Spatio-temporal correlations in aqueous systems: computational studies of static and dynamic heterogeneity by 2D-IR spectroscopy

Local heterogeneity is ubiquitous in natural aqueous systems. It can be caused locally by external biomolecular subsystems like proteins, DNA, micelles and reverse micelles, nanoscopic materials etc., but can also be intrinsic to the thermodynamic nature of the aqueous solution itself (like binary mixtures or at the gas-liquid interface). The altered dynamics of water in the presence of such diverse surfaces has attracted considerable attention in recent years. As these interfaces are quite narrow, only a few molecular layers thick, they are hard to study by conventional methods. The recent development of two dimensional infra-red (2D-IR) spectroscopy allows us to estimate length and time scales of such dynamics fairly accurately. In this work, we present a series of interesting studies employing two dimensional infra-red spectroscopy (2D-IR) to investigate (i) the heterogeneous dynamics of water inside reverse micelles of varying sizes, (ii) supercritical water near the Widom line that is known to exhibit pronounced density fluctuations and also study (iii) the collective and local polarization fluctuation of water molecules in the presence of several different proteins. The spatio-temporal correlation of confined water molecules inside reverse micelles of varying sizes is well captured through the spectral diffusion of corresponding 2D-IR spectra. In the case of supercritical water also, we observe a strong signature of dynamic heterogeneity from the elongated nature of the 2D-IR spectra. In this case the relaxation is ultrafast. We find remarkable agreement between the different tools employed to study the relaxation of density heterogeneity. For aqueous protein solutions, we find that the calculated dielectric constant of the respective systems unanimously shows a noticeable increment compared to that of neat water. However, the `effective' dielectric constant for successive layers shows significant variation, with the layer adjacent to the protein having a much lower value. Relaxation is also slowest at the surface. We find that the dielectric constant achieves the bulk value at distances more than 3 nm from the surface of the protein.

Prediction of Queue Waiting Times for Metascheduling on Parallel Batch Systems

Prediction of queue waiting times of jobs submitted to production parallel batch systems is important to provide overall estimates to users and can also help meta-schedulers make scheduling decisions. In this work, we have developed a framework for predicting ranges of queue waiting times for jobs by employing multi-class classification of similar jobs in history. Our hierarchical prediction strategy first predicts the point wait time of a job using dynamic k-Nearest Neighbor (kNN) method. It then performs a multi-class classification using Support Vector Machines (SVMs) among all the classes of the jobs. The probabilities given by the SVM for the class predicted using k-NN and its neighboring classes are used to provide a set of ranges of predicted wait times with probabilities. We have used these predictions and probabilities in a meta-scheduling strategy that distributes jobs to different queues/sites in a multi-queue/grid environment for minimizing wait times of the jobs. Experiments with different production supercomputer job traces show that our prediction strategies can give correct predictions for about 77-87% of the jobs, and also result in about 12% improved accuracy when compared to the next best existing method. Experiments with our meta-scheduling strategy using different production and synthetic job traces for various system sizes, partitioning schemes and different workloads, show that the meta-scheduling strategy gives much improved performance when compared to existing scheduling policies by reducing the overall average queue waiting times of the jobs by about 47%.

Fault Tolerance on Large Scale Systems using Adaptive Process Replication

Exascale systems of the future are predicted to have mean time between failures (MTBF) of less than one hour. At such low MTBFs, employing periodic checkpointing alone will result in low efficiency because of the high number of application failures resulting in large amount of lost work due to rollbacks. In such scenarios, it is highly necessary to have proactive fault tolerance mechanisms that can help avoid significant number of failures. In this work, we have developed a mechanism for proactive fault tolerance using partial replication of a set of application processes. Our fault tolerance framework adaptively changes the set of replicated processes periodically based on failure predictions to avoid failures. We have developed an MPI prototype implementation, PAREP-MPI that allows changing the replica set. We have shown that our strategy involving adaptive process replication significantly outperforms existing mechanisms providing up to 20 percent improvement in application efficiency even for exascale systems.

Post-earthquake behaviour of footings employing densification to mitigate liquefaction

In situ densification is a popular technique to protect shallow foundations from the effects of earthquake-induced liquefaction, current design being based on semiempirical rules. Poor understanding of the mechanisms governing the performance of soil-structure systems during and after earthquakes inhibits the use of narrow densified zones, which could contribute to optimise the use of densification if the increase in post-earthquake settlement is restrained. Therefore this paper investigates the long-term behaviour of a footing built on densified ground and surrounded by liquefiable ground, centrifuge experiments being used to identify the mechanisms occurring in the ground during and after a seismic simulation. The differential excess pore pressure generated in the ground during the shaking and the processes of vertical stress concentration and subsequent redistribution observed under the footing dominate the system behaviour. The results enlighten the complex mechanisms determining the post-earthquake settlement when densification is carried out to mitigate liquefaction effects. The improvement in performance resulting from widening the zone of densification is rationally explained which encourages the development of new design concepts that may enhance the future use of densification as a liquefaction resistance measure. © 2007 Thomas Telford Ltd.

Surface effects in simple molecular systems

This thesis examines two problems concerned with surface effects in simple molecular systems. The first is the problem associated with the interaction of a fluid with a solid boundary, and the second originates from the interaction of a liquid with its own vapor.

For a fluid in contact with a solid wall, two sets of integro-differential equations, involving the molecular distribution functions of the system, are derived. One of these is a particular form of the well-known Bogolyubov-Born-Green-Kirkwood-Yvon equations. For the second set, the derivation, in contrast with the formulation of the B.B.G.K.Y. hierarchy, is independent of the pair-potential assumption. The density of the fluid, expressed as a power series in the uniform fluid density, is obtained by solving these equations under the requirement that the wall be ideal.

The liquid-vapor interface is analyzed with the aid of equations that describe the density and pair-correlation function. These equations are simplified and then solved by employing the superposition and the low vapor density approximations. The solutions are substituted into formulas for the surface energy and surface tension, and numerical results are obtained for selected systems. Finally, the liquid-vapor system near the critical point is examined by means of the lowest order B.B.G.K.Y. equation.

Design of carbon nanotubes based microwave applications employing mechanical resonance analysis

Carbon nanotubes (CNTs) have good mechanical properties and unique structural, electronic, thermal, and optical characteristics. In this work, we present the results of our investigations of a resonator device based on embedded vertical CNT arrays. The device's design is based on the mechanical resonance of the tubes. CoventorWare FEA tools have been used to simulate the mechanical resonance frequencies of the vertical nanotubes arrays integrated on a silicon substrate. ©2008 IEEE.

A matter of life and death: sociomateriality, information systems and critical care

Sociomateriality has been attracting growing attention in the Organization Studies and Information Systems literatures since 2007, with more than 140 journal articles now referring to the concept. Over 80 percent of these articles have been published since January 2011 and almost all cite the work of Orlikowski (2007, 2010; Orlikowski and Scott 2008) as the source of the concept. Only a few, however, address all of the notions that Orlikowski suggests are entailed in sociomateriality, namely materiality, inseparability, relationality, performativity, and practices, with many employing the concept quite selectively. The contribution of sociomateriality to these literatures is, therefore, still unclear. Drawing on evidence from an ongoing study of the adoption of a computer-based clinical information system in a hospital critical care unit, this paper explores whether the notions, individually and collectively, offer a distinctive and coherent account of the relationship between the social and the material that may be useful in Information Systems research. It is argued that if sociomateriality is to be more than simply a label for research employing a number of loosely related existing theoretical approaches, then studies employing the concept need to pay greater attention to the notions entailed in it and to differences in their interpretation.

Improving the Accessibility of Lightweight Formal Verification Systems

In research areas involving mathematical rigor, there are numerous benefits to adopting a formal representation of models and arguments: reusability, automatic evaluation of examples, and verification of consistency and correctness. However, broad accessibility has not been a priority in the design of formal verification tools that can provide these benefits. We propose a few design criteria to address these issues: a simple, familiar, and conventional concrete syntax that is independent of any environment, application, or verification strategy, and the possibility of reducing workload and entry costs by employing features selectively. We demonstrate the feasibility of satisfying such criteria by presenting our own formal representation and verification system. Our system’s concrete syntax overlaps with English, LATEX and MediaWiki markup wherever possible, and its verifier relies on heuristic search techniques that make the formal authoring process more manageable and consistent with prevailing practices. We employ techniques and algorithms that ensure a simple, uniform, and flexible definition and design for the system, so that it easy to augment, extend, and improve.

Capturing the overarm throw in darts employing wireless inertial measurement

This work employs a custom built body area network of wireless inertial measurement technology to conduct a biomechanical analysis of precision targeted throwing in competitive and recreational darts. The solution is shown to be capable of measuring key biomechanical factors including speed, acceleration and timing. These parameters are subsequently correlated with scoring performance to determine the affect each variable has on outcome. For validation purposes an optical 3D motion capture system provides a complete kinematic model of the subject and enables concurrent benchmarking of the 'gold standard' optical inertial measurement system with the more affordable and proactive wireless inertial measurement solution developed as part of this work.

Energy storage systems for wave energy converters and microgrids

The thesis initially gives an overview of the wave industry and the current state of some of the leading technologies as well as the energy storage systems that are inherently part of the power take-off mechanism. The benefits of electrical energy storage systems for wave energy converters are then outlined as well as the key parameters required from them. The options for storage systems are investigated and the reasons for examining supercapacitors and lithium-ion batteries in more detail are shown. The thesis then focusses on a particular type of offshore wave energy converter in its analysis, the backward bent duct buoy employing a Wells turbine. Variable speed strategies from the research literature which make use of the energy stored in the turbine inertia are examined for this system, and based on this analysis an appropriate scheme is selected. A supercapacitor power smoothing approach is presented in conjunction with the variable speed strategy. As long component lifetime is a requirement for offshore wave energy converters, a computer-controlled test rig has been built to validate supercapacitor lifetimes to manufacturer’s specifications. The test rig is also utilised to determine the effect of temperature on supercapacitors, and determine application lifetime. Cycle testing is carried out on individual supercapacitors at room temperature, and also at rated temperature utilising a thermal chamber and equipment programmed through the general purpose interface bus by Matlab. Application testing is carried out using time-compressed scaled-power profiles from the model to allow a comparison of lifetime degradation. Further applications of supercapacitors in offshore wave energy converters are then explored. These include start-up of the non-self-starting Wells turbine, and low-voltage ride-through examined to the limits specified in the Irish grid code for wind turbines. These applications are investigated with a more complete model of the system that includes a detailed back-to-back converter coupling a permanent magnet synchronous generator to the grid. Supercapacitors have been utilised in combination with battery systems for many applications to aid with peak power requirements and have been shown to improve the performance of these energy storage systems. The design, implementation, and construction of coupling a 5 kW h lithium-ion battery to a microgrid are described. The high voltage battery employed a continuous power rating of 10 kW and was designed for the future EV market with a controller area network interface. This build gives a general insight to some of the engineering, planning, safety, and cost requirements of implementing a high power energy storage system near or on an offshore device for interface to a microgrid or grid.

Characterisation of freeze-dried wafers and solvent evaporated films as potential drug delivery systems to mucosal surfaces

Freeze-dried (lyophilised) wafers and solvent cast films from sodium alginate (ALG) and sodium carboxymethylcellulose (CMC) have been developed as potential drug delivery systems for mucosal surfaces including wounds. The wafers (ALG, CMC) and films (CMC) were prepared by freeze-drying and drying in air (solvent evaporation) respectively, aqueous gels of the polymers containing paracetamol as a model drug. Microscopic architecture was examined using scanning electron microscopy, hydration characteristics with confocal laser scanning microscopy and dynamic vapour sorption. Texture analysis was employed to investigate mechanical characteristics of the wafers during compression. Differential scanning calorimetry was used to investigate polymorphic changes of paracetamol occurring during formulation of the wafers and films. The porous freeze-dried wafers exhibited higher drug loading and water absorption capacity than the corresponding solvent evaporated films. Moisture absorption, ease of hydration and mechanical behaviour were affected by the polymer and drug concentration. Two polymorphs of paracetamol were observed in the wafers and films, due to partial conversion of the original monoclinic to the orthorhombic polymorph during the formulation process. The results showed the potential of employing the freeze-dried wafers and solvent evaporated films in diverse mucosal applications due to their ease of hydration and based on different physical mechanical properties exhibited by both type of formulations.

In vitro-in vivo correlations of self-emulsifying drug delivery systems combining the dynamic lipolysis model and neuro-fuzzy networks

The aim of the current study was to evaluate the potential of the dynamic lipolysis model to simulate the absorption of a poorly soluble model drug compound, probucol, from three lipid-based formulations and to predict the in vitro-in vivo correlation (IVIVC) using neuro-fuzzy networks. An oil solution and two self-micro and nano-emulsifying drug delivery systems were tested in the lipolysis model. The release of probucol to the aqueous (micellar) phase was monitored during the progress of lipolysis. These release profiles compared with plasma profiles obtained in a previous bioavailability study conducted in mini-pigs at the same conditions. The release rate and extent of release from the oil formulation were found to be significantly lower than from SMEDDS and SNEDDS. The rank order of probucol released (SMEDDS approximately SNEDDS > oil formulation) was similar to the rank order of bioavailability from the in vivo study. The employed neuro-fuzzy model (AFM-IVIVC) achieved significantly high prediction ability for different data formations (correlation greater than 0.91 and prediction error close to zero), without employing complex configurations. These preliminary results suggest that the dynamic lipolysis model combined with the AFM-IVIVC can be a useful tool in the prediction of the in vivo behavior of lipid-based formulations.

Improved Linear Transmit Processing for Single-User and Multi-User MIMO Communications Systems

In this paper, we propose a novel linear transmit precoding strategy for multiple-input, multiple-output (MIMO) systems employing improper signal constellations. In particular, improved zero-forcing (ZF) and minimum mean square error (MMSE) precoders are derived based on modified cost functions, and are shown to achieve a superior performance without loss of spectrum efficiency compared to the conventional linear and nonlinear precoders. The superiority of the proposed precoders over the conventional solutions are verified by both simulation and analytical results. The novel approach to precoding design is also applied to the case of an imperfect channel estimate with a known error covariance as well as to the multi-user scenario where precoding based on the nullspace of channel transmission matrix is employed to decouple multi-user channels. In both cases, the improved precoding schemes yield significant performance gain compared to the conventional counterparts.

Iterative Receiver Design for MIMO Systems with Improper Signal Constellations

In this paper, we propose a novel iterative receiver
strategy for uncoded multiple-input, multiple-output (MIMO)
systems employing improper signal constellations. The proposed
scheme is shown to achieve superior performance and faster
convergence without the loss of spectrum efficiency compared
to the conventional iterative receivers. The superiority of this
novel approach over conventional solutions is verified by both
simulation and analytical results.

The RMT method for many-electron atomic systems in intense short-pulse laser light

We describe a new ab initio method for solving the time-dependent Schrödinger equation for multi-electron atomic systems exposed to intense short-pulse laser light. We call the method the R-matrix with time-dependence (RMT) method. Our starting point is a finite-difference numerical integrator (HELIUM), which has proved successful at describing few-electron atoms and atomic ions in strong laser fields with high accuracy. By exploiting the R-matrix division-of-space concept, we bring together a numerical method most appropriate to the multi-electron finite inner region (R-matrix basis set) and a different numerical method most appropriate to the one-electron outer region (finite difference). In order to exploit massively parallel supercomputers efficiently, we time-propagate the wavefunction in both regions by employing Arnoldi methods, originally developed for HELIUM.