Swarms of computational resources and swarms of tasks for building reliable systems

Space applications demand the need for building reliable systems. Autonomic computing defines such reliable systems as self-managing systems. The work reported in this paper combines agent based and swarm robotic approaches leading to swarm-array computing, a novel technique to achieve autonomy for distributed parallel computing systems. Two swarm-array computing approaches based on swarms of computational resources and swarms of tasks are explored. FPGA is considered as the computing system. The feasibility of the two proposed approaches that binds the computing system and the task together is simulated on the SeSAm multi-agent simulator.

Investigating feasible tools for swarm pattern transformation

Abstract-The work reported in this paper is motivated by the need for developing swarm pattern transformation methodologies. Two methods, namely a macroscopic method and a mathematical method are investigated for pattern transformation. The first method is based on macroscopic parameters while the second method is based on both microscopic and macroscopic parameters. A formal definition to pattern transformation considering four special cases of transformation is presented. Simulations on a physics simulation engine are used to confirm the feasibility of the proposed transformation methods. A brief comparison between the two methods is also presented.

Solving optimal control problems with state constraints using nonlinear programming and simulation tools

This paper illustrates how nonlinear programming and simulation tools, which are available in packages such as MATLAB and SIMULINK, can easily be used to solve optimal control problems with state- and/or input-dependent inequality constraints. The method presented is illustrated with a model of a single-link manipulator. The method is suitable to be taught to advanced undergraduate and Master's level students in control engineering.

Landscape state machines: Tools for evolutionary algorithm performance analyses and landscape/algorithm mapping

Many evolutionary algorithm applications involve either fitness functions with high time complexity or large dimensionality (hence very many fitness evaluations will typically be needed) or both. In such circumstances, there is a dire need to tune various features of the algorithm well so that performance and time savings are optimized. However, these are precisely the circumstances in which prior tuning is very costly in time and resources. There is hence a need for methods which enable fast prior tuning in such cases. We describe a candidate technique for this purpose, in which we model a landscape as a finite state machine, inferred from preliminary sampling runs. In prior algorithm-tuning trials, we can replace the 'real' landscape with the model, enabling extremely fast tuning, saving far more time than was required to infer the model. Preliminary results indicate much promise, though much work needs to be done to establish various aspects of the conditions under which it can be most beneficially used. A main limitation of the method as described here is a restriction to mutation-only algorithms, but there are various ways to address this and other limitations.

Computational complexity of weighted splitting schemes on parallel computers

In models of complicated physical-chemical processes operator splitting is very often applied in order to achieve sufficient accuracy as well as efficiency of the numerical solution. The recently rediscovered weighted splitting schemes have the great advantage of being parallelizable on operator level, which allows us to reduce the computational time if parallel computers are used. In this paper, the computational times needed for the weighted splitting methods are studied in comparison with the sequential (S) splitting and the Marchuk-Strang (MSt) splitting and are illustrated by numerical experiments performed by use of simplified versions of the Danish Eulerian model (DEM).

The eMinerals Collaboratory: Tools and Experience

Collaboratories provide an environment where researchers at distant locations work together at tackling important scientific and industrial problems. In this paper we outline the tools and principles used to form the eMinerals collaboratory, and discuss the experience, from within, of working towards establishing the eMinerals project team as a functioning virtual organisation. Much of the emphasis of this paper is on experience with the IT tools. We introduce a new application sharing tool.

Tools for regularizing Array Designs

This paper makes a contribution in bridging the theory and practice of the polyhedral model for designing parallel algorithms. Although the theory of polyhedral model is well developed, designers of massively parallel algorithms are unable to benefit from the theory due to the lack of software tools that incorporate the wide range of transformations that are possible in the model. The Uniformization tool that we developed was the first to integrate a number of techniques and to completely automate the transformation step allowing designers to explore a wide range of feasible designs from high-level specifications.

Parallel implementation and one year experiments with the Danish Eulerian Model

Large scale air pollution models are powerful tools, designed to meet the increasing demand in different environmental studies. The atmosphere is the most dynamic component of the environment, where the pollutants can be moved quickly on far distnce. Therefore the air pollution modeling must be done in a large computational domain. Moreover, all relevant physical, chemical and photochemical processes must be taken into account. In such complex models operator splitting is very often applied in order to achieve sufficient accuracy as well as efficiency of the numerical solution. The Danish Eulerian Model (DEM) is one of the most advanced such models. Its space domain (4800 × 4800 km) covers Europe, most of the Mediterian and neighboring parts of Asia and the Atlantic Ocean. Efficient parallelization is crucial for the performance and practical capabilities of this huge computational model. Different splitting schemes, based on the main processes mentioned above, have been implemented and tested with respect to accuracy and performance in the new version of DEM. Some numerical results of these experiments are presented in this paper.

Comparison of the computational cost of a Monte Carlo and deterministic algorithm for computing bilinear forms of matrix powers

In this paper we consider bilinear forms of matrix polynomials and show that these polynomials can be used to construct solutions for the problems of solving systems of linear algebraic equations, matrix inversion and finding extremal eigenvalues. An almost Optimal Monte Carlo (MAO) algorithm for computing bilinear forms of matrix polynomials is presented. Results for the computational costs of a balanced algorithm for computing the bilinear form of a matrix power is presented, i.e., an algorithm for which probability and systematic errors are of the same order, and this is compared with the computational cost for a corresponding deterministic method.

Computational chemistry for elucidating protein function: energetics and dynamics of myoglobin-ligand systems

State-of-the-art computational methodologies are used to investigate the energetics and dynamics of photodissociated CO and NO in myoglobin (Mb···CO and Mb···NO). This includes the combination of molecular dynamics, ab initio MD, free energy sampling, and effective dynamics methods to compare the results with studies using X-ray crystallography and ultrafast spectroscopy metho ds. It is shown that modern simulation techniques along with careful description of the intermolecular interactions can give quantitative agreement with experiments on complex molecular systems. Based on this agreement predictions for as yet uncharacterized species can be made.

Correlations for gas-phase reactions of NO3, OH and O3 with alkenes: an update

Methods are developed for predicting rate coefficients for reactions of initiators of tropospheric oxidation with unsaturated compounds that are abundant in the atmosphere; prognostic tools of this kind are essential for atmospheric chemists and modellers. To pursue the aim of exploring such tools, the kinetics of reactions of NO3, OH and O-3 with a series of alkenes are examined for correlations relating the logarithms of the rate coefficients to the energies of the highest occupied molecular orbitals (HOMOs) of the alkenes. A comparison of the values predicted by the correlations with experimental data (where the latter exist) allowed us to assess the reliability of our method. We used a series of theoretical methods to calculate the HOMO energies, and found that higher computational effort improves the agreement of the predicted rate coefficients with experimental values, especially for reactions of NO3 with alkenes that possess vinyllic halogen substituents. As a consequence, it is expedient to suggest new correlations to replace those presented by us and others that were based on the lower level of theory. We propose the following correlations for the reactions of NO3, OH and O-3 with alkenes: ln(k(NO3)/cm(3) molecule(-1) s(-1)) = 6.40(E-HOMO/eV) + 31.69, ln(k(OH)/cm(3) molecule(-1) s(-1)) = 1.21 (E-HOMO/eV)-12.34 and ln(k(O3)/cm(3) molecule(-1) s(-1)) = 3.28(E-HOMO/eV)-6.78. These new correlations have been developed using the larger experimental data sets now available, and the impact of the extended data on the quality of the correlations is examined in the paper. Atmospheric lifetimes have been calculated from both experimental and estimated rate coefficients to provide an overview of removal efficiencies for different classes of alkenes with respect to oxidative processes initiated by NO3, OH and O-3. A figure is presented to show the spatial scales over which alkenes may survive transport in competition with attack by NO3, OH and O-3. Removal by NO3 or OH is always more important than removal by O-3, and reactions with NO3 dominate for scales up to a few hundred metres.

Electronic properties of 4,4 ',5,5 '-tetramethyl-2,2 '-biphosphinine (tmbp) in the redox series fac-[Mn(Br)(CO)(3)(tmbp)], [Mn(CO)(3)(tmbp)](2), and [Mn(CO)(3)(tmbp)](-): crystallographic, spectroelectrochemical, and DFT computational study

Stepwise electrochemical reduction of the complex fac-[Mn(Br)(CO)(3)(tmbp)] (tmbp = 4,4',5,5'-tetramethyl-2,2'-biphosphinine) produces the dimer [Mn(CO)(3)(tmbp)](2) and the five-coordinate anion [Mn(CO)(3)(tmbp)](-). All three members of the redox series have been characterized by single-crystal X-ray diffraction. The crystallographic data provide valuable insight into the localization of the added electrons on the (carbonyl)manganese and tmbp centers. In particular, the formulation of the two-electron-reduced anion as [Mn-0(CO)(3)(tmbp(-))](-) also agrees with the analysis of its IR nu(CO) wavenumbers and with the results of density functional theoretical (DFT) MO calculations on this compound. The strongly delocalized pi-bonding in the anion stabilizes its five-coordinate geometry and results in the appearance of several mixed Mn-to-tmbp charge-transfer/IL(tmbp) transitions in the near-UV-vis spectral region. A thorough voltammetric and UV-vis/IR spectroelectrochemical study of the reduction path provided evidence for a direct formation of [Mn(CO)(3)(tmbp)](-) via a two-electron ECE mechanism involving the [Mn(CO)(3)(tmbp)](.) radical transient. At ambient temperature [Mn(CO)(3)(tmbp)](-) reacts rapidly with nonreduced fac-[Mn(Br)(CO)(3)(tmbp)] to produce [Mn(CO)(3)(tmbp)](2). Comparison with the analogous 2,2'-bipyridine complexes has revealed striking similarity in the bonding properties and reactivity, despite the stronger pi-acceptor character of the tmbp ligand.

Titanocene anticancer complexes and their binding mode of action to human serum albumin: a computational study

Due to the pivotal role played by human serum albumin (HSA) in the transport and cytotoxicity of titanocene complexes, a docking study has been performed on a selected set of titanocene complexes to aid in the current understanding of the potential mode of action of these titanocenes upon binding HSA. Analysis of the docking results has revealed potential binding at the known drug binding sites in HSA and has provided some explanation for the specificity and subsequent cytotoxicity of these titanocenes. Additionally, a new alternative binding site for these titanocenes has been postulated.