" Nonlinear Signal Processing of Electroencephalogram .' Application in the Study of Neurodynamics. "

Interfacings of various subjects generate new field ofstudy and research that help in advancing human knowledge. One of the latest of such fields is Neurotechnology, which is an effective amalgamation of neuroscience, physics, biomedical engineering and computational methods. Neurotechnology provides a platform to interact physicist; neurologist and engineers to break methodology and terminology related barriers. Advancements in Computational capability, wider scope of applications in nonlinear dynamics and chaos in complex systems enhanced study of neurodynamics. However there is a need for an effective dialogue among physicists, neurologists and engineers. Application of computer based technology in the field of medicine through signal and image processing, creation of clinical databases for helping clinicians etc are widely acknowledged. Such synergic effects between widely separated disciplines may help in enhancing the effectiveness of existing diagnostic methods. One of the recent methods in this direction is analysis of electroencephalogram with the help of methods in nonlinear dynamics. This thesis is an effort to understand the functional aspects of human brain by studying electroencephalogram. The algorithms and other related methods developed in the present work can be interfaced with a digital EEG machine to unfold the information hidden in the signal. Ultimately this can be used as a diagnostic tool.

A Comparative Study of Convective Parameterization Schemes in WRF-NMM Model

Severe local storms, including tornadoes, damaging hail and wind gusts, frequently occur over the eastern and northeastern states of India during the pre-monsoon season (March-May). Forecasting thunderstorms is one of the most difficult tasks in weather prediction, due to their rather small spatial and temporal extension and the inherent non-linearity of their dynamics and physics. In this paper, sensitivity experiments are conducted with the WRF-NMM model to test the impact of convective parameterization schemes on simulating severe thunderstorms that occurred over Kolkata on 20 May 2006 and 21 May 2007 and validated the model results with observation. In addition, a simulation without convective parameterization scheme was performed for each case to determine if the model could simulate the convection explicitly. A statistical analysis based on mean absolute error, root mean square error and correlation coefficient is performed for comparisons between the simulated and observed data with different convective schemes. This study shows that the prediction of thunderstorm affected parameters is sensitive to convective schemes. The Grell-Devenyi cloud ensemble convective scheme is well simulated the thunderstorm activities in terms of time, intensity and the region of occurrence of the events as compared to other convective schemes and also explicit scheme

Reliability Estimation of Open Source Software based Computational Systems

Software systems are progressively being deployed in many facets of human life. The implication of the failure of such systems, has an assorted impact on its customers. The fundamental aspect that supports a software system, is focus on quality. Reliability describes the ability of the system to function under specified environment for a specified period of time and is used to objectively measure the quality. Evaluation of reliability of a computing system involves computation of hardware and software reliability. Most of the earlier works were given focus on software reliability with no consideration for hardware parts or vice versa. However, a complete estimation of reliability of a computing system requires these two elements to be considered together, and thus demands a combined approach. The present work focuses on this and presents a model for evaluating the reliability of a computing system. The method involves identifying the failure data for hardware components, software components and building a model based on it, to predict the reliability. To develop such a model, focus is given to the systems based on Open Source Software, since there is an increasing trend towards its use and only a few studies were reported on the modeling and measurement of the reliability of such products. The present work includes a thorough study on the role of Free and Open Source Software, evaluation of reliability growth models, and is trying to present an integrated model for the prediction of reliability of a computational system. The developed model has been compared with existing models and its usefulness of is being discussed.

Theoretical study of magnetism, structure and chemical order in transition-metal alloy clusters

Research on transition-metal nanoalloy clusters composed of a few atoms is fascinating by their unusual properties due to the interplay among the structure, chemical order and magnetism. Such nanoalloy clusters, can be used to construct nanometer devices for technological applications by manipulating their remarkable magnetic, chemical and optical properties. Determining the nanoscopic features exhibited by the magnetic alloy clusters signifies the need for a systematic global and local exploration of their potential-energy surface in order to identify all the relevant energetically low-lying magnetic isomers. In this thesis the sampling of the potential-energy surface has been performed by employing the state-of-the-art spin-polarized density-functional theory in combination with graph theory and the basin-hopping global optimization techniques. This combination is vital for a quantitative analysis of the quantum mechanical energetics. The first approach, i.e., spin-polarized density-functional theory together with the graph theory method, is applied to study the Fe$_m$Rh$_n$ and Co$_m$Pd$_n$ clusters having $N = m+n \leq 8$ atoms. We carried out a thorough and systematic sampling of the potential-energy surface by taking into account all possible initial cluster topologies, all different distributions of the two kinds of atoms within the cluster, the entire concentration range between the pure limits, and different initial magnetic configurations such as ferro- and anti-ferromagnetic coupling. The remarkable magnetic properties shown by FeRh and CoPd nanoclusters are attributed to the extremely reduced coordination number together with the charge transfer from 3$d$ to 4$d$ elements. The second approach, i.e., spin-polarized density-functional theory together with the basin-hopping method is applied to study the small Fe$_6$, Fe$_3$Rh$_3$ and Rh$_6$ and the larger Fe$_{13}$, Fe$_6$Rh$_7$ and Rh$_{13}$ clusters as illustrative benchmark systems. This method is able to identify the true ground-state structures of Fe$_6$ and Fe$_3$Rh$_3$ which were not obtained by using the first approach. However, both approaches predict a similar cluster for the ground-state of Rh$_6$. Moreover, the computational time taken by this approach is found to be significantly lower than the first approach. The ground-state structure of Fe$_{13}$ cluster is found to be an icosahedral structure, whereas Rh$_{13}$ and Fe$_6$Rh$_7$ isomers relax into cage-like and layered-like structures, respectively. All the clusters display a remarkable variety of structural and magnetic behaviors. It is observed that the isomers having similar shape with small distortion with respect to each other can exhibit quite different magnetic moments. This has been interpreted as a probable artifact of spin-rotational symmetry breaking introduced by the spin-polarized GGA. The possibility of combining the spin-polarized density-functional theory with some other global optimization techniques such as minima-hopping method could be the next step in this direction. This combination is expected to be an ideal sampling approach having the advantage of avoiding efficiently the search over irrelevant regions of the potential energy surface.

Experimental and CFD study on low temperature drying of loose and compressed bulks

Die Trocknung ist eines der am häufigsten verwendeten Verfahren, um die Haltbarkeit von landwirtschaftlichen Gütern zu verlängern. Von den vielen gebräuchlichen Trocknungsarten ist die Konvektionstrocknung, die Luft als Energie- und Feuchteträger verwendet, weiterhin die wichtigste. Trotz ihrer Nachteile und ihres hohen spezifischen Energieverbrauchs sind Satztrockner für die Getreide-, Kräuter- und Heutrocknung noch weit verbreitet. Ferner werden Konvektionstrockner gemeinhin zur künstlichen Trocknung eingesetzt. Diese Arbeit ist Teil eines Forschungsprojekts, welches eine sorptionsgestützte solare Trocknung von landwirtschaftlichen Gütern untersucht. Bei dieser wird kühle feuchte Luft in Kontakt mit einer konzentrierten hygroskopischen Salzlösung gebracht. Während dieses Prozesses wird die Luft entfeuchtet und mit Hilfe der freigesetzten Verdampfungsenthalpie erwärmt. Die Anwendung dieses Verfahrens zur Trocknung landwirtschaftlicher Güter ist besonders interessant für Produkte, die bei niedrigen Temperaturen verarbeitet werden, um ihre Qualität nicht negativ zu beeinflussen. Bei allen energieintensiven Prozessen und vor allem bei der Verwendung von Solarenergie ist ein effizienter Energieverbrauch äußerst wichtig für den technischen und ökonomischen Erfolg. Eine ungleichmäßige Trocknung ist oftmals bei Satztrocknern zu beobachten, was die Energieeffizienz negativ beeinflusst. Aus diesem Grund lag im agrartechnischen Teil des Projekts der Schwerpunkt auf der Trocknung bei niedrigen Temperaturen und geringer Luftfeuchte, die der Sorptionsprozess liefert, sowie auf der Verbesserung der Luftverteilung und der Gleichmäßigkeit der Trocknung in lockeren und verdichteten Schüttungen. Es wurden Dünnschicht-Trocknungsexperminente für Blattsellerie bei unterschiedlichen Lufttemperaturen und unterschiedlicher relativer Luftfeuchte durchgeführt. Die Ergebnisse zeigen eindeutig, dass nicht nur die Lufttemperatur einen großen Einfluss auf die Trocknungsgeschwindigkeit hat, sondern auch die relative Luftfeuchte. Dies ist vor allem bei niedrigen Temperaturen, wie sie vom Sorptionssystem geliefert werden, der Fall. Um die Luftverteilung und Gleichmäßigkeit der Trocknung lockerer Schüttungen zu untersuchen, wurde ein Kistentrockner experimentell und in Strömungssimulationen getestet. Die Leistung des ursprünglichen Trockners wurde signifikant durch einfache Veränderungen des Designs verbessert. Diese stellten einen gleichmäßigeren Luftstrom durch das Produkt sicher. Die Trocknung von Heu-Rundballen stellt eine Herausforderung dar, da diese sehr stark verdichtet sind und die Dichte innerhalb eines Ballens stark schwankt. Strömungs- und Trocknungssimulationen so wie experimentelle Messungen zeigten, dass das Trocknerdesign einen großen Einfluss auf die Gleichmäßigkeit der Trocknung hat. Bei den einfachsten Trocknervarianten war die Verteilung auch bei optimal gepressten Ballen unzureichend, während komplexere Trockner eine gleichmäßigere Trocknung erzielten. Jedoch werden auch hier die Ergebnisse stark von der Verteilung der Dichte im Ballen beeinflusst, welche in der Praxis weiterhin nicht ideal ist. Abschließend wurde, um den Trocknungsfortschritt zu überwachen, eine Methodik getestet, bei der zur Messung des durchschnittlichen aktuellen Feuchtegehalts des Produktes psychrometrische Messungen und Messungen des Luftstroms in kurzen Abständen durchgeführt wurden. Die Menge des tatsächlich entfernten Wassers stimmte in den meisten Fällen gut mit der geschätzten Menge überein. Jedoch hängt der Erfolg dieser Methode stark von der Genauigkeit der Messfühler ab.

Stimulus Simplification and Object Representation: A Modeling Study

Tsunoda et al. (2001) recently studied the nature of object representation in monkey inferotemporal cortex using a combination of optical imaging and extracellular recordings. In particular, they examined IT neuron responses to complex natural objects and "simplified" versions thereof. In that study, in 42% of the cases, optical imaging revealed a decrease in the number of activation patches in IT as stimuli were "simplified". However, in 58% of the cases, "simplification" of the stimuli actually led to the appearance of additional activation patches in IT. Based on these results, the authors propose a scheme in which an object is represented by combinations of active and inactive columns coding for individual features. We examine the patterns of activation caused by the same stimuli as used by Tsunoda et al. in our model of object recognition in cortex (Riesenhuber 99). We find that object-tuned units can show a pattern of appearance and disappearance of features identical to the experiment. Thus, the data of Tsunoda et al. appear to be in quantitative agreement with a simple object-based representation in which an object's identity is coded by its similarities to reference objects. Moreover, the agreement of simulations and experiment suggests that the simplification procedure used by Tsunoda (2001) is not necessarily an accurate method to determine neuronal tuning.

Electronic couplings and on-site energies for hole transfer in DNA: systematic quantum mechanical/molecular dynamic study

The electron hole transfer (HT) properties of DNA are substantially affected by thermal fluctuations of the π stack structure. Depending on the mutual position of neighboring nucleobases, electronic coupling V may change by several orders of magnitude. In the present paper, we report the results of systematic QM/molecular dynamic (MD) calculations of the electronic couplings and on-site energies for the hole transfer. Based on 15 ns MD trajectories for several DNA oligomers, we calculate the average coupling squares 〈 V2 〉 and the energies of basepair triplets X G+ Y and X A+ Y, where X, Y=G, A, T, and C. For each of the 32 systems, 15 000 conformations separated by 1 ps are considered. The three-state generalized Mulliken-Hush method is used to derive electronic couplings for HT between neighboring basepairs. The adiabatic energies and dipole moment matrix elements are computed within the INDO/S method. We compare the rms values of V with the couplings estimated for the idealized B -DNA structure and show that in several important cases the couplings calculated for the idealized B -DNA structure are considerably underestimated. The rms values for intrastrand couplings G-G, A-A, G-A, and A-G are found to be similar, ∼0.07 eV, while the interstrand couplings are quite different. The energies of hole states G+ and A+ in the stack depend on the nature of the neighboring pairs. The X G+ Y are by 0.5 eV more stable than X A+ Y. The thermal fluctuations of the DNA structure facilitate the HT process from guanine to adenine. The tabulated couplings and on-site energies can be used as reference parameters in theoretical and computational studies of HT processes in DNA

Dihydrogen bonds: a study

Un pont de dihidrogen (dihydrogen bond,DHB) és un tipus de pont d'hidrogen atípic que s'estableix entre un hidrur metàl·lic i un donador de protons com un grup OH o NH. Els ponts de dihidrogen són claus en les característiques geomètriques i altres propietats de compostos que en presenten tan de molècules petites com el dímer de NH3BH3, com d'estructures superiors més complicades com complexes metàl·lics o sòlids. Poden ser útils aplicats a certes molècules o síntesis moleculars per a obtenir nous materials amb propietats o característiques fetes a mida. El treball d'aquesta tesi està orientat a millorar la comprensió dels ponts de dihidrogen, aprofundint en certs aspectes de la seva naturalesa atòmica/molecular utilitzant mètodes teòrics basats en la química física quàntica.

Electronic structure of point defects in controlled self-doping of the TiO2 (110) surface: Combined photoemission spectroscopy and density functional theory study

Point defects in metal oxides such as TiO2 are key to their applications in numerous technologies. The investigation of thermally induced nonstoichiometry in TiO2 is complicated by the difficulties in preparing and determining a desired degree of nonstoichiometry. We study controlled self-doping of TiO2 by adsorption of 1/8 and 1/16 monolayer Ti at the (110) surface using a combination of experimental and computational approaches to unravel the details of the adsorption process and the oxidation state of Ti. Upon adsorption of Ti, x-ray and ultraviolet photoemission spectroscopy (XPS and UPS) show formation of reduced Ti. Comparison of pure density functional theory (DFT) with experiment shows that pure DFT provides an inconsistent description of the electronic structure. To surmount this difficulty, we apply DFT corrected for on-site Coulomb interaction (DFT+U) to describe reduced Ti ions. The optimal value of U is 3 eV, determined from comparison of the computed Ti 3d electronic density of states with the UPS data. DFT+U and UPS show the appearance of a Ti 3d adsorbate-induced state at 1.3 eV above the valence band and 1.0 eV below the conduction band. The computations show that the adsorbed Ti atom is oxidized to Ti2+ and a fivefold coordinated surface Ti atom is reduced to Ti3+, while the remaining electron is distributed among other surface Ti atoms. The UPS data are best fitted with reduced Ti2+ and Ti3+ ions. These results demonstrate that the complexity of doped metal oxides is best understood with a combination of experiment and appropriate computations.

Use of essential and molecular dynamics to study gamma B-crystallin unfolding after non-enzymic post-translational modifications

Essential and Molecular Dynamics (ED/MD) have been used to model the conformational changes of a protein implicated in a conformational disease-cataract, the largest cause of blindness in the world-after non-enzymic post-translational modification. Cyanate modification did not significantly alter flexibility, while the Schiff's base adduct produced a more flexible N-terminal domain, and intra-secondary structure regions, than either the cyanate adduct or the native structure. Glycation also increased linker flexibility and disrupted the charge network. A number of post-translational adducts showed structural disruption around Cys15 and increased linker flexibility; this may be important in subsequent protein aggregation. Our modelling results are in accord with experimental evidence, and show that ED/MD is a useful tool in modelling conformational changes in proteins implicated in disease processes. (C) 2003 Published by Elsevier Ltd.

Solid phases of cyclopentane: combined experimental and simulation study

The phase diagram of cyclopentane has been studied by powder neutron diffraction, providing diffraction patterns for phases I, II, and III, over a range of temperatures and pressures. The putative phase IV was not observed. The structure of the ordered phase III has been solved by single-crystal diffraction. Computational modeling reveals that there are many equienergetic ordered structures for cyclopentane within a small energy range. Molecular dynamics simulations reproduce the structures and diffraction patterns for phases I and III and also show an intermediate disordered phase, which is used to interpret phase II.

A comparative study of Java and C performance in two large-scale parallel applications

In the 1990s the Message Passing Interface Forum defined MPI bindings for Fortran, C, and C++. With the success of MPI these relatively conservative languages have continued to dominate in the parallel computing community. There are compelling arguments in favour of more modern languages like Java. These include portability, better runtime error checking, modularity, and multi-threading. But these arguments have not converted many HPC programmers, perhaps due to the scarcity of full-scale scientific Java codes, and the lack of evidence for performance competitive with C or Fortran. This paper tries to redress this situation by porting two scientific applications to Java. Both of these applications are parallelized using our thread-safe Java messaging system—MPJ Express. The first application is the Gadget-2 code, which is a massively parallel structure formation code for cosmological simulations. The second application uses the finite-domain time-difference method for simulations in the area of computational electromagnetics. We evaluate and compare the performance of the Java and C versions of these two scientific applications, and demonstrate that the Java codes can achieve performance comparable with legacy applications written in conventional HPC languages. Copyright © 2009 John Wiley & Sons, Ltd.

Effects of dendritic morphology on CA3 pyramidal cell electrophysiology: a simulation study

We investigated the effect of morphological differences on neuronal firing behavior within the hippocampal CA3 pyramidal cell family by using three-dimensional reconstructions of dendritic morphology in computational simulations of electrophysiology. In this paper, we report for the first time that differences in dendritic structure within the same morphological class can have a dramatic influence on the firing rate and firing mode (spiking versus bursting and type of bursting). Our method consisted of converting morphological measurements from three-dimensional neuroanatomical data of CA3 pyramidal cells into a computational simulator format. In the simulation, active channels were distributed evenly across the cells so that the electrophysiological differences observed in the neurons would only be due to morphological differences. We found that differences in the size of the dendritic tree of CA3 pyramidal cells had a significant qualitative and quantitative effect on the electrophysiological response. Cells with larger dendritic trees: (1) had a lower burst rate, but a higher spike rate within a burst, (2) had higher thresholds for transitions from quiescent to bursting and from bursting to regular spiking and (3) tended to burst with a plateau. Dendritic tree size alone did not account for all the differences in electrophysiological responses. Differences in apical branching, such as the distribution of branch points and terminations per branch order, appear to effect the duration of a burst. These results highlight the importance of considering the contribution of morphology in electrophysiological and simulation studies.

Dynamic stall for a Vertical Axis Wind Turbine in a two-dimensional study

The last few years have proved that Vertical Axis Wind Turbines (VAWTs) are more suitable for urban areas than Horizontal Axis Wind Turbines (HAWTs). To date, very little has been published in this area to assess good performance and lifetime of VAWTs either in open or urban areas. At low tip speed ratios (TSRs<5), VAWTs are subjected to a phenomenon called 'dynamic stall'. This can really affect the fatigue life of a VAWT if it is not well understood. The purpose of this paper is to investigate how CFD is able to simulate the dynamic stall for 2-D flow around VAWT blades. During the numerical simulations different turbulence models were used and compared with the data available on the subject. In this numerical analysis the Shear Stress Transport (SST) turbulence model seems to predict the dynamic stall better than the other turbulence models available. The limitations of the study are that the simulations are based on a 2-D case with constant wind and rotational speeds instead of considering a 3-D case with variable wind speeds. This approach was necessary for having a numerical analysis at low computational cost and time. Consequently, in the future it is strongly suggested to develop a more sophisticated model that is a more realistic simulation of a dynamic stall in a three-dimensional VAWT.

Advances in sequential data assimilation and numerical weather forecasting: an Ensemble Transform Kalman-Bucy Filter, a study on clustering in deterministic Ensemble Square Root Filters, and a test of a new time stepping scheme in an atmospheric model

This dissertation deals with aspects of sequential data assimilation (in particular ensemble Kalman filtering) and numerical weather forecasting. In the first part, the recently formulated Ensemble Kalman-Bucy (EnKBF) filter is revisited. It is shown that the previously used numerical integration scheme fails when the magnitude of the background error covariance grows beyond that of the observational error covariance in the forecast window. Therefore, we present a suitable integration scheme that handles the stiffening of the differential equations involved and doesn’t represent further computational expense. Moreover, a transform-based alternative to the EnKBF is developed: under this scheme, the operations are performed in the ensemble space instead of in the state space. Advantages of this formulation are explained. For the first time, the EnKBF is implemented in an atmospheric model. The second part of this work deals with ensemble clustering, a phenomenon that arises when performing data assimilation using of deterministic ensemble square root filters in highly nonlinear forecast models. Namely, an M-member ensemble detaches into an outlier and a cluster of M-1 members. Previous works may suggest that this issue represents a failure of EnSRFs; this work dispels that notion. It is shown that ensemble clustering can be reverted also due to nonlinear processes, in particular the alternation between nonlinear expansion and compression of the ensemble for different regions of the attractor. Some EnSRFs that use random rotations have been developed to overcome this issue; these formulations are analyzed and their advantages and disadvantages with respect to common EnSRFs are discussed. The third and last part contains the implementation of the Robert-Asselin-Williams (RAW) filter in an atmospheric model. The RAW filter is an improvement to the widely popular Robert-Asselin filter that successfully suppresses spurious computational waves while avoiding any distortion in the mean value of the function. Using statistical significance tests both at the local and field level, it is shown that the climatology of the SPEEDY model is not modified by the changed time stepping scheme; hence, no retuning of the parameterizations is required. It is found the accuracy of the medium-term forecasts is increased by using the RAW filter.