Application of Computational Fluid Dynamics in Modeling Blood Flow in Human Thoracic Aorta

The aim of this study was to simulate blood flow in thoracic human aorta and understand the role of flow dynamics in the initialization and localization of atherosclerotic plaque in human thoracic aorta. The blood flow dynamics in idealized and realistic models of human thoracic aorta were numerically simulated in three idealized and two realistic thoracic aorta models. The idealized models of thoracic aorta were reconstructed with measurements available from literature, and the realistic models of thoracic aorta were constructed by image processing Computed Tomographic (CT) images. The CT images were made available by South Karelia Central Hospital in Lappeenranta. The reconstruction of thoracic aorta consisted of operations, such as contrast adjustment, image segmentations, and 3D surface rendering. Additional design operations were performed to make the aorta model compatible for the numerical method based computer code. The image processing and design operations were performed with specialized medical image processing software. Pulsatile pressure and velocity boundary conditions were deployed as inlet boundary conditions. The blood flow was assumed homogeneous and incompressible. The blood was assumed to be a Newtonian fluid. The simulations with idealized models of thoracic aorta were carried out with Finite Element Method based computer code, while the simulations with realistic models of thoracic aorta were carried out with Finite Volume Method based computer code. Simulations were carried out for four cardiac cycles. The distribution of flow, pressure and Wall Shear Stress (WSS) observed during the fourth cardiac cycle were extensively analyzed. The aim of carrying out the simulations with idealized model was to get an estimate of flow dynamics in a realistic aorta model. The motive behind the choice of three aorta models with distinct features was to understand the dependence of flow dynamics on aorta anatomy. Highly disturbed and nonuniform distribution of velocity and WSS was observed in aortic arch, near brachiocephalic, left common artery, and left subclavian artery. On the other hand, the WSS profiles at the roots of branches show significant differences with geometry variation of aorta and branches. The comparison of instantaneous WSS profiles revealed that the model with straight branching arteries had relatively lower WSS compared to that in the aorta model with curved branches. In addition to this, significant differences were observed in the spatial and temporal profiles of WSS, flow, and pressure. The study with idealized model was extended to study blood flow in thoracic aorta under the effects of hypertension and hypotension. One of the idealized aorta models was modified along with the boundary conditions to mimic the thoracic aorta under the effects of hypertension and hypotension. The results of simulations with realistic models extracted from CT scans demonstrated more realistic flow dynamics than that in the idealized models. During systole, the velocity in ascending aorta was skewed towards the outer wall of aortic arch. The flow develops secondary flow patterns as it moves downstream towards aortic arch. Unlike idealized models, the distribution of flow was nonplanar and heavily guided by the artery anatomy. Flow cavitation was observed in the aorta model which was imaged giving longer branches. This could not be properly observed in the model with imaging containing a shorter length for aortic branches. The flow circulation was also observed in the inner wall of the aortic arch. However, during the diastole, the flow profiles were almost flat and regular due the acceleration of flow at the inlet. The flow profiles were weakly turbulent during the flow reversal. The complex flow patterns caused a non-uniform distribution of WSS. High WSS was distributed at the junction of branches and aortic arch. Low WSS was distributed at the proximal part of the junction, while intermedium WSS was distributed in the distal part of the junction. The pulsatile nature of the inflow caused oscillating WSS at the branch entry region and inner curvature of aortic arch. Based on the WSS distribution in the realistic model, one of the aorta models was altered to induce artificial atherosclerotic plaque at the branch entry region and inner curvature of aortic arch. Atherosclerotic plaque causing 50% blockage of lumen was introduced in brachiocephalic artery, common carotid artery, left subclavian artery, and aortic arch. The aim of this part of the study was first to study the effect of stenosis on flow and WSS distribution, understand the effect of shape of atherosclerotic plaque on flow and WSS distribution, and finally to investigate the effect of lumen blockage severity on flow and WSS distributions. The results revealed that the distribution of WSS is significantly affected by plaque with mere 50% stenosis. The asymmetric shape of stenosis causes higher WSS in branching arteries than in the cases with symmetric plaque. The flow dynamics within thoracic aorta models has been extensively studied and reported here. The effects of pressure and arterial anatomy on the flow dynamic were investigated. The distribution of complex flow and WSS is correlated with the localization of atherosclerosis. With the available results we can conclude that the thoracic aorta, with complex anatomy is the most vulnerable artery for the localization and development of atherosclerosis. The flow dynamics and arterial anatomy play a role in the localization of atherosclerosis. The patient specific image based models can be used to diagnose the locations in the aorta vulnerable to the development of arterial diseases such as atherosclerosis.

DYNAMICS OF LEAF FALL FROM RIPARIAN VEGETATION AND THE ACCUMULATION IN BENTHIC STOCK IN NEOTROPICAL STREAMS1

ABSTRACT Considering the importance of the riparian vegetation leaves as an energetic source to first order streams, the aim of the present study was to evaluate the leaf biomass contribution to the system and its temporal dynamics. With this purpose, monthly samples from July 2008 to June 2009 were collected using four sampling devices installed in three streams, in order to collect the vertical, lateral and terrestrial loads, and the benthic stock. We tested the following hypothesis: (1) leaf biomass input is higher after hydric stress periods; and (2) benthic stock biomass increase with higher loads from vertical and lateral entrances. Leaves represented 71.9% (on average) of all sampled allochthonous matter, with seasonal significant variation along the studied year. Peaks of leaf input were registered in September-October, after an increase in rainfall, and also in January, after a decrease in rainfall. Leaf input was higher in the lateral load.

DYNAMICS AND PREDICTION OF DIAMETRIC STRUCTURE IN TWO ATLANTIC FOREST FRAGMENTS IN NORTHEASTERN BRAZIL

ABSTRACT Monitoring analyses aim to understand the processes that drive changes in forest structure and, along with prediction studies, may assist in the management planning and conservation of forest remnants. The objective of this study was to analyze the forest dynamics in two Atlantic rainforest fragments in Pernambuco, Brazil, and to predict their future forest diameter structure using the Markov chain model. We used continuous forest inventory data from three surveys in two forest fragments of 87 ha (F1) and 388 ha (F2). We calculated the annual rates of mortality and recruitment, the mean annual increment, and the basal area for each of the 3-year periods. Data from the first and second surveys were used to project the third inventory measurements, which were compared to the observed values in the permanent plots using chi-squared tests (a = 0.05). In F1, a decrease in the number of individuals was observed due to mortality rates being higher than recruitment rates; however, there was an increase in the basal area. In this fragment, the fit to the Markov model was adequate. In F2, there was an increase in both the basal area and the number of individuals during the 6-year period due to the recruitment rate exceeding the mortality rate. For this fragment, the fit of the model was unacceptable. Hence, for the studied fragments, the demographic rates influenced the stem density more than the floristic composition. Yet, even with these intense dynamics, both fragments showed active growth.

Non-Markovian Dynamics in Continuous Variable Quantum Systems

The present manuscript represents the completion of a research path carried forward during my doctoral studies in the University of Turku. It contains information regarding my scientific contribution to the field of open quantum systems, accomplished in collaboration with other scientists. The main subject investigated in the thesis is the non-Markovian dynamics of open quantum systems with focus on continuous variable quantum channels, e.g. quantum Brownian motion models. Non-Markovianity is here interpreted as a manifestation of the existence of a flow of information exchanged by the system and environment during the dynamical evolution. While in Markovian systems the flow is unidirectional, i.e. from the system to the environment, in non-Markovian systems there are time windows in which the flow is reversed and the quantum state of the system may regain coherence and correlations previously lost. Signatures of a non-Markovian behavior have been studied in connection with the dynamics of quantum correlations like entanglement or quantum discord. Moreover, in the attempt to recognisee non-Markovianity as a resource for quantum technologies, it is proposed, for the first time, to consider its effects in practical quantum key distribution protocols. It has been proven that security of coherent state protocols can be enhanced using non-Markovian properties of the transmission channels. The thesis is divided in two parts: in the first part I introduce the reader to the world of continuous variable open quantum systems and non-Markovian dynamics. The second part instead consists of a collection of five publications inherent to the topic.

Detection of soybean planted areas through orbital images based on culture spectral dynamics

The soybean is important to the economy of Brazil, so the estimation of the planted area and the production with higher antecedence and reliability becomes essential. Techniques related to Remote Sensing may help to obtain this information at lower cost and less subjectivity in relation to traditional surveys. The aim of this study is to estimate the planted area with soybean culture in the crop of 2008/2009 in cities in the west of the state of Paraná, in Brazil, based on the spectral dynamics of the culture and through the use of the specific system of analysis for images of Landsat 5/TM satellite. The obtained results were satisfactory, because the classification supervised by Maximum Verisimilitude - MaxVer along with the techniques of the specific system of analysis for satellite images has allowed an estimate of soybean planted area (soybean mask), obtaining values ​​of the metrics of Global Accuracy with an average of 79.05% and Kappa Index over 63.50% in all cities. The monitoring of a reference area was of great importance for determining the vegetative phase in which the culture is more different from the other targets, facilitating the choice of training samples (ROIs) and avoiding misclassifications.

Non-Markovian Dynamics and the Quantum-To-Classical Transition for Quantum Brownian Motion

In this Thesis I discuss the dynamics of the quantum Brownian motion model in harmonic potential. This paradigmatic model has an exact solution, making it possible to consider also analytically the non-Markovian dynamics. The issues covered in this Thesis are themed around decoherence. First, I consider decoherence as the mediator of quantum-to-classical transition. I examine five different definitions for nonclassicality of quantum states, and show how each definition gives qualitatively different times for the onset of classicality. In particular I have found that all characterizations of nonclassicality, apart from one based on the interference term in the Wigner function, result in a finite, rather than asymptotic, time for the emergence of classicality. Second, I examine the diverse effects which coupling to a non-Markovian, structured reservoir, has on our system. By comparing different types of Ohmic reservoirs, I derive some general conclusions on the role of the reservoir spectrum in both the short-time and the thermalization dynamics. Finally, I apply these results to two schemes for decoherence control. Both of the methods are based on the non-Markovian properties of the dynamics.

Structural modelling of liquid ZrO2 and glassy B2O3 by using AB INITIO Molecular Dynamics method

Atomic structure of ZrO2 and B2O3 was investigated in this work. New data under extreme conditions (T = 3100 K) was obtained for the liquid ZrO2 structure. A fractional number of boron was investigated for glassy structure of B2O3. It was shown that it is possible to obtain an agreement for the fractional number between NMR and DFT techniques using a suitable initial configuration.

Spin-Dynamics in Cold Gases of 87Rb and Atomic Hydrogen. The spins they are a-changin’

In this thesis the dynamics of cold gaseous atoms is studied. Two different atomic species and two different experimental techniques have been used. In the first part of the thesis experiments with Bose-Einstein condensates of Rb-87 are presented. In these experiments the methods of laser cooling and magnetic trapping of atoms were utilized. An atom chip was used as the experimental technique for implementation of magnetic trapping. The atom chip is a small integrated instrument allowing accurate and detailed manipulation of the atoms. The experiments with Rb-87 probed the behaviour of a falling beam of atoms outcoupled from the Bose-Einstein condensate by electromagnetic field induced spin flips. In the experiments a correspondence between the phases of the outcoupling radio frequency field and the falling beam of atoms was found. In the second part of the thesis experiments of spin dynamics in cold atomic hydrogen gas are discussed. The experiments with atomic hydrogen are conducted in a cryostat using a dilution refrigerator as the cooling method. These experiments concentrated on explaining and quantifying modulations in the electron spin resonance spectra of doubly polarized atomic hydrogen. The modifications to the previous experimental setup are described and the observation of electron spin waves is presented. The observed spin wave modes were caused by the identical spin rotation effect. These modes have a strong dependence on the spatial profile of the polarizing magnetic field. We also demonstrated confinement of these modes in regions of strong magnetic field and manipulated their spatial distribution by changing the position of the field maximum.

Photoexcitation dynamics in organic solar cell donor/acceptor systems

Solceller presenteras ofta som ett miljövänligt alternativ för energiproduktion. Det största hindret för en bredare ibruktagning av kiselbaserade solceller är deras höga pris. I och med upptäckten av ledande och halvledande organiska (kolbaserade) molekyler och polymerer har ett nytt forskningsområde, organisk elektronik, vuxit fram. Den stora fördelen med organisk elektronik är att de använda materialen oftast är lösliga. Tillverkning av elektroniska komponenter kan då göras med hjälp av konventionella trycktekniker där bläcket ersatts med upplösta organiska material. Detta har potential att betydligt sänka priset för solceller. Nackdelen med organisk elektronik är att de använda materialen är komplexa, och de fysikaliska processerna i dem likaså. I min avhandling har jag studerat fotofysiken i två polymerer, P3HT och APFO3, som kan användas för att tillverka organiska solceller. Blandade med fullerenderivatet PCBM, som är en stark elektronacceptor, fås ett material som effektivt producerar elektroner och hål under belysning. I praktiken bidrar dock inte alla skapade laddningar till strömmen ur solcellen. Elektronerna och hålen kan förbli bundna till varandra i olika exciterade tillstånd, och även de som är fria kan träffa på motsatta laddningar under vägen till kontakterna och rekombinera. Centralt i mitt arbete har varit att identifiera olika typer av exciterade tillstånd i dessa solcellsmaterial, samt att bestämma deras livstider och rekombination. Metoden för detta har varit s.k. fotoinducerad absorption, som mäter fotoexcitationernas absorptioner i infraröda våglängdsområdet. De två viktigaste resultaten som presenteras i avhandlingen är en ratekvationsmodell för fotoexcitationsdynamiken i APFO3 på ultrasnabba tidsskalor (femtosekund - microsekund) och bildandet av en rekombinationshämmande dipol vid gränsytan för P3HT och PCBM som följd av värmebehandling. Dessa resultat bidrar till förståelsen av de fotofysikaliska processerna i relaterade material.

Dispersal and metacommunity dynamics in a soft-sediment benthic system : how well is the seafloor connected?

Connectivity depends on rates of dispersal between communities. For marine soft-sediment communities continued small-scale dispersal as post-larvae and as adults can be equally important in maintaining community composition, as initial recruitment of substrate by pelagic larvae. In this thesis post-larval dispersal strategies of benthic invertebrates, as well as mechanisms by which communities are connected were investigated. Such knowledge on dispersal is scarce, due to the difficulties in actually measuring dispersal directly in nature, and dispersal has not previously been quantified in the Baltic Sea. Different trap-types were used underwater to capture dispersing invertebrates at different sites, while in parallel measuring waves and currents. Local community composition was found to change predictably under varying rates of dispersal and physical connectivity (waves and currents). This response was, however, dependent on dispersal-related traits of taxa. Actively dispersing taxa will be relatively better at maintaining their position, as they are not as dependent on hydrodynamic conditions for dispersal and will be less prone to be passively transported by currents. Taxa also dispersed in relative proportions that were distinctly different from resident community composition and a significant proportion (40 %) of taxa were found to lack a planktonic larval life-stage. Community assembly was re-started in a large-scale manipulative field experiment over one year across several sites, which revealed how patterns of community composition (α-, β- and λ-diversity) change depending on rates of dispersal. Results also demonstrated that in response to small-scale disturbance, initial recruitment was by nearby-dominant species after which other species arrived from successively further away. At later assembly time, the number of coexisting species increased beyond what was expected purely by local niche requirements (species sorting), transferring regional differences in community composition (β-diversity) to the local scale (α-diversity, mass effect). Findings of this thesis complement more theoretical studies in metacommunity ecology by demonstrating that understanding how and when individuals disperse relative to underlying environmental heterogeneity is key to interpreting how patterns of diversity change across different spatial scales. Such information from nature is critical when predicting responses to, for example, different types of disturbances or management actions in conservation.

JNK, a versatile regulator of kinesin-1 transport and cytoskeleton dynamics

C-Jun N-terminal kinase (JNK) is traditionally recognized as a crucial factor in stress response and inducer of apoptosis upon various stimulations. Three isoforms build the JNK subfamily of MAPK; generally expressed JNK1 and JNK2 and brain specific JNK3. Degenerative potency placed JNK in the spotlight as potential pharmacological option for intervention. Unfortunately, adverse effects of potential drugs and observation that expression of only JNK2 and JNK3 are induced upon stress, restrained initial enthusiasm. Notably, JNK1 demonstrated atypical high constitutive activity in neurons that is not responsive to cellular stresses and indicated existence of physiological activity. This thesis aimed at revealing the physiological functions of JNK1 in actin homeostasis through novel effector MARCKS-Like 1 (MARCKSL1) protein, neuronal trafficking mediated by major kinesin-1 motor protein and microtubule (MT) dynamics via STMN2/SCG10. The screen for novel physiological JNK substrates revealed specific phosphorylation of C-terminal end of MARCKSL1 at S120, T148 and T183 both ex vivo and in vitro. By utilizing site-specific mutagenesis, various actin dynamics and migrations assays we were able to demonstrate that JNK1 phosphorylation specifically facilitates F-actin bundling and thus filament stabilisation. Consecutively, this molecular mechanism was proved to enhance formation of filopodia; cell surface projections that allow cell sensing surrounding environment and migrate efficiently. Our results visualize JNK dependent and MARCKSL1 executed induction of filopodia in neurons and fibroblast indicating general mechanism. Subsequently, inactivation of JNK action on MARCKSL1 shifts cellular actin machinery into lamellipodial dynamic arrangement. Tuning of actin cytoskeleton inevitably melds with cell migration. We observed that both active JNK and JNK pseudo-phosphorylated form of MARCKSL1 reduce actin turnover in intact cells leading to overall diminished cell motility. We demonstrate that tumour transformed cells from breast, prostate, lung and muscle-derived cancers upregulate MARCKSL1. We showed on the example of prostate cancer PC-3 cell line that JNK phosphorylation negatively controls MARCKSL1 ability to induce migration, which precedes cancer cell metastasis. The second round of identification of JNK physiological substrates resulted in detection of predominant motor protein kinesin-1 (Kif5). Mass spectrometry detailed analysis showed evident endogenous phosphorylation of kinesin-1 on S176 within motor domain that interacts with MT. In vitro phosphorylation of bacterially expressed kinesin heavy chain by JNK isoforms displayed higher specificity of JNK1 when compared to JNK3. Since, JNK1 is constitutively active in neurons it signified physiological aspect of kinesin-1 regulation. Subsequent biochemical examination revealed that kinesin-1, when not phosphorylated on JNK site, exhibits much higher affinity toward MTs. Expression of the JNK non-phosphorable kinesin-1 mutant in intact cells as well as in vitro single molecule imaging using total internal reflection fluorescence microscopy indicated that the mutant loses normal speed and is not able to move processively into proper cellular compartments. We identify novel kinesin-1 cargo protein STMN2/SCG10, which along with known kinesin-1 cargo BDNF is showing impaired trafficking when JNK activity is inhibited. Our data postulates that constitutive JNK activity in neurons is crucial for unperturbed physiologically relevant transport of kinesin-1 dependant cargo. Additionally, my work helps to validate another novel physiological JNK1 effector STMN2/SCG10 as determinant of axodendritic neurites dynamics in the developing brain through regulation of MT turnover. We show successively that this increased MT dynamics is crucial during developmental radial migration when brain layering occurs. Successively, we are able to show that introduction of JNK phosphorylation mimicking STMN2/SCG10 S62/73D mutant rescues completely JNK1 genetic deletion migration phenotype. We prove that STMN2/SCG10 is predominant JNK effector responsible for MT depolymerising activity and neurite length during brain development. Summarizing, this work describes identification of three novel JNK substrates MARCKSL1, kinesin-1 and STMN2/SCG10 and investigation of their roles in cytoskeleton dynamics and cargo transport. This data is of high importance to understand physiological meaning of JNK activity, which might have an adverse effect during pharmaceutical intervention aiming at blocking pathological JNK action.

Trypanosoma vivax infection dynamics in a cattle herd maintained in a transition area between Pantanal lowlands and highlands of Mato Grosso do Sul, Brazil

Trypanosoma vivax outbreaks in beef cattle in the Pantanal region of Mato Grosso do Sul state, Brazil, causes relevant economical impact due to weight loss, abortion and mortality. Cattle moved from the Pantanal to adjacent areas of this ecosystem for breeding and fattening is a common feature. Therefore an epidemiological study on breeding cows in the transition area between Pantanal lowland and adjacent highlands of Mato Grosso do Sul was performed to determine the T. vivax infection dynamics and outbreak risk. Three experimental groups were formed: Group 1 consisted of cows parasitologically negative by the Woo test and in the enzyme-linked immunosorbent assay for T. vivax antibody detection (Tv-ELISA-Ab); Group 2 parasitologically negative and positive in the Tv-ELISA-Ab; and in Group 3 cows were parasitologically positive and with positive reactions in the Tv-ELISA-Ab. During 24 months, the cows' dislodgment between the above established groups was monitored by Woo test and Tv-ELISA-Ab exams. The tabanid population was also monitored and the highest number occurred during the rainy season. Although parasitemias were detected only in the first four samplings of the experimental period, the cows could be considered as trypanotolerant, because no clinical signs were observed. Despite the higher T. vivax incidence during the dry season, no disease symptoms were seen. Even though T. vivax epidemiological situation in the herd was characterized as endemic with seasonal variation, the probability of outbreaks was null within the conditions of the study.

Detection and dynamics of porcine circovirus 2 shedding in semen using conventional and real-time PCR

The dynamics of porcine circovirus type 2 (PCV2) shedding in semen of naturally infected boars was studied. Semen was collected serially each 15 or 20 days during 62 days from 5 boars from a herd and from 11 boars from an artificial insemination center. All boars were positive for PCV2 DNA by nested polymerase chain reaction of raw semen in at least two sampling dates, and most of them had detectable shedding in all sampling dates. Real-time quantitative PCR was performed in 23 samples. All samples showed low amounts of PCV2 DNA, ranging from 98 to 652 PCV2 copies/mL. No differences between the frequencies of PCV2 DNA shed in semen were found considering herds and age of boars. PCV2 shedding in the semen can occur continuously or intermittently up to 60 days in naturally infected boars at 12 to 42 months old in absence of PCV2 clinical signs. These results demonstrate sporadic and long-term shedding patterns of low amounts of PCV2 DNA in semen from naturally infected boars.

A Soft Contact Collision Method For Real-Time Simulation of Triangularized Geometries in Multibody Dynamics

When modeling machines in their natural working environment collisions become a very important feature in terms of simulation accuracy. By expanding the simulation to include the operation environment, the need for a general collision model that is able to handle a wide variety of cases has become central in the development of simulation environments. With the addition of the operating environment the challenges for the collision modeling method also change. More simultaneous contacts with more objects occur in more complicated situations. This means that the real-time requirement becomes more difficult to meet. Common problems in current collision modeling methods include for example dependency on the geometry shape or mesh density, calculation need increasing exponentially in respect to the number of contacts, the lack of a proper friction model and failures due to certain configurations like closed kinematic loops. All these problems mean that the current modeling methods will fail in certain situations. A method that would not fail in any situation is not very realistic but improvements can be made over the current methods.

Non-Markovian dynamics and quantum information probes

This Thesis discusses the phenomenology of the dynamics of open quantum systems marked by non-Markovian memory effects. Non-Markovian open quantum systems are the focal point of a flurry of recent research aiming to answer, e.g., the following questions: What is the characteristic trait of non-Markovian dynamical processes that discriminates it from forgetful Markovian dynamics? What is the microscopic origin of memory in quantum dynamics, and how can it be controlled? Does the existence of memory effects open new avenues and enable accomplishments that cannot be achieved with Markovian processes? These questions are addressed in the publications forming the core of this Thesis with case studies of both prototypical and more exotic models of open quantum systems. In the first part of the Thesis several ways of characterizing and quantifying non-Markovian phenomena are introduced. Their differences are then explored using a driven, dissipative qubit model. The second part of the Thesis focuses on the dynamics of a purely dephasing qubit model, which is used to unveil the origin of non-Markovianity for a wide class of dynamical models. The emergence of memory is shown to be strongly intertwined with the structure of the spectral density function, as further demonstrated in a physical realization of the dephasing model using ultracold quantum gases. Finally, as an application of memory effects, it is shown that non- Markovian dynamical processes facilitate a novel phenomenon of timeinvariant discord, where the total quantum correlations of a system are frozen to their initial value. Non-Markovianity can also be exploited in the detection of phase transitions using quantum information probes, as shown using the physically interesting models of the Ising chain in a transverse field and a Coulomb chain undergoing a structural phase transition.