Scalable Visualization of Galaxies, Oceans, and Brains

One of the challenges in scientific visualization is to generate software libraries suitable for the large-scale data emerging from tera-scale simulations and instruments. We describe the efforts currently under way at SDSC and NPACI to address these challenges. The scope of the SDSC project spans data handling, graphics, visualization, and scientific application domains. Components of the research focus on the following areas: intelligent data storage, layout and handling, using an associated ���Floor-Plan��� (meta data); performance optimization on parallel architectures; extension of SDSC���s scalable, parallel, direct volume renderer to allow perspective viewing; and interactive rendering of fractional images (���imagelets���), which facilitates the examination of large datasets. These concepts are coordinated within a data-visualization pipeline, which operates on component data blocks sized to fit within the available computing resources. A key feature of the scheme is that the meta data, which tag the data blocks, can be propagated and applied consistently. This is possible at the disk level, in distributing the computations across parallel processors; in ���imagelet��� composition; and in feature tagging. The work reflects the emerging challenges and opportunities presented by the ongoing progress in high-performance computing (HPC) and the deployment of the data, computational, and visualization Grids.

Bifurcation in growth patterns for arrays of parallel Griffith, edge and sliding cracks

This paper presents the recent finding by Muhlhaus et al [1] that bifurcation of crack growth patterns exists for arrays of two-dimensional cracks. This bifurcation is a result of the nonlinear effect due to crack interaction, which is, in the present analysis, approximated by the dipole asymptotic or pseudo-traction method. The nonlinear parameter for the problem is the crack length/ spacing ratio lambda = a/h. For parallel and edge crack arrays under far field tension, uniform crack growth patterns (all cracks having same size) yield to nonuniform crack growth patterns (i.e. bifurcation) if lambda is larger than a critical value lambda(cr) (note that such bifurcation is not found for collinear crack arrays). For parallel and edge crack arrays respectively, the value of lambda(cr) decreases monotonically from (2/9)(1/2) and (2/15.096)(1/2) for arrays of 2 cracks, to (2/3)(1/2)/pi and (2/5.032)(1/2)/pi for infinite arrays of cracks. The critical parameter lambda(cr) is calculated numerically for arrays of up to 100 cracks, whilst discrete Fourier transform is used to obtain the exact solution of lambda(cr) for infinite crack arrays. For geomaterials, bifurcation can also occurs when array of sliding cracks are under compression.

Response (re-)programming in aging: A kinematic analysis

Background. Age-related motor slowing may reflect either motor programming deficits, poorer movement execution, or mere strategic preferences for online guidance of movement. We controlled such preferences, limiting the extent to which movements could be programmed. Methods. Twenty-four young and 24 older adults performed a line drawing task that allowed movements to he prepared in advance in one case (i.e., cue initially available indicating target location) and not in another (i.e., no cue initially available as to target location). Participants connected large or small targets illuminated by light-emitting diodes upon a graphics tablet that sampled pen tip position at 200 Hz. Results. Older adults had a disproportionate difficulty initiating movement when prevented from programming in advance. Older adults produced slower, less efficient movements, particularly when prevented from programming under greater precision requirements. Conclusions. The slower movements of older adults do not simply reflect a preference for online control, as older adults have less efficient movements when forced to reprogram their movements. Age-related motor slowing kinematically resembles that seen in patients with cerebellar dysfunction.

The effect of imposed and self-selected computer monitor height on posture and gaze angle

Objective: The objectives were to determine the postural consequences of varying computer monitor height and to describe self-selected monitor heights and postures. Design: The design involved experimental manipulation of computer monitor height, description of self-selected heights, and measurement of posture and gaze angles. Background. Disagreement exists with regard to the appropriate height of computer monitors. It is known that users alter both head orientation and gaze angle in response to changes in monitor height; however the relative contribution of atlanto-occipital and cervical flexion to the change in head rotation is unknown. No information is available with regard to self-selected monitor heights. Methods. Twelve students performed a tracking task with the monitor placed at three different heights. The subjects then completed eight trials in which monitor height was first self-selected. Sagittal postural and gaze angle data were determined by digitizing markers defining a two-dimensional three-link model of the trunk, cervical spine and head. Results. The 27 degrees change in monitor height imposed was, on average, accommodated by 18 degrees of head inclination and a 9 degrees change in gaze angle relative to the head. The change in head inclination was achieved by a 6 degrees change in trunk inclination, a 4 degrees change in cervical flexion, and a 7 degrees change in atlanto-occipital flexion. The self-selected height varied depending on the initial monitor height and inclination. Conclusions. Self-selected monitor heights were lower than current 'eye-level' recommendations. Lower monitor heights are likely to reduce both visual and musculoskeletal discomfort. Relevance Musculoskeletal and visual discomfort may be reduced by placing computer monitors lower than currently recommended. (C) 1998 Elsevier Science Ltd. All rights reserved.

CXTANNEAL: an improved program for estimating solute transport parameters

CXTANNEAL is a program for analysing contaminant transport in soils. The code, written in Fortran 77, is a modified version of CXTFIT, a commonly used package for estimating solute transport parameters in soils. The improvement of the present code is that it includes simulated annealing as the optimization technique for curve fitting. Tests with hypothetical data show that CXTANNEAL performs better than the original code in searching for optimal parameter estimates. To reduce the computational time, a parallel version of CXTANNEAL (CXTANNEAL_P) was also developed. (C) 1999 Elsevier Science Ltd. All rights reserved.

RWMODEL II: Computer simulation of the Rescorla-Wagner model of Pavlovian conditioning

RWMODEL II simulates the Rescorla-Wagner model of Pavlovian conditioning. It is written in Delphi and runs under Windows 3.1 and Windows 95. The program was designed for novice and expert users and can be employed in teaching, as well as in research. It is user friendly and requires a minimal level of computer literacy but is sufficiently flexible to permit a wide range of simulations. It allows the display of empirical data, against which predictions from the model can be validated.

Optimal release strategies for biological control agents: an application of stochastic dynamic programming to population management

1. Establishing biological control agents in the field is a major step in any classical biocontrol programme, yet there are few general guidelines to help the practitioner decide what factors might enhance the establishment of such agents. 2. A stochastic dynamic programming (SDP) approach, linked to a metapopulation model, was used to find optimal release strategies (number and size of releases), given constraints on time and the number of biocontrol agents available. By modelling within a decision-making framework we derived rules of thumb that will enable biocontrol workers to choose between management options, depending on the current state of the system. 3. When there are few well-established sites, making a few large releases is the optimal strategy. For other states of the system, the optimal strategy ranges from a few large releases, through a mixed strategy (a variety of release sizes), to many small releases, as the probability of establishment of smaller inocula increases. 4. Given that the probability of establishment is rarely a known entity, we also strongly recommend a mixed strategy in the early stages of a release programme, to accelerate learning and improve the chances of finding the optimal approach.

Target similarity effects: Support for the parallel distributed processing assumptions

Recent research has begun to provide support for the assumptions that memories are stored as a composite and are accessed in parallel (Tehan & Humphreys, 1998). New predictions derived from these assumptions and from the Chappell and Humphreys (1994) implementation of these assumptions were tested. In three experiments, subjects studied relatively short lists of words. Some of the Lists contained two similar targets (thief and theft) or two dissimilar targets (thief and steal) associated with the same cue (ROBBERY). AS predicted, target similarity affected performance in cued recall but not free association. Contrary to predictions, two spaced presentations of a target did not improve performance in free association. Two additional experiments confirmed and extended this finding. Several alternative explanations for the target similarity effect, which incorporate assumptions about separate representations and sequential search, are rejected. The importance of the finding that, in at least one implicit memory paradigm, repetition does not improve performance is also discussed.

Numerical modelling of single-layer folding: clarification of an issue regarding the possible effect of computer codes and the influence of initial irregularities

The influence of initial perturbation geometry and material propel-ties on final fold geometry has been investigated using finite-difference (FLAC) and finite-element (MARC) numerical models. Previous studies using these two different codes reported very different folding behaviour although the material properties, boundary conditions and initial perturbation geometries were similar. The current results establish that the discrepancy was not due to the different computer codes but due to the different strain rates employed in the two previous studies (i.e. 10(-6) s(-1) in the FLAC models and 10(-14) s(-1) in the MARC models). As a result, different parts of the elasto-viscous rheological field were bring investigated. For the same material properties, strain rate and boundary conditions, the present results using the two different codes are consistent. A transition in Folding behaviour, from a situation where the geometry of initial perturbation determines final fold shape to a situation where material properties control the final geometry, is produced using both models. This transition takes place with increasing strain rate, decreasing elastic moduli or increasing viscosity (reflecting in each case the increasing influence of the elastic component in the Maxwell elastoviscous rheology). The transition described here is mechanically feasible but is associated with very high stresses in the competent layer (on the order of GPa), which is improbable under natural conditions. (C) 2000 Elsevier Science Ltd. All rights reserved.

Parallel processing and image analysis in the eyes of mantis shrimps

The compound eyes of mantis shrimps, a group of tropical marine crustaceans, incorporate principles of serial and parallel processing of visual information that may be applicable to artificial imaging systems. Their eyes include numerous specializations for analysis of the spectral and polarizational properties of light, and include more photoreceptor classes for analysis of ultraviolet light, color, and polarization than occur in any other known visual system. This is possible because receptors in different regions of the eye are anatomically diverse and incorporate unusual structural features, such as spectral filters, not seen in other compound eyes. Unlike eyes of most other animals, eyes of mantis shrimps must move to acquire some types of visual information and to integrate color and polarization with spatial vision. Information leaving the retina appears to be processed into numerous parallel data streams leading into the central nervous system, greatly reducing the analytical requirements at higher levels. Many of these unusual features of mantis shrimp vision may inspire new sensor designs for machine vision

Using stochastic dynamic programming to determine optimal fire management for Banksia ornata

1. A model of the population dynamics of Banksia ornata was developed, using stochastic dynamic programming (a state-dependent decision-making tool), to determine optimal fire management strategies that incorporate trade-offs between biodiversity conservation and fuel reduction. 2. The modelled population of B. ornata was described by its age and density, and was exposed to the risk of unplanned fires and stochastic variation in germination success. 3. For a given population in each year, three management strategies were considered: (i) lighting a prescribed fire; (ii) controlling the incidence of unplanned fire; (iii) doing nothing. 4. The optimal management strategy depended on the state of the B. ornata population, with the time since the last fire (age of the population) being the most important variable. Lighting a prescribed fire at an age of less than 30 years was only optimal when the density of seedlings after a fire was low (< 100 plants ha(-1)) or when there were benefits of maintaining a low fuel load by using more frequent fire. 5. Because the cost of management was assumed to be negligible (relative to the value of the persistence of the population), the do-nothing option was never the optimal strategy, although lighting prescribed fires had only marginal benefits when the mean interval between unplanned fires was less than 20-30 years.

Assisting decision-making in Queensland barley production through chance constrained programming

A chance constrained programming model is developed to assist Queensland barley growers make varietal and agronomic decisions in the face of changing product demands and volatile production conditions. Unsuitable or overlooked in many risk programming applications, the chance constrained programming approach nonetheless aptly captures the single-stage decision problem faced by barley growers of whether to plant lower-yielding but potentially higher-priced malting varieties, given a particular expectation of meeting malting grade standards. Different expectations greatly affect the optimal mix of malting and feed barley activities. The analysis highlights the suitability of chance constrained programming to this specific class of farm decision problem.

An L-system-based plant modeling language

Cpfg is a program for simulating and visualizing plant development, based on the theory of L-systems. A special-purpose programming language, used to specify plant models, is an essential feature of cpfg. We review postulates of L-system theory that have influenced the design of this language. We then present the main constructs of this language, and evaluate it from a user's perspective.

Modelling socially optimal land allocations for sugar cane growing in North Queensland: a linked mathematical programming and choice modelling study

A modelling framework is developed to determine the joint economic and environmental net benefits of alternative land allocation strategies. Estimates of community preferences for preservation of natural land, derived from a choice modelling study, are used as input to a model of agricultural production in an optimisation framework. The trade-offs between agricultural production and environmental protection are analysed using the sugar industry of the Herbert River district of north Queensland as an example. Spatially-differentiated resource attributes and the opportunity costs of natural land determine the optimal tradeoffs between production and conservation for a range of sugar prices.

Structuring real-time Object-Z specifications

This paper presents a means of structuring specifications in real-time Object-Z: an integration of Object-Z with the timed refinement calculus. Incremental modification of classes using inheritance and composition of classes to form multi-component systems are examined. Two approaches to the latter are considered: using Object-Z's notion of object instantiation and introducing a parallel composition operator similar to those found in process algebras. The parallel composition operator approach is both more concise and allows more general modelling of concurrency. Its incorporation into the existing semantics of real-time Object-Z is presented.