Nanopatterning by solid-state dewetting on reconstructed ceramic surfaces

We demonstrate ordered array formation of Au nanoparticles by controlled solid-state dewetting of a metal film on stepped alumina substrates. In situ transmission electron microscopy studies reveal that the dewetting process starts with nucleation of ordered dry regions on the substrate. The chemical potential difference between concave and convex surface regions induces anisotropic metal diffusion leading to the formation of nanowires in the valleys. The nanowires fragment due to Rayleigh instability forming arrays of metal nanoparticles on the substrate. The length scale of reconstruction relative to the starting film thickness is an important parameter in controlling the spatial order of the nanoparticles.

Evolution of three-dimensional character across the Lan+1NinO3n+1 homologous series with increase in n1

Electrical and magnetic properties of La3Ni2O7 and La4Ni3O10 have been investigated in comparison with those of La2NiO4, LaNiO3, and LaSrNiO4. The results suggest an increasing 3-dimensional character across the homologous series Lan+1NinO3n+1 with increase in n. Accordingly, the electrical resistivity decreases in the order La3Ni2O7, La4Ni3O10, and LaNiO3 and this trend is suggested to be related to the percolation threshold. Magnetic properties of these oxides also show some interesting trends across the series.

Computational Methods for Reconstruction and Analysis of Genome-Scale Metabolic Networks

Metabolism is the cellular subsystem responsible for generation of energy from nutrients and production of building blocks for larger macromolecules. Computational and statistical modeling of metabolism is vital to many disciplines including bioengineering, the study of diseases, drug target identification, and understanding the evolution of metabolism. In this thesis, we propose efficient computational methods for metabolic modeling. The techniques presented are targeted particularly at the analysis of large metabolic models encompassing the whole metabolism of one or several organisms. We concentrate on three major themes of metabolic modeling: metabolic pathway analysis, metabolic reconstruction and the study of evolution of metabolism. In the first part of this thesis, we study metabolic pathway analysis. We propose a novel modeling framework called gapless modeling to study biochemically viable metabolic networks and pathways. In addition, we investigate the utilization of atom-level information on metabolism to improve the quality of pathway analyses. We describe efficient algorithms for discovering both gapless and atom-level metabolic pathways, and conduct experiments with large-scale metabolic networks. The presented gapless approach offers a compromise in terms of complexity and feasibility between the previous graph-theoretic and stoichiometric approaches to metabolic modeling. Gapless pathway analysis shows that microbial metabolic networks are not as robust to random damage as suggested by previous studies. Furthermore the amino acid biosynthesis pathways of the fungal species Trichoderma reesei discovered from atom-level data are shown to closely correspond to those of Saccharomyces cerevisiae. In the second part, we propose computational methods for metabolic reconstruction in the gapless modeling framework. We study the task of reconstructing a metabolic network that does not suffer from connectivity problems. Such problems often limit the usability of reconstructed models, and typically require a significant amount of manual postprocessing. We formulate gapless metabolic reconstruction as an optimization problem and propose an efficient divide-and-conquer strategy to solve it with real-world instances. We also describe computational techniques for solving problems stemming from ambiguities in metabolite naming. These techniques have been implemented in a web-based sofware ReMatch intended for reconstruction of models for 13C metabolic flux analysis. In the third part, we extend our scope from single to multiple metabolic networks and propose an algorithm for inferring gapless metabolic networks of ancestral species from phylogenetic data. Experimenting with 16 fungal species, we show that the method is able to generate results that are easily interpretable and that provide hypotheses about the evolution of metabolism.

Single-resolution and multiresolution extended-Kalman-filter-based reconstruction approaches to optical refraction tomography

The problem of reconstruction of a refractive-index distribution (RID) in optical refraction tomography (ORT) with optical path-length difference (OPD) data is solved using two adaptive-estimation-based extended-Kalman-filter (EKF) approaches. First, a basic single-resolution EKF (SR-EKF) is applied to a state variable model describing the tomographic process, to estimate the RID of an optically transparent refracting object from noisy OPD data. The initialization of the biases and covariances corresponding to the state and measurement noise is discussed. The state and measurement noise biases and covariances are adaptively estimated. An EKF is then applied to the wavelet-transformed state variable model to yield a wavelet-based multiresolution EKF (MR-EKF) solution approach. To numerically validate the adaptive EKF approaches, we evaluate them with benchmark studies of standard stationary cases, where comparative results with commonly used efficient deterministic approaches can be obtained. Detailed reconstruction studies for the SR-EKF and two versions of the MR-EKF (with Haar and Daubechies-4 wavelets) compare well with those obtained from a typically used variant of the (deterministic) algebraic reconstruction technique, the average correction per projection method, thus establishing the capability of the EKF for ORT. To the best of our knowledge, the present work contains unique reconstruction studies encompassing the use of EKF for ORT in single-resolution and multiresolution formulations, and also in the use of adaptive estimation of the EKF's noise covariances. (C) 2010 Optical Society of America

“Empire is a state of mind” – Imagining Eurasia in Russia –

Työssäni tarkastelen venäläistä neo-euraasianistista liikettä ja tapoja joilla liikkeen aktivistit rakentavat Euraasiasta yhtenäistä kokonaisuutta ja imperiumia. Keskeisiä tutkimuskysymyksiäni ovat: Mikä imperiumi on ja mitkä ovat sen keskeisiä motivaatioita ja teemoja? Kuinka imperiumin idea rakentuu tai käsitetään ja tämän voi tulkita? Minkälaisia seurauksia voi tulkita heidän tavallaan Euraasia nähdä olevan? Materiaalina käytän haastatteluja, jotka on kerätty Moskovassa keväällä 2008, ja liikkeen kirjallisia tuotoksia (lehdet ja Internet -sivut). Neo-euraasianistisella liikkeellä tarkoitan tässä työssä Kansainvälistä Euraasianistista liikettä (Meždunarodnoe Evrazijskoe Dviženie) ja sen alahaaraa Euraasianistista Nuorisoliittoa (Evrazijskij Sojuz Molodëži). Liike perustettiin virallisesti 2003, mutta rakentaa vahvasti historiallista yhteyttä 1930 -luvun klassiseen eurasianismiin. Tämän lisäksi sen diskurssissa on paljon neuvostoliittolaisia, fasistisia, uuskonservatiivisia ja nationalistisia piirteitä. Liikkeen johtohahmo on filosofi-geopoliitikko Alexandr Dugin. Työn tausta-ajatuksena minua kiinnostaa etenkin nk. älymystön tai intelligenttien vaikutus nationalismiin tai sosiaalisia ryhmiä määrittelevien diskurssien kehitykseen ja muutokseen.Tarkastelen materiaalia diskurssianalyyttisesta näkökulmasta. Näen diskurssianalyysin sen tutkimisena, miten sosiaalista todellisuutta tuotetaan erilaisissa sosiaalisissa käytännöissä. Samalla näiden diskurssien tutkiminen, foucautlaisen perinteen myötä, tarkastelee kriittisesti niiden tuottamia (aktualisoituneita sekä potentiaalisia) valtasuhteita. Käytän työssäni myös Benedict Andersonin kuvitellun yhteisön (imagined communities) käsitettä, joka auttaa hahmottamaan tapaa, jolla tutkimuskohteeni rakentavat imperiumia yhteisönä. Aktivistien puheessa imperiumi (imperiâ) tulee esiin pääasiallisesti positiivisesti ja ”heidän omanaan,” kun taas termi imperialismi (imperializm) pääosin negatiivisena, liittyen etenkin keskeisenä vihollisena pidettyihin Yhdysvaltoihin. Esiin nousee monta toisiinsa liittyvää teemaa, jotka jaottelen viideksi pääteemaksi. Näistä tarkastelen lähemmin imperiumia ”kaikkien kansojen hyväntekijänä (poliittinen puoli)”, ulkoisen voiman lähteenä (historiallis-geopoliittinen puoli) sekä kollektiivisen subjektin luojana (imperialistis-nationalistinen puoli). Pyrin kontekstualisoimaan diskurssin ja tarkastelemaan tapoja, joilla se ammentaa motiiveja myös historiallis-kulttuurisista tavoista hahmottaa aluetta ja sen asukkaita. Käsittelen myös kansan, kansakunnan, etnoksen ja nationalismin käsitteitä ja sitä, miten ne nousevat neo-eurasianistisessa diskursissa esiin. Imperiaalisen nationalismin (imperskij nacionalizm) käsite auttaa ymmärtämään niitä tapoja, jolla liike tekee sekä pesäeroa nationalismiin että samalla hyödyntää monia nationalistisen diskurssin perusteemoja. Eräs liikkeen diskurssin keskeisistä eroista niin sanottuun nationalismin valtavirtaan on ”kansakunnan (naciâ)” käsitteen vahva negatiivinen konnotaatio. Sen vastakohtana esiin nostetaan vahvasti kansan (narod) käsite. Samalla kuitenkin etnisen venäläisen (russkij) käsitettä käytetään tavallista laajemmin ja kattavammin kuin tavallisesti, ja ennen kaikkea Venäjä nousee imperiumin keskeisimmäksi tekijäksi. Euraasialaiseen imperiumiin liitetyistä positiivistista mielikuvista käsittelen tarkemmin monikansallisuuden ja kansojen kodin ideaa, joka nousee mielestäni huomattavaksi retoriseksi taustaksi kaikessa materiaalissa. Tähän liittyy vahvasti myös saman teeman sivujuonne, eli imperiumin ”vapauttava” rooli. Tulkitsen, että liikkeen imperiumi -diskurssilla on instrumentaalinen luonne: se legitimoi aktivistien vaatimuksia varsinkin entisen Neuvostoliiton alueen suhteen. ”Euraasialaisen kansan” ajatus toimii mahdollisena Euraasiaa yhteisenä tekijänä ”Neuvostokansan” tilalla. Sen taustalla materiaalistani päätellen siintävät kuitenkin enemmänkin Venäjä ja venäläis -spesifit vaateet kuin koko Euraasia. Pohdin myös kansakunnan (nation) hyljeksimisen syitä ja käsitteen sopivuutta Venäjälle, kuten myös venäläisyyden käsitteiden kerrostuneisuutta. Kokonaisuudessaan imperiumi tuli esiin abstraktina, utopistisena ja ”totaalisena” kokonaisuutena.

Composite MR image reconstruction and unaliasing for general trajectories using neural networks

In rapid parallel magnetic resonance imaging, the problem of image reconstruction is challenging. Here, a novel image reconstruction technique for data acquired along any general trajectory in neural network framework, called ``Composite Reconstruction And Unaliasing using Neural Networks'' (CRAUNN), is proposed. CRAUNN is based on the observation that the nature of aliasing remains unchanged whether the undersampled acquisition contains only low frequencies or includes high frequencies too. Here, the transformation needed to reconstruct the alias-free image from the aliased coil images is learnt, using acquisitions consisting of densely sampled low frequencies. Neural networks are made use of as machine learning tools to learn the transformation, in order to obtain the desired alias-free image for actual acquisitions containing sparsely sampled low as well as high frequencies. CRAUNN operates in the image domain and does not require explicit coil sensitivity estimation. It is also independent of the sampling trajectory used, and could be applied to arbitrary trajectories as well. As a pilot trial, the technique is first applied to Cartesian trajectory-sampled data. Experiments performed using radial and spiral trajectories on real and synthetic data, illustrate the performance of the method. The reconstruction errors depend on the acceleration factor as well as the sampling trajectory. It is found that higher acceleration factors can be obtained when radial trajectories are used. Comparisons against existing techniques are presented. CRAUNN has been found to perform on par with the state-of-the-art techniques. Acceleration factors of up to 4, 6 and 4 are achieved in Cartesian, radial and spiral cases, respectively. (C) 2010 Elsevier Inc. All rights reserved.

A determination of the structure of the intramolecular charge transfer state of 4-dimethylaminobenzonitrile (DMABN) by time-resolved resonance Raman spectroscopy

Picosecond time-resolved resonance Raman spectra of the A (intramolecular charge transfer, ICT) state of DMABN, DMABN-d(6) and DMABN-N-15 have been obtained. The isotopic shifts identify the nu (s)(ph-N) mode as a band at 1281 cm(-1). The similar to 96 cm(-1) downshift of this mode from its ground state frequency rules out the electronic coupling PICT model and unequivocally supports the electronic decoupling TICT model. However, our results suggest some pyramidal character of the A state amino conformation.

Solid state structural and solution studies on the formation of a flexible cavity for anions by copper(I) and 1,2-bis(diphenylphosphino)ethane

Copper(l) complexes of 1,2-bis(diphenylphosphino)ethane (dppe) with a stoichiometry Cu-2(dppe)(3)(X)(2) [X- = CN- (1), SCN- (2), NO3- (3)] are obtained from direct reactions of CuX and dppe. The complexes are structurally and spectroscopically (NMR and IR) characterized. The structure of the [Cu-2(dPPe)(3)](2+) dication is similar to the structural motif observed in many other complexes with a chelating dppe and a bridging dppe connecting two copper centers. In complexes 1 -3, the anions are confined to the cavity formed by the phosphines which force a monodentate coordination mode despite the predominant bidentate/bridging character of the anions. The coordination angles rather than the thermochemical radii dictate the steric requirement of anions. While the solution behavior of 3, with nitrate, is similar to complexes studied earlier, complexes with pseudohalides exhibit new solution behavior. (C) 2002 Elsevier Science Ltd. All rights reserved.

Interplay of localized and itinerant character of Ru ions: Tl2Ru2O7 versus Hg2Ru2O7

We carry out a comparative study of the electronic structure of two pyrochlore ruthenate compounds, Tl2Ru2O7 and Hg2Ru2O7, in terms of first principles calculations. Our study reveals the Ru d electrons in Hg2Ru2O7 to be much more delocalized compared to that in Tl2Ru2O7. The subtle change in the Ru-d bandwidths in the two compounds, triggered by the differences in Hg 5d-Ru 4d hybridization compared to that of Tl 5d-Ru 4d, bring in the observed differences in behavior. Our study further shows that the development of long range noncollinear antiferromagnetic structure at low temperature is sufficient to produce the insulating solution in Hg2Ru2O7, in line with the prediction from recent nuclear magnetic resonance study.

Advances in Image Reconstruction Methods for Real-Time Magnetic Resonance Thermometry

Magnetic Resonance Imaging (MRI) has been widely used in cancer treatment planning, which takes the advantage of high-resolution and high-contrast provided by it. The raw data collected in the MRI can also be used to obtain the temperature maps and has been explored for performing MR thermometry. This review article describes the methods that are used in performing MR thermometry, with an emphasis on reconstruction methods that are useful to obtain these temperature maps in real-time for large region of interest. This article also proposes a prior-image constrained reconstruction method for temperature reconstruction in MR thermometry, and a systematic comparison using ex-vivo tissue experiments with state of the art reconstruction method is presented.

B-Spline potential function for maximum a-posteriori image reconstruction in fluorescence microscopy

An iterative image reconstruction technique employing B-Spline potential function in a Bayesian framework is proposed for fluorescence microscopy images. B-splines are piecewise polynomials with smooth transition, compact support and are the shortest polynomial splines. Incorporation of the B-spline potential function in the maximum-a-posteriori reconstruction technique resulted in improved contrast, enhanced resolution and substantial background reduction. The proposed technique is validated on simulated data as well as on the images acquired from fluorescence microscopes (widefield, confocal laser scanning fluorescence and super-resolution 4Pi microscopy). A comparative study of the proposed technique with the state-of-art maximum likelihood (ML) and maximum-a-posteriori (MAP) with quadratic potential function shows its superiority over the others. B-Spline MAP technique can find applications in several imaging modalities of fluorescence microscopy like selective plane illumination microscopy, localization microscopy and STED. (C) 2015 Author(s).

Geometric documentation and reconstruction of the church of the Monastery of San Prudencio (La Rioja, Spain)

[EN] Data contained in this record come from the following accademic activity (from which it is possible to locate additional records related with the Monastery):

Dimorfismo sexual e polimorfismo no gênero Ptychoderes Schoenherr, 1823 (Coleoptera Anthribidae, Anthribinae, Ptychoderini)

O dimorfismo sexual exibido por machos polifênicos em algumas espécies do gênero Ptychoderes envolve variação no rostro, antena e ventritos. A existência de polifenismo pode ser um importante componente no processo evolutivo por meio de novidades morfológicas e comportamentais. O objetivo desse estudo foi determinar a variação em caracteres morfométricos, polifenismo em machos, variação de estruturas com conhecido dimorfismo sexual, possíveis padrões alométricos e testar estas inferências para Ptychoderes através do mapeamento do dimorfismo sexual e de machos em uma reconstrução filogenética de Ptychoderes usando Mesquite 2.04. Foram medidas 23 variáveis morfométricas em 510 espécimes com as seguintes análises realizadas: análises de cluster, analises de componentes principais (PCA), analise de variáveis canônicas (AVC), análise de regressão por eixo maior reduzido (RMA). Cada tipo de dimorfismo foi mapeado em uma filogenia prévia como dois estados separados usando parcimônia. Para todas as espécies o dimorfismo sexual apresentou diferenças significativas entre os sexos com relação aos segmentos antenais (II- X).O compriemtno do rosto e ventrito V foram confirmados como indicativos de dimorfismo sexual (exceto em P. jordani). A única espécie em que não ocorreu machos polifenicos foi P. depressus. Nas outras espécies machos grandes e pequenos diferem significantemente para muitas variáveis com similaridades e diferenças. Na ACP, o primeiro componente (PC1) apresentou alta porcentagem de variância nos dados de todas as espécies; apresentou loadings de mesmo sinal sugerindo diferenças relacionadas ao tamanho para as espécies P. jordani, P. depressus, P. virgatus, P. mixtus e P. callosus e para as espécies P. viridanus, P. antiquus, P. elongates e P. nebulosus apresentou loadings positivos e negativos sugerindo diferenças relacionadas a forma (alometria). O PC2 apresentou loadings positivos e negativos para todas as espécies, um provável componente alométricos. A AVC confirmou os grupos: machos grandes, machos pequenos e fêmeas quando estes ocorreram. Nós encontramos diferentes padrões alométricos para todas as espécies com diferenças e semelhanças entre as espécies. Todos esses resultados confirmam a hipótese de polifenismo em machos e dimorfismo sexual para Ptychhoderes. A análise dos padrões alométricos para o dimorfismo sexual revelou alometria positiva para o comprimento do rostro (CR1) em machos e fêmeas, com os ventritos apenas em machos. Padrões alométricos positivos relacionados ao polifenismo nos antenômeros foram confirmados para os machos grandes e pequenos de quase todas as espécies exceto em P. nebulosus. O ancestral de clados na filogenia de Ptychoderes foi inferido para machos polifênicos (exceto P. depressus) com variáveis no rostro, antenas e ventritos indicativas de dimorfismo sexual com alometria positiva. Estes padrões poderiam estar ligados com o comportamento de proteção das fêemeas realizados por machos grandes durante a oviposição.

Parity-dependent State Engineering and Tomography in the ultrastrong coupling regime

Reaching the strong coupling regime of light-matter interaction has led to an impressive development in fundamental quantum physics and applications to quantum information processing. Latests advances in different quantum technologies, like superconducting circuits or semiconductor quantum wells, show that the ultrastrong coupling regime (USC) can also be achieved, where novel physical phenomena and potential computational benefits have been predicted. Nevertheless, the lack of effective decoupling mechanism in this regime has so far hindered control and measurement processes. Here, we propose a method based on parity symmetry conservation that allows for the generation and reconstruction of arbitrary states in the ultrastrong coupling regime of light-matter interactions. Our protocol requires minimal external resources by making use of the coupling between the USC system and an ancillary two-level quantum system.

Fourier analysis and gabor filtering for texture analysis and local reconstruction of general shapes

Since the pioneering work of Gibson in 1950, Shape- From-Texture has been considered by researchers as a hard problem, mainly due to restrictive assumptions which often limit its applicability. We assume a very general stochastic homogeneity and perspective camera model, for both deterministic and stochastic textures. A multi-scale distortion is efficiently estimated with a previously presented method based on Fourier analysis and Gabor filters. The novel 3D reconstruction method that we propose applies to general shapes, and includes non-developable and extensive surfaces. Our algorithm is accurate, robust and compares favorably to the present state of the art of Shape-From- Texture. Results show its application to non-invasively study shape changes with laid-on textures, while rendering and retexturing of cloth is suggested for future work. © 2009 IEEE.