Towards input/output-free modelling of linear infinite-dimensional systems in continuous time

This dissertation describes a networking approach to infinite-dimensional systems theory, where there is a minimal distinction between inputs and outputs. We introduce and study two closely related classes of systems, namely the state/signal systems and the port-Hamiltonian systems, and describe how they relate to each other. Some basic theory for these two classes of systems and the interconnections of such systems is provided. The main emphasis lies on passive and conservative systems, and the theoretical concepts are illustrated using the example of a lossless transfer line. Much remains to be done in this field and we point to some directions for future studies as well.

Frequency-Domain and Wide-Pulse Time-Domain Measurements of Lanthanide Luminescence and Lanthanide-Based Resonance Energy Transfer

Resonance energy transfer (RET) is a non-radiative transfer of the excitation energy from the initially excited luminescent donor to an acceptor. The requirements for the resonance energy transfer are: i) the spectral overlap between the donor emission spectrum and the acceptor absorption spectrum, ii) the close proximity of the donor and the acceptor, and iii) the suitable relative orientations of the donor emission and the acceptor absorption transition dipoles. As a result of the RET process the donor luminescence intensity and the donor lifetime are decreased. If the acceptor is luminescent, a sensitized acceptor emission appears. The rate of RET depends strongly on the donor–acceptor distance (r) and is inversely proportional to r6. The distance dependence of RET is utilized in binding assays. The proximity requirement and the selective detection of the RET-modified emission signal allow homogeneous separation free assays. The term lanthanide-based RET is used when luminescent lanthanide compounds are used as donors. The long luminescence lifetimes, the large Stokes’ shifts and the intense, sharply-spiked emission spectra of the lanthanide donors offer advantages over the conventional organic donor molecules. Both the organic lanthanide chelates and the inorganic up-converting phosphor (UCP) particles have been used as donor labels in the RET based binding assays. In the present work lanthanide luminescence and lanthanide-based resonance energy transfer phenomena were studied. Luminescence lifetime measurements had an essential role in the research. Modular frequency-domain and time-domain luminometers were assembled and used successfully in the lifetime measurements. The frequency-domain luminometer operated in the low frequency domain ( 100 kHz) and utilized a novel dual-phase lock-in detection of the luminescence. One of the studied phenomena was the recently discovered non-overlapping fluorescence resonance energy transfer (nFRET). The studied properties were the distance and temperature dependences of nFRET. The distance dependence was found to deviate from the Förster theory and a clear temperature dependence was observed whereas conventional RET was completely independent of the temperature. Based on the experimental results two thermally activated mechanisms were proposed for the nFRET process. The work with the UCP particles involved the measurement of the luminescence properties of the UCP particles synthesized in our laboratory. The goal of the UCP particle research is to develop UCP donor labels for binding assays. In the present work the effect of the dopant concentrations and the core–shell structure on the total up-conversion luminescence intensity, the red–green emission ratio, and the luminescence lifetime was studied. Also the non-radiative nature of the energy transfer from the UCP particle donors to organic acceptors was demonstrated for the first time in aqueous environment and with a controlled donor–acceptor distance.

Detection of Pathologic Changes Following Traumatic Brain Injury Using Magnetic Resonance Imaging

Background: Approximately two percent of Finns have sequels after traumatic brain injury (TBI), and many TBI patients are young or middle-aged. The high rate of unemployment after TBI has major economic consequences for society, and traumatic brain injury often has remarkable personal consequences, as well. Structural imaging is often needed to support the clinical TBI diagnosis. Accurate early diagnosis is essential for successful rehabilition and, thus, may also influence the patient’s outcome. Traumatic axonal injury and cortical contusions constitute the majority of traumatic brain lesions. Several studies have shown magnetic resonance imaging (MRI) to be superior to computed tomography (CT) in the detection of these lesions. However, traumatic brain injury often leads to persistent symptoms even in cases with few or no findings in conventional MRI. Aims and methods: The aim of this prospective study was to clarify the role of conventional MRI in the imaging of traumatic brain injury, and to investigate how to improve the radiologic diagnostics of TBI by using more modern diffusion-weighted imaging (DWI) and diffusion tensor imaging (DTI) techniques. We estimated, in a longitudinal study, the visibility of the contusions and other intraparenchymal lesions in conventional MRI at one week and one year after TBI. We used DWI-based measurements to look for changes in the diffusivity of the normal-appearing brain in a case-control study. DTI-based tractography was used in a case-control study to evaluate changes in the volume, diffusivity, and anisotropy of the long association tracts in symptomatic TBI patients with no visible signs of intracranial or intraparenchymal abnormalities on routine MRI. We further studied the reproducibility of different tools to identify and measure white-matter tracts by using a DTI sequence suitable for clinical protocols. Results: Both the number and extent of visible traumatic lesions on conventional MRI diminished significantly with time. Slightly increased diffusion in the normal-appearing brain was a common finding at one week after TBI, but it was not significantly associated with the injury severity. Fractional anisotropy values, that represent the integrity of the white-matter tracts, were significantly diminished in several tracts in TBI patients compared to the control subjects. Compared to the cross-sectional ROI method, the tract-based analyses had better reproducibility to identify and measure white-matter tracts of interest by means of DTI tractography. Conclusions: As conventional MRI is still applied in clinical practice, it should be carried out soon after the injury, at least in symptomatic patients with negative CT scan. DWI-related brain diffusivity measurements may be used to improve the documenting of TBI. DTI tractography can be used to improve radiologic diagnostics in a symptomatic TBI sub-population with no findings on conventional MRI. Reproducibility of different tools to quantify fibre tracts vary considerably, which should be taken into consideration in the clinical DTI applications.

Homogeneous assay technologies in drug screening: Quenching Resonance Energy Transfer (QRET) technique

Information gained from the human genome project and improvements in compound synthesizing have increased the number of both therapeutic targets and potential lead compounds. This has evolved a need for better screening techniques to have a capacity to screen number of compound libraries against increasing amount of targets. Radioactivity based assays have been traditionally used in drug screening but the fluorescence based assays have become more popular in high throughput screening (HTS) as they avoid safety and waste problems confronted with radioactivity. In comparison to conventional fluorescence more sensitive detection is obtained with time-resolved luminescence which has increased the popularity of time-resolved fluorescence resonance energy transfer (TR-FRET) based assays. To simplify the current TR-FRET based assay concept the luminometric homogeneous single-label utilizing assay technique, Quenching Resonance Energy Transfer (QRET), was developed. The technique utilizes soluble quencher to quench non-specifically the signal of unbound fraction of lanthanide labeled ligand. One labeling procedure and fewer manipulation steps in the assay concept are saving resources. The QRET technique is suitable for both biochemical and cell-based assays as indicated in four studies:1) ligand screening study of β2 -adrenergic receptor (cell-based), 2) activation study of Gs-/Gi-protein coupled receptors by measuring intracellular concentration of cyclic adenosine monophosphate (cell-based), 3) activation study of G-protein coupled receptors by observing the binding of guanosine-5’-triphosphate (cell membranes), and 4) activation study of small GTP binding protein Ras (biochemical). Signal-to-background ratios were between 2.4 to 10 and coefficient of variation varied from 0.5 to 17% indicating their suitability to HTS use.

Acceleration of Solar Energetic Particles in coronal shocks through self-generated turbulence

The acceleration of solar energetic particles (SEPs) by flares and coronal mass ejections (CMEs) has been a major topic of research for the solar-terrestrial physics and geophysics communities for decades. This thesis discusses theories describing first-order Fermi acceleration of SEPs through repeated crossings at a CME-driven shock. We propose that particle trapping occurs through self-generated Alfvén waves, leading to a turbulent trapping region in front of the shock. Decelerating coronal shocks are shown to be capable of efficient SEP acceleration, provided seed particle injection is sufficient. Quasi-parallel shocks are found to inject thermal particles with good efficiency. The roles of minimum injection velocities, cross-field diffusion, downstream scattering efficiency and cross-shock potential are investigated in detail, with downstream isotropisation timescales having a major effect on injection efficiency. Accelerated spectra of heavier elements up to iron are found to exhibit significantly harder spectra than protons. Accelerated spectra cut-off energies are found to scale proportional to (Q/A)^1.5, which is explained through analysis of the spectral shape of amplified Alfvénic turbulence. Acceleration times to different threshold energies are found to be non-linear, indicating that self-consistent time-dependent simulations are required in order to expose the full extent of acceleration dynamics. The well-established quasilinear theory (QLT) of particle scattering is investigated by comparing QLT scattering coefficients with those found via full-orbit simulations. QLT is found to overemphasise resonance conditions. This finding supports the simplifications implemented in the presented coronal shock acceleration (CSA) simulation software. The CSA software package is used to simulate a range of acceleration scenarios. The results are found to be in agreement with well-established particle acceleration theory. At the same time, new spatial and temporal dynamics of particle population trapping and wave evolution are revealed.

Linear prediction in optical spectroscopy

A linear prediction procedure is one of the approved numerical methods of signal processing. In the field of optical spectroscopy it is used mainly for extrapolation known parts of an optical signal in order to obtain a longer one or deduce missing signal samples. The first is needed particularly when narrowing spectral lines for the purpose of spectral information extraction. In the present paper the coherent anti-Stokes Raman scattering (CARS) spectra were under investigation. The spectra were significantly distorted by the presence of nonlinear nonresonant background. In addition, line shapes were far from Gaussian/Lorentz profiles. To overcome these disadvantages the maximum entropy method (MEM) for phase spectrum retrieval was used. The obtained broad MEM spectra were further underwent the linear prediction analysis in order to be narrowed.

Quantitative Magnetic Resonance Imaging of the Liver and Heart In Iron Overload

Systemic iron overload (IO) is considered a principal determinant in the clinical outcome of different forms of IO and in allogeneic hematopoietic stem cell transplantation (alloSCT). However, indirect markers for iron do not provide exact quantification of iron burden, and the evidence of iron-induced adverse effects in hematological diseases has not been established. Hepatic iron concentration (HIC) has been found to represent systemic IO, which can be quantified safely with magnetic resonance imaging (MRI), based on enhanced transverse relaxation. The iron measurement methods by MRI are evolving. The aims of this study were to implement and optimise the methodology of non-invasive iron measurement with MRI to assess the degree and the role of IO in the patients. An MRI-based HIC method (M-HIC) and a transverse relaxation rate (R2*) from M-HIC images were validated. Thereafter, a transverse relaxation rate (R2) from spin-echo imaging was calibrated for IO assessment. Two analysis methods, visual grading and rSI, for a rapid IO grading from in-phase and out-of-phase images were introduced. Additionally, clinical iron indicators were evaluated. The degree of hepatic and cardiac iron in our study patients and IO as a prognostic factor in patients undergoing alloSCT were explored. In vivo and in vitro validations indicated that M-HIC and R2* are both accurate in the quantification of liver iron. R2 was a reliable method for HIC quantification and covered a wider HIC range than M-HIC and R2*. The grading of IO was able to be performed rapidly with the visual grading and rSI methods. Transfusion load was more accurate than plasma ferritin in predicting transfusional IO. In patients with hematological disorders, the prevalence of hepatic IO was frequent, opposite to cardiac IO. Patients with myelodysplastic syndrome were found to be the most susceptible to IO. Pre-transplant IO predicted severe infections during the early post-transplant period, in contrast to the reduced risk of graft-versus-host disease. Iron-induced, poor transplantation results are most likely to be mediated by severe infections.

Comparison of Different Concentrated Solar Power Collector Designs and Development of a Linear Fresnel Solar Collector Model

Concentrated solar power (CSP) is a renewable energy technology, which could contribute to overcoming global problems related to pollution emissions and increasing energy demand. CSP utilizes solar irradiation, which is a variable source of energy. In order to utilize CSP technology in energy production and reliably operate a solar field including thermal energy storage system, dynamic simulation tools are needed in order to study the dynamics of the solar field, to optimize production and develop control systems. The object of this Master’s Thesis is to compare different concentrated solar power technologies and configure a dynamic solar field model of one selected CSP field design in the dynamic simulation program Apros, owned by VTT and Fortum. The configured model is based on German Novatec Solar’s linear Fresnel reflector design. Solar collector components including dimensions and performance calculation were developed, as well as a simple solar field control system. The preliminary simulation results of two simulation cases under clear sky conditions were good; the desired and stable superheated steam conditions were maintained in both cases, while, as expected, the amount of steam produced was reduced in the case having lower irradiation conditions. As a result of the model development process, it can be concluded, that the configured model is working successfully and that Apros is a very capable and flexible tool for configuring new solar field models and control systems and simulating solar field dynamic behaviour.

From Unspecific Quenching to Specific Signaling: Functional GTPase Assays Utilizing Quenching Resonance Energy Transfer (QRET) Technology

The aim of the work presented in this study was to demonstrate the wide applicability of a single-label quenching resonance energy transfer (QRET) assay based on time-resolved lanthanide luminescence. QRET technology is proximity dependent method utilizing weak and unspecific interaction between soluble quencher molecule and lanthanide chelate. The interaction between quencher and chelate is lost when the ligand binds to its target molecule. The properties of QRET technology are especially useful in high throughput screening (HTS) assays. At the beginning of this study, only end-point type QRET technology was available. To enable efficient study of enzymatic reactions, the QRET technology was further developed to enable measurement of reaction kinetics. This was performed using proteindeoxyribonuclei acid (DNA) interaction as a first tool to monitor reaction kinetics. Later, the QRET was used to study nucleotide exchange reaction kinetics and mutation induced effects to the small GTPase activity. Small GTPases act as a molecular switch shifting between active GTP bound and inactive GDP bound conformation. The possibility of monitoring reaction kinetics using the QRET technology was evaluated using two homogeneous assays: a direct growth factor detection assay and a nucleotide exchange monitoring assay with small GTPases. To complete the list, a heterogeneous assay for monitoring GTP hydrolysis using small GTPases, was developed. All these small GTPase assays could be performed using nanomolar protein concentrations without GTPase pretreatment. The results from these studies demonstrated that QRET technology can be used to monitor reaction kinetics and further enable the possibility to use the same method for screening.

Modification of commercial poly-lactide for extrusion coated food packaging applications

Poly-L-lactide (PLLA) is a widely used sustainable and biodegradable alternative to replace synthetic non-degradable plastic materials in the packaging industry. Conversely, its processing properties are not always optimal, e.g. insufficient melt strength at higher temperatures (necessary in extrusion coating processes). This thesis reports on research to improve properties of commercial PLLA grade (3051D from NatureWorks), to satisfy and extend end-use applications, such as food packaging by blending with modified PLLA. Adjustment of the processability by chain branching of commercial poly-L-lactide initiated by peroxide was evaluated. Several well-defined branched structures with four arms (sPLLA) were synthesized using pentaerythritol as a tetra-functional initiator. Finally, several block copolymers consisting of polyethylene glycol and PLLA (i.e. PEGLA) were produced to obtain a well extruded material with improved heat sealing properties. Reactive extrusion of poly-L-lactide was carried out in the presence of 0.1, 0.3 and 0.5 wt% of various peroxides [tert-butyl-peroxybenzoate (TBPB), 2,5-dimethyl-2,5-(tert-butylperoxy)-hexane (Lupersol 101; LOL1) and benzoyl peroxide (BPO)] at 190C. The peroxide-treated PLLAs showed increased complex viscosity and storage modulus at lower frequencies, indicating the formation of branched/cross linked architectures. The material property changes were dependent on the peroxide, and the used peroxide concentration. Gel fraction analysis showed that the peroxides, afforded different gel contents, and especially 0.5 wt% peroxide, produced both an extremely high molar mass, and a cross linked structure, not perhaps well suited for e.g. further use in a blending step. The thermal behavior was somewhat unexpected as the materials prepared with 0.5 wt% peroxide showed the highest ability for crystallization and cold crystallization, despite substantial cross linking. The peroxide-modified PLLA, i.e. PLLA melt extruded with 0.3 wt% of TBPB and LOL1 and 0.5 wt% BPO was added to linear PLLA in ratios of 5, 15 and 30 wt%. All blends showed increased zero shear viscosity, elastic nature (storage modulus) and shear sensitivity. All blends remained amorphous, though the ability of annealing was improved slightly. Extrusion coating on paperboard was conducted with PLLA, and peroxide-modified PLLA blends (90:10). All blends were processable, but only PLLA with 0.3 wt% of LOL1 afforded a smooth high quality surface with improved line speed. Adhesion levels between fiber and plastic, as well as heat seal performance were marginally reduced compared with pure 3051D. The water vapor transmission measurements (WVTR) of the blends containing LOL1 showed acceptable levels, only slightly lower than for comparable PLLA 3051D. A series of four-arm star-shaped poly-L-lactide (sPLLA) with different branch length was synthesized by ring opening polymerization (ROP) of L-lactide using pentaerythritol as initiator and stannous octoate as catalyst. The star-shaped polymers were further blended with its linear resin and studied for their melt flow and thermal properties. Blends containing 30 wt% of sPLLA with low molecular weight (30 wt%; Mwtotal: 2500 g mol-1 and 15000 g mol-1) showed lower zero shear viscosity and significantly increased shear thinning, while at the same time slightly increased crystallization of the blend. However, the amount of crystallization increased significantly with the higher molecular weight sPLLA, therefore the star-shaped structure may play a role as nucleating agent. PLLA-polyethylene glycol–PLLA triblock copolymers (PEGLA) with different PLLA block length were synthesized and their applicability as blends with linear PLLA (3051D NatureWorks) was investigated with the intention of improving heat-seal and adhesion properties of extrusion-coated paperboard. PLLA-PEG-PLLA was obtained by ring opening polymerization (ROP) of L-lactide using PEG (molecular weight 6000 g mol-1) as an initiator, and stannous octoate as catalyst. The structures of the PEGLAs were characterized by proton nuclear magnetic resonance spectroscopy (1H-NMR). The melt flow and thermal properties of all PEGLAs and their blends were evaluated using dynamic rheology, and differential scanning calorimeter (DSC). All blends containing 30 wt% of PEGLAs showed slightly higher zero shear viscosity, higher shear thinning and increased melt elasticity (based on tan delta). Nevertheless, no significant changes in thermal properties were distinguished. High molecular weight PEGLAs were used in extrusion coating line with 3051D without problems.

The solutions and tunneling properties for a linear potential and an inverted harmonic oscillator in an infinite well

In this work we look at two different 1-dimensional quantum systems. The potentials for these systems are a linear potential in an infinite well and an inverted harmonic oscillator in an infinite well. We will solve the Schrödinger equation for both of these systems and get the energy eigenvalues and eigenfunctions. The solutions are obtained by using the boundary conditions and numerical methods. The motivation for our study comes from experimental background. For the linear potential we have two different boundary conditions. The first one is the so called normal boundary condition in which the wave function goes to zero on the edge of the well. The second condition is called derivative boundary condition in which the derivative of the wave function goes to zero on the edge of the well. The actual solutions are Airy functions. In the case of the inverted oscillator the solutions are parabolic cylinder functions and they are solved only using the normal boundary condition. Both of the potentials are compared with the particle in a box solutions. We will also present figures and tables from which we can see how the solutions look like. The similarities and differences with the particle in a box solution are also shown visually. The figures and calculations are done using mathematical software. We will also compare the linear potential to a case where the infinite wall is only on the left side. For this case we will also show graphical information of the different properties. With the inverted harmonic oscillator we will take a closer look at the quantum mechanical tunneling. We present some of the history of the quantum tunneling theory, its developers and finally we show the Feynman path integral theory. This theory enables us to get the instanton solutions. The instanton solutions are a way to look at the tunneling properties of the quantum system. The results are compared with the solutions of the double-well potential which is very similar to our case as a quantum system. The solutions are obtained using the same methods which makes the comparison relatively easy. All in all we consider and go through some of the stages of the quantum theory. We also look at the different ways to interpret the theory. We also present the special functions that are needed in our solutions, and look at the properties and different relations to other special functions. It is essential to notice that it is possible to use different mathematical formalisms to get the desired result. The quantum theory has been built for over one hundred years and it has different approaches. Different aspects make it possible to look at different things.