Virtual models of the HLA class I antigen processing pathway

Antigen recognition by cytotoxic CD8 T cells is dependent upon a number of critical steps in MHC class I antigen processing including proteosomal cleavage, TAP transport into the endoplasmic reticulum, and MHC class 1 binding. Based on extensive experimental data relating to each of these steps there is now the capacity to model individual antigen processing steps with a high degree of accuracy. This paper demonstrates the potential to bring together models of individual antigen processing steps, for example proteosome cleavage, TAP transport, and MHC binding, to build highly informative models of functional pathways. In particular, we demonstrate how an artificial neural network model of TAP transport was used to mine a HLA-binding database so as to identify H LA-binding peptides transported by TAP. This integrated model of antigen processing provided the unique insight that HLA class I alleles apparently constitute two separate classes: those that are TAP-efficient for peptide loading (HLA-B27, -A3, and -A24) and those that are TAP-inefficient (HLA-A2, -B7, and -B8). Hence, using this integrated model we were able to generate novel hypotheses regarding antigen processing, and these hypotheses are now capable of being tested experimentally. This model confirms the feasibility of constructing a virtual immune system, whereby each additional step in antigen processing is incorporated into a single modular model. Accurate models of antigen processing have implications for the study of basic immunology as well as for the design of peptide-based vaccines and other immunotherapies. (C) 2004 Elsevier Inc. All rights reserved.

Virtual plants - integrating architectural and physiological models

Recent advances in computer technology have made it possible to create virtual plants by simulating the details of structural development of individual plants. Software has been developed that processes plant models expressed in a special purpose mini-language based on the Lindenmayer system formalism. These models can be extended from their architectural basis to capture plant physiology by integrating them with crop models, which estimate biomass production as a consequence of environmental inputs. Through this process, virtual plants will gain the ability to react to broad environmental conditions, while crop models will gain a visualisation component. This integration requires the resolution of the fundamentally different time scales underlying the approaches. Architectural models are usually based on physiological time; each time step encompasses the same amount of development in the plant, without regard to the passage of real time. In contrast, physiological models are based in real time; the amount of development in a time step is dependent on environmental conditions during the period. This paper provides a background on the plant modelling language, then describes how widely-used concepts of thermal time can be implemented to resolve these time scale differences. The process is illustrated using a case study. (C) 1997 Elsevier Science Ltd.

Communicating trustworthiness and building trust in interorganizational virtual organizations

We propose a theory of trust in interorganizational virtual organizations that focuses on how trustworthiness can be communicated and trust built in this environment. The theory highlights three issues that must be dealt with if the potential obstacles to the development of trust in the virtual context are to be overcome. These are communication of trustworthiness facilitated by reliable Information and Communication Technology (ICT), establishment of a common business understanding, and strong business ethics. We propose four specific propositions relating to these issues, and suggest topics to be explored in future research. (C) 2001 Elsevier Science Inc. All rights reserved.

Simulation of insect movement with respect to plant architecture and morphogenesis

Developments in computer and three dimensional (3D) digitiser technologies have made it possible to keep track of the broad range of data required to simulate an insect moving around or over the highly heterogeneous habitat of a plant's surface. Properties of plant parts vary within a complex canopy architecture, and insect damage can induce further changes that affect an animal's movements, development and likelihood of survival. Models of plant architectural development based on Lindenmayer systems (L-systems) serve as dynamic platforms for simulation of insect movement, providing ail explicit model of the developing 3D structure of a plant as well as allowing physiological processes associated with plant growth and responses to damage to be described and Simulated. Simple examples of the use of the L-system formalism to model insect movement, operating Lit different spatial scales-from insects foraging on an individual plant to insects flying around plants in a field-are presented. Such models can be used to explore questions about the consequences of changes in environmental architecture and configuration on host finding, exploitation and its population consequences. In effect this model is a 'virtual ecosystem' laboratory to address local as well as landscape-level questions pertinent to plant-insect interactions, taking plant architecture into account. (C) 2002 Elsevier Science B.V. All rights reserved.

Database technologies for l-system simulations in virtual plant applications on bioinformatics

One of the most important advantages of database systems is that the underlying mathematics is rich enough to specify very complex operations with a small number of statements in the database language. This research covers an aspect of biological informatics that is the marriage of information technology and biology, involving the study of real-world phenomena using virtual plants derived from L-systems simulation. L-systems were introduced by Aristid Lindenmayer as a mathematical model of multicellular organisms. Not much consideration has been given to the problem of persistent storage for these simulations. Current procedures for querying data generated by L-systems for scientific experiments, simulations and measurements are also inadequate. To address these problems the research in this paper presents a generic process for data-modeling tools (L-DBM) between L-systems and database systems. This paper shows how L-system productions can be generically and automatically represented in database schemas and how a database can be populated from the L-system strings. This paper further describes the idea of pre-computing recursive structures in the data into derived attributes using compiler generation. A method to allow a correspondence between biologists' terms and compiler-generated terms in a biologist computing environment is supplied. Once the L-DBM gets any specific L-systems productions and its declarations, it can generate the specific schema for both simple correspondence terminology and also complex recursive structure data attributes and relationships.

Determination of lifter design, speed and filling effects in AG mills by 3D DEM

The power required to operate large gyratory mills often exceeds 10 MW. Hence, optimisation of the power consumption will have a significant impact on the overall economic performance and environmental impact of the mineral processing plant. In most of the published models of tumbling mills (e.g. [Morrell, S., 1996. Power draw of wet tumbling mills and its relationship to charge dynamics, Part 2: An empirical approach to modelling of mill power draw. Trans. Inst. Mining Metall. (Section C: Mineral Processing Ext. Metall.) 105, C54-C62. Austin, L.G., 1990. A mill power equation for SAG mills. Miner. Metall. Process. 57-62]), the effect of lifter design and its interaction with mill speed and filling are not incorporated. Recent experience suggests that there is an opportunity for improving grinding efficiency by choosing the appropriate combination of these variables. However, it is difficult to experimentally determine the interactions of these variables in a full scale mill. Although some work has recently been published using DEM simulations, it was basically. limited to 2D. The discrete element code, Particle Flow Code 3D (PFC3D), has been used in this work to model the effects of lifter height (525 cm) and mill speed (50-90% of critical) on the power draw and frequency distribution of specific energy (J/kg) of normal impacts in a 5 m diameter autogenous (AG) mill. It was found that the distribution of the impact energy is affected by the number of lifters, lifter height, mill speed and mill filling. Interactions of lifter design, mill speed and mill filling are demonstrated through three dimensional distinct element methods (3D DEM) modelling. The intensity of the induced stresses (shear and normal) on lifters, and hence the lifter wear, is also simulated. (C) 2004 Elsevier Ltd. All rights reserved.

A parallel implementation of the lattice solid model for the simulation of rock mechanics and earthquake dynamics

The Lattice Solid Model has been used successfully as a virtual laboratory to simulate fracturing of rocks, the dynamics of faults, earthquakes and gouge processes. However, results from those simulations show that in order to make the next step towards more realistic experiments it will be necessary to use models containing a significantly larger number of particles than current models. Thus, those simulations will require a greatly increased amount of computational resources. Whereas the computing power provided by single processors can be expected to increase according to Moore's law, i.e., to double every 18-24 months, parallel computers can provide significantly larger computing power today. In order to make this computing power available for the simulation of the microphysics of earthquakes, a parallel version of the Lattice Solid Model has been implemented. Benchmarks using large models with several millions of particles have shown that the parallel implementation of the Lattice Solid Model can achieve a high parallel-efficiency of about 80% for large numbers of processors on different computer architectures.

The correspondence framework for 3D surface matching algorithms

Beyond the inherent technical challenges, current research into the three dimensional surface correspondence problem is hampered by a lack of uniform terminology, an abundance of application specific algorithms, and the absence of a consistent model for comparing existing approaches and developing new ones. This paper addresses these challenges by presenting a framework for analysing, comparing, developing, and implementing surface correspondence algorithms. The framework uses five distinct stages to establish correspondence between surfaces. It is general, encompassing a wide variety of existing techniques, and flexible, facilitating the synthesis of new correspondence algorithms. This paper presents a review of existing surface correspondence algorithms, and shows how they fit into the correspondence framework. It also shows how the framework can be used to analyse and compare existing algorithms and develop new algorithms using the framework's modular structure. Six algorithms, four existing and two new, are implemented using the framework. Each implemented algorithm is used to match a number of surface pairs. Results demonstrate that the correspondence framework implementations are faithful implementations of existing algorithms, and that powerful new surface correspondence algorithms can be created. (C) 2004 Elsevier Inc. All rights reserved.