Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Efficient on the fly calculation of time correlation functions in computer simulations

Time correlation functions yield profound information about the dynamics of a physical system and hence are frequently calculated in computer simulations. For systems whose dynamics span a wide range of time, currently used methods require significant computer time and memory. In this paper, we discuss the multiple-tau correlator method for the efficient calculation of accurate time correlation functions on the fly during computer simulations. The multiple-tau correlator is efficacious in terms of computational requirements and can be tuned to the desired level of accuracy. Further, we derive estimates for the error arising from the use of the multiple-tau correlator and extend it for use in the calculation of mean-square particle displacements and dynamic structure factors. The method described here, in hardware implementation, is routinely used in light scattering experiments but has not yet found widespread use in computer simulations.

Relating computer tasks to existing knowledge to improve accessibility for older adults

Routine computer tasks are often difficult for older adult computer users to learn and remember. People tend to learn new tasks by relating new concepts to existing knowledge. However, even for 'basic' computer tasks there is little, if any, existing knowledge on which older adults can base their learning. This paper investigates a custom file management interface that was designed to aid discovery and learnability by providing interface objects that are familiar to the user. A study was conducted which examined the differences between older and younger computer users when undertaking routine file management tasks using the standard Windows desktop as compared with the custom interface. Results showed that older adult computer users requested help more than ten times as often as younger users when using a standard windows/mouse configuration, made more mistakes and also required significantly more confirmations than younger users. The custom interface showed improvements over standard Windows/mouse, with fewer confirmations and less help being required. Hence, there is potential for an interface that closely mimics the real world to improve computer accessibility for older adults, aiding self-discovery and learnability.

Handling single node failures using agents in computer clusters

The work reported in this paper is motivated towards handling single node failures for parallel summation algorithms in computer clusters. An agent based approach is proposed in which a task to be executed is decomposed to sub-tasks and mapped onto agents that traverse computing nodes. The agents intercommunicate across computing nodes to share information during the event of a predicted node failure. Two single node failure scenarios are considered. The Message Passing Interface is employed for implementing the proposed approach. Quantitative results obtained from experiments reveal that the agent based approach can handle failures more efficiently than traditional failure handling approaches.

Measuring departures from Hardy-Weinberg: a Markov chain Monte Carlo method for estimating the inbreeding coefficient

Many well-established statistical methods in genetics were developed in a climate of severe constraints on computational power. Recent advances in simulation methodology now bring modern, flexible statistical methods within the reach of scientists having access to a desktop workstation. We illustrate the potential advantages now available by considering the problem of assessing departures from Hardy-Weinberg (HW) equilibrium. Several hypothesis tests of HW have been established, as well as a variety of point estimation methods for the parameter which measures departures from HW under the inbreeding model. We propose a computational, Bayesian method for assessing departures from HW, which has a number of important advantages over existing approaches. The method incorporates the effects-of uncertainty about the nuisance parameters--the allele frequencies--as well as the boundary constraints on f (which are functions of the nuisance parameters). Results are naturally presented visually, exploiting the graphics capabilities of modern computer environments to allow straightforward interpretation. Perhaps most importantly, the method is founded on a flexible, likelihood-based modelling framework, which can incorporate the inbreeding model if appropriate, but also allows the assumptions of the model to he investigated and, if necessary, relaxed. Under appropriate conditions, information can be shared across loci and, possibly, across populations, leading to more precise estimation. The advantages of the method are illustrated by application both to simulated data and to data analysed by alternative methods in the recent literature.

Computer generation and quantitative morphometric analysis of virtual neurons

An important goal in computational neuroanatomy is the complete and accurate simulation of neuronal morphology. We are developing computational tools to model three-dimensional dendritic structures based on sets of stochastic rules. This paper reports an extensive, quantitative anatomical characterization of simulated motoneurons and Purkinje cells. We used several local and global algorithms implemented in the L-Neuron and ArborVitae programs to generate sets of virtual neurons. Parameters statistics for all algorithms were measured from experimental data, thus providing a compact and consistent description of these morphological classes. We compared the emergent anatomical features of each group of virtual neurons with those of the experimental database in order to gain insights on the plausibility of the model assumptions, potential improvements to the algorithms, and non-trivial relations among morphological parameters. Algorithms mainly based on local constraints (e.g., branch diameter) were successful in reproducing many morphological properties of both motoneurons and Purkinje cells (e.g. total length, asymmetry, number of bifurcations). The addition of global constraints (e.g., trophic factors) improved the angle-dependent emergent characteristics (average Euclidean distance from the soma to the dendritic terminations, dendritic spread). Virtual neurons systematically displayed greater anatomical variability than real cells, suggesting the need for additional constraints in the models. For several emergent anatomical properties, a specific algorithm reproduced the experimental statistics better than the others did. However, relative performances were often reversed for different anatomical properties and/or morphological classes. Thus, combining the strengths of alternative generative models could lead to comprehensive algorithms for the complete and accurate simulation of dendritic morphology.

Surface based hypothesis verification in intensity images using geometric and appearance data

In this paper we discuss current work concerning Appearance-based and CAD-based vision; two opposing vision strategies. CAD-based vision is geometry based, reliant on having complete object centred models. Appearance-based vision builds view dependent models from training images. Existing CAD-based vision systems that work with intensity images have all used one and zero dimensional features, for example lines, arcs, points and corners. We describe a system we have developed for combining these two strategies. Geometric models are extracted from a commercial CAD library of industry standard parts. Surface appearance characteristics are then learnt automatically by observing actual object instances. This information is combined with geometric information and is used in hypothesis evaluation. This augmented description improves the systems robustness to texture, specularities and other artifacts which are hard to model with geometry alone, whilst maintaining the advantages of a geometric description.

Implementation of VR systems: a comparison between the early adoption of CAD and current uptake of VR

Use of new technologies, such as virtual reality (VR), is important to corporations, yet understanding of their successful implementation is insuf. ciently developed. In this paper a case study is used to analyse the introduction of VR use in a British housebuilding company. Although the implementation was not successful in the manner initially anticipated, the study provides insight into the process of change, the constraints that inhibit implementation and the relationship between new technology and work organization. Comparison is made with the early use of CAD and similarities and differences between empirical . ndings of the case study and the previous literature are discussed.

Virtual reality as a visualisation tool: benefits and constraints

The benefits and applications of virtual reality (VR) in the construction industry have been investigated for almost a decade. However, the practical implementation of VR in the construction industry has yet to reach maturity owing to technical constraints. The need for effective information management presents challenges: both transfer of building data to, and organisation of building information within, the virtual environment require consideration. This paper reviews the applications and benefits of VR in the built environment field and reports on a collaboration between Loughborough University and South Bank University to overcome constraints on the use of the overall VR model for whole lifecycle visualisation. The work at each research centre is concerned with an aspect of information management within VR applications for the built environment, and both data transfer and internal data organisation have been investigated. In this paper, similarities and differences between computer-aided design (CAD) and VR packages are first discussed. Three different approaches to the creation of VR models during the design stage are identified and described, with a view to providing sharing understanding across the interdiscipliary groups involved. The suitable organisation of building information within the virtual environment is then further investigated. This work focused on the visualisation of the degradation of a building, through its lifespan, with the view to provide a visual aid for developing an effective and economic project maintenance programme. Finally consideration is given to the potential of emerging standards to facilitate an integrated use of VR. The convergence towards similar data structures in VR and other construction packages may enable visualisation to be better utilised in the overall lifecycle model.

Computer intensive methods in control and signal processing: the curse of dimensionality

This volume is based upon the 2nd IEEE European Workshop on Computer-Intensive Methods in Control and Signal Processing, held in Prague, August 1996.

Queue-based agent communication architecture for intelligent human-like computer interfaces

Human-like computer interaction systems requires far more than just simple speech input/output. Such a system should communicate with the user verbally, using a conversational style language. It should be aware of its surroundings and use this context for any decisions it makes. As a synthetic character, it should have a computer generated human-like appearance. This, in turn, should be used to convey emotions, expressions and gestures. Finally, and perhaps most important of all, the system should interact with the user in real time, in a fluent and believable manner.