for cirrhosis of the liver and hepatocellular carcinoma. HCV is classified in six major genotypes and more than 70 subtypes. In Colombian blood banks, serum samples were tested for anti-HCV antibodies using a third-generation ELISA. The aim of this study was to characterize the viral sequences in plasma of 184 volunteer blood donors who attended the ""Banco Nacional de Sangre de la Cruz Roja Colombiana,`` Bogota, Colombia. Three different HCV genomic regions were amplified by nested PCR. The first of these was a segment of 180 bp of the 5`UTR region to confirm the previous diagnosis by ELISA. From those that were positive to the 5`UTR region, two further segments were amplified for genotyping and subtyping by phylogenetic analysis: a segment of 380 bp from the NS5B region; and a segment of 391 bp from the E1 region. The distribution of HCV subtypes was: 1b (82.8%), 1a (5.7%), 2a (5.7%), 2b (2.8%), and 3a (2.8%). By applying Bayesian Markov chain Monte Carlo simulation, it was estimated that HCV-1b was introduced into Bogota around 1950. Also, this subtype spread at an exponential rate between about 1970 to about 1990, after which transmission of HCV was reduced by anti-HCV testing of this population. Among Colombian blood donors, HCV genotype 1b is the most frequent genotype, especially in large urban conglomerates such as Bogota, as is the case in other South American countries. J. Med. Virol. 82: 1889-1898, 2010. (C) 2010 Wiley-Liss, Inc.

Canine population dynamics: the potential effect of sterilization campaigns

Objective. To analyze, through mathematical modeling, the potential ability of sterilization campaigns to reduce the population density of pet dogs. Methods. Mathematical models were constructed to simulate the canine population dynamics and project the results of control strategies based on several sterilization rates. Results. Even at high sterilization rates (for example, 0.80 year(-1)), it would take approximately 5 years to reduce density by 20%. Even so, other sources of population growth, such as the importing of dogs from other geographic areas, could outweigh the effects of a sterilization program. Conclusions. A program`s effectiveness is contingent upon not only on the sterilization rate, but also the rate of population growth. Sterilization campaigns may potentially reduce population density, but this reduction may not be immediately evident.

Enzymology, structure, and dynamics of acetohydroxy acid isomeroreductase

Acetohydroxy acid isomeroreductase is a key enzyme involved in the biosynthetic pathway of the amino acids isoleucine, valine, and leucine. This enzyme is of great interest in agrochemical research because it is present only in plants and microorganisms, making it a potential target for specific herbicides and fungicides. Moreover, it catalyzes an unusual two-step reaction that is of great fundamental interest. With a view to characterizing both the mechanism of inhibition by potential herbicides and the complex reaction mechanism, various techniques of enzymology, molecular biology, mass spectrometry, X-ray crystallography, and theoretical simulation have been used. The results and conclusions of these studies are described briefly in this paper.

Simulation of Oxford University Gun Tunnel performance using a quasi-one-dimensional model

The performance of the Oxford University Gun Tunnel has been estimated using a quasi-one-dimensional simulation of the facility gas dynamics. The modelling of the actual facility area variations so as to adequately simulate both shock reflection and flow discharge processes has been considered in some detail. Test gas stagnation pressure and temperature histories are compared with measurements at two different operating conditions - one with nitrogen and the other with carbon dioxide as the test gas. It is demonstrated that both the simulated pressures and temperatures are typically within 3% of the experimental measurements.

Universal quantum computation and simulation using any entangling Hamiltonian and local unitaries

What interactions are sufficient to simulate arbitrary quantum dynamics in a composite quantum system? We provide an efficient algorithm to simulate any desired two-body Hamiltonian evolution using any fixed two-body entangling n-qubit Hamiltonian and local unitary operations. It follows that universal quantum computation can be performed using any entangling interaction and local unitary operations.

An atomistic simulation of solid state sintering using Monte Carlo methods

This paper presents results on the simulation of the solid state sintering of copper wires using Monte Carlo techniques based on elements of lattice theory and cellular automata. The initial structure is superimposed onto a triangular, two-dimensional lattice, where each lattice site corresponds to either an atom or vacancy. The number of vacancies varies with the simulation temperature, while a cluster of vacancies is a pore. To simulate sintering, lattice sites are picked at random and reoriented in terms of an atomistic model governing mass transport. The probability that an atom has sufficient energy to jump to a vacant lattice site is related to the jump frequency, and hence the diffusion coefficient, while the probability that an atomic jump will be accepted is related to the change in energy of the system as a result of the jump, as determined by the change in the number of nearest neighbours. The jump frequency is also used to relate model time, measured in Monte Carlo Steps, to the actual sintering time. The model incorporates bulk, grain boundary and surface diffusion terms and includes vacancy annihilation on the grain boundaries. The predictions of the model were found to be consistent with experimental data, both in terms of the microstructural evolution and in terms of the sintering time. (C) 2002 Elsevier Science B.V. All rights reserved.

Tillering in grain sorghum over a wide range of population densities: Modelling dynamics of tiller fertility

The prediction of tillering is poor or absent in existing sorghum crop models even though fertile tillers contribute significantly to grain yield. The objective of this study was to identify general quantitative relationships underpinning tiller dynamics of sorghum for a broad range of assimilate availabilities. Emergence, phenology, leaf area development and fertility of individual main calms and tillers were quantified weekly in plants grown at one of four plant densities ranging from two to 16 plants m(-2). On any given day, a tiller was considered potentially fertile (a posteriori) if its number of leaves continued to increase thereafter. The dynamics of potentially fertile tiller number per plant varied greatly with plant density, but could generally be described by three determinants, stable across plant densities: tiller emergence rate aligned with leaf ligule appearance rate; cessation of tiller emergence occurred at a stable leaf area index; and rate of decrease in potentially fertile tillers was linearly related to the ratio of realized to potential leaf area growth. Realized leaf area growth is the measured increase in leaf area, whereas potential leaf area growth is the estimated increase in leaf area if all potentially fertile tillers were to continue to develop. Procedures to predict this ratio, by estimating realized leaf area per plant from intercepted radiation and potential leaf area per plant from the number and type of developing axes, are presented. While it is suitable for modelling tiller dynamics in grain sorghum, this general framework needs to be validated by testing it in different environments and for other cultivars. (C) 2002 Annals of Botany Company.