Supergravity models of (3+1)-dimensional QCD

The most general black M5-brane solution of eleven-dimensional supergravity (with a flat R4 spacetime in the brane and a regular horizon) is characterized by charge, mass and two angular momenta. We use this metric to construct general dual models of large-N QCD (at strong coupling) that depend on two free parameters. The mass spectrum of scalar particles is determined analytically (in the WKB approximation) and numerically in the whole two-dimensional parameter space. We compare the mass spectrum with analogous results from lattice calculations, and find that the supergravity predictions are close to the lattice results everywhere on the two dimensional parameter space except along a special line. We also examine the mass spectrum of the supergravity Kaluza-Klein (KK) modes and find that the KK modes along the compact D-brane coordinate decouple from the spectrum for large angular momenta. There are however KK modes charged under a U(1)×U(1) global symmetry which do not decouple anywhere on the parameter space. General formulas for the string tension and action are also given.

Energy-momentum tensor for scalar fields coupled to the dilaton in two dimensions

We clarify some issues related to the evaluation of the mean value of the energy-momentum tensor for quantum scalar fields coupled to the dilaton field in two-dimensional gravity. Because of this coupling, the energy-momentum tensor for matter is not conserved and therefore it is not determined by the trace anomaly. We discuss different approximations for the calculation of the energy-momentum tensor and show how to obtain the correct amount of Hawking radiation. We also compute cosmological particle creation and quantum corrections to the Newtonian potential.

Lämmönsiirron numeerinen laskenta profiloidulle kanavalle.

Työn tavoitteena oli tutkia aaltomaisen profiloinnin vaikutusta suorien jäähdytyskanavien lämmönsiirtoon ja painehäviöön. Erilaisia profiileja oli kymmenen kappaletta ja ne olivat 5mm leveitä ja 30cm pitkiä kukin. Ne laskettiin kolmeulotteisina tapauksina FINFLO-virtausratkaisijalla kolmella eri Reynoldsin luvulla, jotka vastasivat laminaarista, osittain turbulenttista ja lähes kokonaan turbulenttista virtausta. Lämmönsiirtoaine oli kuiva +30°C ilma ja profiloinnin toteutustapa oli toisiaan sivuavat ympyräkaaret kolmella erilaisella säteen arvolla ja kolmella erilaisella aallonpituuden arvolla. Lisäksi laskettiin saman levyisen tasokanavan arvot jokaisella Reynoldsin luvulla kaksiulotteisina tapauksina. Näitä profiloimattomia kanavia pidettiin referenssitapauksina. Tuloksena havaittiin että profiloimalla saadaan yksiselitteisesti suurempi lämpöteho ulos samasta tilavuudesta. Lämmönsiirtokerroin kasvaa profiloinnin avulla parhaimmillaan n. 20% käytetystä turbulenssimallista tai lämmönsiirtokertoimen määritelmästä riippumatta. Painehäviö kasvaa myös aina, mutta kitkakerroin voi hieman pienentyä. Profiilin varsinaisena hyvyyskriteerinä pidettiin lämmönsiirtokertoimen ja kitkakertoimen suhdetta h/f. Se osoittautui riippuvaksi Reynoldsin luvusta ja turbulenssimallista; ASM ja Chien k-έ -mallit ennustavat transitioetäisyyden eri tavalla. Laminaarisilla virtauksilla h/f :n vaihtelu oli vähäistä; suhde vaihteli vain ±5% eri profiilien kesken. ASM-mallilla havaittiin sekundääripyörteilyä, ehkä siksi että se mallintaa anisotrooppisen turbulenssin. Chien k-έ malli ennusti suuremman ja aikaisemmin alkavan turbulenttisuuden kuin ASM. Lisäksi havaittiin mm. että tietyillä profiileilla muodostuu kanavan kapeimpaan kohtaan selvä virtausnopeuden paikallinen minimi seinämän läheisyyden takia.

Modeling the transport phenomena within arterial wall: porous media approach

The transport of macromolecules, such as low-density lipoprotein (LDL), and their accumulation in the layers of the arterial wall play a critical role in the creation and development of atherosclerosis. Atherosclerosis is a disease of large arteries e.g., the aorta, coronary, carotid, and other proximal arteries that involves a distinctive accumulation of LDL and other lipid-bearing materials in the arterial wall. Over time, plaque hardens and narrows the arteries. The flow of oxygen-rich blood to organs and other parts of the body is reduced. This can lead to serious problems, including heart attack, stroke, or even death. It has been proven that the accumulation of macromolecules in the arterial wall depends not only on the ease with which materials enter the wall, but also on the hindrance to the passage of materials out of the wall posed by underlying layers. Therefore, attention was drawn to the fact that the wall structure of large arteries is different than other vessels which are disease-resistant. Atherosclerosis tends to be localized in regions of curvature and branching in arteries where fluid shear stress (shear rate) and other fluid mechanical characteristics deviate from their normal spatial and temporal distribution patterns in straight vessels. On the other hand, the smooth muscle cells (SMCs) residing in the media layer of the arterial wall respond to mechanical stimuli, such as shear stress. Shear stress may affect SMC proliferation and migration from the media layer to intima. This occurs in atherosclerosis and intimal hyperplasia. The study of blood flow and other body fluids and of heat transport through the arterial wall is one of the advanced applications of porous media in recent years. The arterial wall may be modeled in both macroscopic (as a continuous porous medium) and microscopic scales (as a heterogeneous porous medium). In the present study, the governing equations of mass, heat and momentum transport have been solved for different species and interstitial fluid within the arterial wall by means of computational fluid dynamics (CFD). Simulation models are based on the finite element (FE) and finite volume (FV) methods. The wall structure has been modeled by assuming the wall layers as porous media with different properties. In order to study the heat transport through human tissues, the simulations have been carried out for a non-homogeneous model of porous media. The tissue is composed of blood vessels, cells, and an interstitium. The interstitium consists of interstitial fluid and extracellular fibers. Numerical simulations are performed in a two-dimensional (2D) model to realize the effect of the shape and configuration of the discrete phase on the convective and conductive features of heat transfer, e.g. the interstitium of biological tissues. On the other hand, the governing equations of momentum and mass transport have been solved in the heterogeneous porous media model of the media layer, which has a major role in the transport and accumulation of solutes across the arterial wall. The transport of Adenosine 5´-triphosphate (ATP) is simulated across the media layer as a benchmark to observe how SMCs affect on the species mass transport. In addition, the transport of interstitial fluid has been simulated while the deformation of the media layer (due to high blood pressure) and its constituents such as SMCs are also involved in the model. In this context, the effect of pressure variation on shear stress is investigated over SMCs induced by the interstitial flow both in 2D and three-dimensional (3D) geometries for the media layer. The influence of hypertension (high pressure) on the transport of lowdensity lipoprotein (LDL) through deformable arterial wall layers is also studied. This is due to the pressure-driven convective flow across the arterial wall. The intima and media layers are assumed as homogeneous porous media. The results of the present study reveal that ATP concentration over the surface of SMCs and within the bulk of the media layer is significantly dependent on the distribution of cells. Moreover, the shear stress magnitude and distribution over the SMC surface are affected by transmural pressure and the deformation of the media layer of the aorta wall. This work reflects the fact that the second or even subsequent layers of SMCs may bear shear stresses of the same order of magnitude as the first layer does if cells are arranged in an arbitrary manner. This study has brought new insights into the simulation of the arterial wall, as the previous simplifications have been ignored. The configurations of SMCs used here with elliptic cross sections of SMCs closely resemble the physiological conditions of cells. Moreover, the deformation of SMCs with high transmural pressure which follows the media layer compaction has been studied for the first time. On the other hand, results demonstrate that LDL concentration through the intima and media layers changes significantly as wall layers compress with transmural pressure. It was also noticed that the fraction of leaky junctions across the endothelial cells and the area fraction of fenestral pores over the internal elastic lamina affect the LDL distribution dramatically through the thoracic aorta wall. The simulation techniques introduced in this work can also trigger new ideas for simulating porous media involved in any biomedical, biomechanical, chemical, and environmental engineering applications.

Conservation Laws in Cellular Automata

Conservation laws in physics are numerical invariants of the dynamics of a system. In cellular automata (CA), a similar concept has already been defined and studied. To each local pattern of cell states a real value is associated, interpreted as the “energy” (or “mass”, or . . . ) of that pattern.The overall “energy” of a configuration is simply the sum of the energy of the local patterns appearing on different positions in the configuration. We have a conservation law for that energy, if the total energy of each configuration remains constant during the evolution of the CA. For a given conservation law, it is desirable to find microscopic explanations for the dynamics of the conserved energy in terms of flows of energy from one region toward another. Often, it happens that the energy values are from non-negative integers, and are interpreted as the number of “particles” distributed on a configuration. In such cases, it is conjectured that one can always provide a microscopic explanation for the conservation laws by prescribing rules for the local movement of the particles. The onedimensional case has already been solved by Fuk´s and Pivato. We extend this to two-dimensional cellular automata with radius-0,5 neighborhood on the square lattice. We then consider conservation laws in which the energy values are chosen from a commutative group or semigroup. In this case, the class of all conservation laws for a CA form a partially ordered hierarchy. We study the structure of this hierarchy and prove some basic facts about it. Although the local properties of this hierarchy (at least in the group-valued case) are tractable, its global properties turn out to be algorithmically inaccessible. In particular, we prove that it is undecidable whether this hierarchy is trivial (i.e., if the CA has any non-trivial conservation law at all) or unbounded. We point out some interconnections between the structure of this hierarchy and the dynamical properties of the CA. We show that positively expansive CA do not have non-trivial conservation laws. We also investigate a curious relationship between conservation laws and invariant Gibbs measures in reversible and surjective CA. Gibbs measures are known to coincide with the equilibrium states of a lattice system defined in terms of a Hamiltonian. For reversible cellular automata, each conserved quantity may play the role of a Hamiltonian, and provides a Gibbs measure (or a set of Gibbs measures, in case of phase multiplicity) that is invariant. Conversely, every invariant Gibbs measure provides a conservation law for the CA. For surjective CA, the former statement also follows (in a slightly different form) from the variational characterization of the Gibbs measures. For one-dimensional surjective CA, we show that each invariant Gibbs measure provides a conservation law. We also prove that surjective CA almost surely preserve the average information content per cell with respect to any probability measure.

Horizontal Grid Size Selection and its Influence on Mesoscale Model Simulations

The use of two-dimensional spectral analysis applied to terrain heights in order to determine characteristic terrain spatial scales and its subsequent use for the objective definition of an adequate grid size required to resolve terrain forcing are presented in this paper. In order to illustrate the influence of grid size, atmospheric flow in a complex terrain area of the Spanish east coast is simulated by the Regional Atmospheric Modeling System (RAMS) mesoscale numerical model using different horizontal grid resolutions. In this area, a grid size of 2 km is required to account for 95% of terrain variance. Comparison among results of the different simulations shows that, although the main wind behavior does not change dramatically, some small-scale features appear when using a resolution of 2 km or finer. Horizontal flow pattern differences are significant both in the nighttime, when terrain forcing is more relevant, and in the daytime, when thermal forcing is dominant. Vertical structures also are investigated, and results show that vertical advection is influenced highly by the horizontal grid size during the daytime period. The turbulent kinetic energy and potential temperature vertical cross sections show substantial differences in the structure of the planetary boundary layer for each model configuration

Dinâmica complexa no sistema bromato/hipofosfito/acetona/manganês e ferroína

New chemical systems have been recently designed for the study of complex phenomena such as oscillatory dynamics in the temporal domain and spatiotemporal pattern formation. Systems derived from oscillators based on the chemistry of bromate are the most extensively studied, with the celebrated Belousov-Zhabotinsky (BZ) reaction being the most popular example. Problems such as the formation of bubbles (CO2) and solid precipitate in the course of the reaction and the occurrence of simply short-lived oscillations under batch conditions are very common and, in some cases, compromise the use of some of these systems. It is investigated in this paper the dynamic behavior of the bromate/hypophosphite/acetone/dual catalyst system, which has been sugested as an interesting alternative to circumvent those inconvenients. In this work, manganese and ferroin are employed as catalysts and the complete system (BrO3-/H2PO2-/acetone/Mn(II)-ferroin) is studied under batch conditions. Temporal symmetry breaking was studied in a reactor under agitation by means of simultaneous records of the potential changes of platinum and Ag/AgBr electrodes, both measured versus a reversible hydrogen electrode. Additionally, spatio-temporal formation of target patterns and spiral waves were obtained when the oscillating mixture was placed in a quasi two-dimensional reactor.

Cardiac disease in systemic lupus erythematosus: prospective study of 70 patients.

A prospective two dimensional and Doppler echocardiographic study of 70 consecutive patients with systemic lupus erythematosus (SLE) and 40 controls was carried out. Forty patients (57%) were found to have echocardiographic disturbance. Valvular abnormalities were detected in 31 patients (44%) and in only two controls (5%). Mitral valve abnormalities were the most common findings (23/70 (33%)) with mild or moderate regurgitation the most frequent lesion (16% and 9% respectively). Three patients (4%) had a morphological echocardiographic pattern suggestive of non-infective verrucous vegetations affecting the mitral valve. No patient had haemodynamically significant clinical valve disease. Pericardial effusion was identified in 19 patients (27%), of whom 14 had mild and clinically silent disease. Myocardial abnormalities were found in 14 patients (20%), but clinical features of myocardial dysfunction were present in only one. Patients with antiphospholipid antibodies were found to have an increased prevalence of endocardial lesions, mainly valvular regurgitation. It is concluded that the inclusion of echocardiography in a study protocol of patients with SLE can identify an important subset of patients with cardiac abnormalities, many of which are clinically silent. In addition, the association of antiphospholipid antibodies with endocardial lesions suggests that these antibodies may have a prominent role in the pathogenetic mechanisms of heart valve disease in SLE.

Cardiac disease in systemic lupus erythematosus. Prospective study of 70 patients.

A prospective two dimensional and Doppler echocardiographic study of 70 consecutive patients with systemic lupus erythematosus (SLE) and 40 controls was carried out. Forty patients (57%) were found to have echocardiographic disturbance. Valvular abnormalities were detected in 31 patients (44%) and in only two controls (5%). Mitral valve abnormalities were the most common findings (23/70 (33%)) with mild or moderate regurgitation the most frequent lesion (16% and 9% respectively). Three patients (4%) had a morphological echocardiographic pattern suggestive of non-infective verrucous vegetations affecting the mitral valve. No patient had haemodynamically significant clinical valve disease. Pericardial effusion was identified in 19 patients (27%), of whom 14 had mild and clinically silent disease. Myocardial abnormalities were found in 14 patients (20%), but clinical features of myocardial dysfunction were present in only one. Patients with antiphospholipid antibodies were found to have an increased prevalence of endocardial lesions, mainly valvular regurgitation. It is concluded that the inclusion of echocardiography in a study protocol of patients with SLE can identify an important subset of patients with cardiac abnormalities, many of which are clinically silent. In addition, the association of antiphospholipid antibodies with endocardial lesions suggests that these antibodies may have a prominent role in the pathogenetic mechanisms of heart valve disease in SLE.

Water storage in wetted strips under irrigated coffee trees with different criteria of irrigation management

The increasing demand for water resources accentuates the need to reduce water waste through a more appropriate irrigation management. In the particular case of irrigated coffee planting, which in recent years presented growth with the predominance of drip irrigation, the improvement of drip irrigation management techniques is a necessity. The proper management of drip irrigation depends on the knowledge of the spatial pattern of soil moisture distribution inside the wetted strip formed under the irrigation lines. In this study, grids of 24 tensiometers were used to determine the water storage within the wetted strip formed under drippers, with a 3.78 L h-1 discharge, evenly spaced by 0.4 m, subjected to two different management criteria (fixed irrigation interval and 60 kPa tension). Estimates of storage based on a one-dimensional analysis, that only considers depth variations, were compared with two-dimensional estimates. The results indicate that for high-frequency irrigation the one-dimensional analysis is not appropriate. However, under less frequent irrigation, the two-dimensional analysis is dispensable, being the one-dimensional sufficient for calculating the water volume stored in the wetted strip.

A Farewell to Flat Biology. Three-dimensional Cell Culture Models in Cancer Drug Target Identification and Validation

Cells of epithelial origin, e.g. from breast and prostate cancers, effectively differentiate into complex multicellular structures when cultured in three-dimensions (3D) instead of conventional two-dimensional (2D) adherent surfaces. The spectrum of different organotypic morphologies is highly dependent on the culture environment that can be either non-adherent or scaffold-based. When embedded in physiological extracellular matrices (ECMs), such as laminin-rich basement membrane extracts, normal epithelial cells differentiate into acinar spheroids reminiscent of glandular ductal structures. Transformed cancer cells, in contrast, typically fail to undergo acinar morphogenic patterns, forming poorly differentiated or invasive multicellular structures. The 3D cancer spheroids are widely accepted to better recapitulate various tumorigenic processes and drug responses. So far, however, 3D models have been employed predominantly in the Academia, whereas the pharmaceutical industry has yet to adopt a more widely and routine use. This is mainly due to poor characterisation of cell models, lack of standardised workflows and high throughput cell culture platforms, and the availability of proper readout and quantification tools. In this thesis, a complete workflow has been established entailing well-characterised 3D cell culture models for prostate cancer, a standardised 3D cell culture routine based on high-throughput-ready platform, automated image acquisition with concomitant morphometric image analysis, and data visualisation, in order to enable large-scale high-content screens. Our integrated suite of software and statistical analysis tools were optimised and validated using a comprehensive panel of prostate cancer cell lines and 3D models. The tools quantify multiple key cancer-relevant morphological features, ranging from cancer cell invasion through multicellular differentiation to growth, and detect dynamic changes both in morphology and function, such as cell death and apoptosis, in response to experimental perturbations including RNA interference and small molecule inhibitors. Our panel of cell lines included many non-transformed and most currently available classic prostate cancer cell lines, which were characterised for their morphogenetic properties in 3D laminin-rich ECM. The phenotypes and gene expression profiles were evaluated concerning their relevance for pre-clinical drug discovery, disease modelling and basic research. In addition, a spontaneous model for invasive transformation was discovered, displaying a highdegree of epithelial plasticity. This plasticity is mediated by an abundant bioactive serum lipid, lysophosphatidic acid (LPA), and its receptor LPAR1. The invasive transformation was caused by abrupt cytoskeletal rearrangement through impaired G protein alpha 12/13 and RhoA/ROCK, and mediated by upregulated adenylyl cyclase/cyclic AMP (cAMP)/protein kinase A, and Rac/ PAK pathways. The spontaneous invasion model tangibly exemplifies the biological relevance of organotypic cell culture models. Overall, this thesis work underlines the power of novel morphometric screening tools in drug discovery.

Thermal radiation in combustion systems

A numerical procedure for solving the nongray radiative transfer equation (RTE) in two-dimensional cylindrical participating media is presented. Nongray effects are treated by using a narrow-band approach. Radiative emission from CO, CO2, H2O, CH4 and soot is considered. The solution procedure is applied to study radiative heat transfer in a premixed CH4-O2, laminar, flame. Temperature, soot and IR-active species molar fraction distributions are allowed to vary in the axial direction of the flame. From the obtained results it is possible to quantify the radiative loss in the flame, as well as the importance of soot radiation as compared to gaseous radiation. Since the solution procedure is developed for a two-dimensional cylindrical geometry, it can be applied to other combustion systems such as furnaces, internal combustion engines, liquid and solid propellant combustion.

Heat Source Estimation with the Conjugate Gradient Method in Inverse Linear Diffusive Problems

In this work, we present the solution of a class of linear inverse heat conduction problems for the estimation of unknown heat source terms, with no prior information of the functional forms of timewise and spatial dependence of the source strength, using the conjugate gradient method with an adjoint problem. After describing the mathematical formulation of a general direct problem and the procedure for the solution of the inverse problem, we show applications to three transient heat transfer problems: a one-dimensional cylindrical problem; a two-dimensional cylindrical problem; and a one-dimensional problem with two plates.

Multicellular spheroids of bone marrow stromal cells: a three-dimensional in vitro culture system for the study of hematopoietic cell migration

Cell fate decisions are governed by a complex interplay between cell-autonomous signals and stimuli from the surrounding tissue. In vivo cells are connected to their neighbors and to the extracellular matrix forming a complex three-dimensional (3-D) microenvironment that is not reproduced in conventional in vitro systems. A large body of evidence indicates that mechanical tension applied to the cytoskeleton controls cell proliferation, differentiation and migration, suggesting that 3-D in vitro culture systems that mimic the in vivo situation would reveal biological subtleties. In hematopoietic tissues, the microenvironment plays a crucial role in stem and progenitor cell survival, differentiation, proliferation, and migration. In adults, hematopoiesis takes place inside the bone marrow cavity where hematopoietic cells are intimately associated with a specialized three 3-D scaffold of stromal cell surfaces and extracellular matrix that comprise specific niches. The relationship between hematopoietic cells and their niches is highly dynamic. Under steady-state conditions, hematopoietic cells migrate within the marrow cavity and circulate in the bloodstream. The mechanisms underlying hematopoietic stem/progenitor cell homing and mobilization have been studied in animal models, since conventional two-dimensional (2-D) bone marrow cell cultures do not reproduce the complex 3-D environment. In this review, we will highlight some of the mechanisms controlling hematopoietic cell migration and 3-D culture systems.

Response curves of deterministic and probabilistic cellular automata in one and two dimensions

One of the most important problems in the theory of cellular automata (CA) is determining the proportion of cells in a specific state after a given number of time iterations. We approach this problem using patterns in preimage sets - that is, the set of blocks which iterate to the desired output. This allows us to construct a response curve - a relationship between the proportion of cells in state 1 after niterations as a function of the initial proportion. We derive response curve formulae for many two-dimensional deterministic CA rules with L-neighbourhood. For all remaining rules, we find experimental response curves. We also use preimage sets to classify surjective rules. In the last part of the thesis, we consider a special class of one-dimensional probabilistic CA rules. We find response surface formula for these rules and experimental response surfaces for all remaining rules.