Adaptive Dynamics of Resource Specialization

Ecological specialization in resource utilization has various facades ranging from nutritional resources via host use of parasites or phytophagous insects to local adaptation in different habitats. Therefore, the evolution of specialization affects the evolution of most other traits, which makes it one of the core issues in the theory of evolution. Hence, the evolution of specialization has gained enormous amounts of research interest, starting already from Darwin’s Origin of species in 1859. Vast majority of the theoretical studies has, however, focused on the mathematically most simple case with well-mixed populations and equilibrium dynamics. This thesis explores the possibilities to extend the evolutionary analysis of resource usage to spatially heterogeneous metapopulation models and to models with non-equilibrium dynamics. These extensions are enabled by the recent advances in the field of adaptive dynamics, which allows for a mechanistic derivation of the invasion-fitness function based on the ecological dynamics. In the evolutionary analyses, special focus is set to the case with two substitutable renewable resources. In this case, the most striking questions are, whether a generalist species is able to coexist with the two specialist species, and can such trimorphic coexistence be attained through natural selection starting from a monomorphic population. This is shown possible both due to spatial heterogeneity and due to non-equilibrium dynamics. In addition, it is shown that chaotic dynamics may sometimes inflict evolutionary suicide or cyclic evolutionary dynamics. Moreover, the relations between various ecological parameters and evolutionary dynamics are investigated. Especially, the relation between specialization and dispersal propensity turns out to be counter-intuitively non-monotonous. This observation served as inspiration to the analysis of joint evolution of dispersal and specialization, which may provide the most natural explanation to the observed coexistence of specialist and generalist species.

Protein dynamics: hydration and cavities

The temperature-pressure behavior of proteins seems to be unique among the biological macromolecules. Thermodynamic as well as kinetic data show the typical elliptical stability diagram. This may be extended by assuming that the unfolded state gives rise to volume and enthalpy-driven liquid-liquid transitions. A molecular interpretation follows from the temperature and the pressure dependence of the hydration and cavities. We suggest that positron annihilation spectroscopy can provide additional quantitative evidence for the contributions of cavities to the dynamics of proteins. Only mature amyloid fibrils that form from unfolded proteins are very resistant to pressure treatment.

Modeling the pressure inactivation dynamics of Escherichia coli

Escherichia coli, as a model microorganism, was treated in phosphate-buffered saline under high hydrostatic pressure between 100 and 300 MPa, and the inactivation dynamics was investigated from the viewpoint of predictive microbiology. Inactivation data were curve fitted by typical predictive models: logistic, Gompertz and Weibull functions. Weibull function described the inactivation curve the best. Two parameters of Weibull function were calculated for each holding pressure and their dependence on holding pressure was obtained by interpolation. With the interpolated parameters, inactivation curves were simulated and compared with the experimental data sets.

Kalman filter for computational market dynamics

Kalman filter is a recursive mathematical power tool that plays an increasingly vital role in innumerable fields of study. The filter has been put to service in a multitude of studies involving both time series modelling and financial time series modelling. Modelling time series data in Computational Market Dynamics (CMD) can be accomplished using the Jablonska-Capasso-Morale (JCM) model. Maximum likelihood approach has always been utilised to estimate the parameters of the JCM model. The purpose of this study is to discover if the Kalman filter can be effectively utilized in CMD. Ensemble Kalman filter (EnKF), with 50 ensemble members, applied to US sugar prices spanning the period of January, 1960 to February, 2012 was employed for this work. The real data and Kalman filter trajectories showed no significant discrepancies, hence indicating satisfactory performance of the technique. Since only US sugar prices were utilized, it would be interesting to discover the nature of results if other data sets are employed.

Influence of He-Ne laser therapy on the dynamics of wound healing in mice treated with anti-inflammatory drugs

We determined the effects of helium-neon (He-Ne) laser irradiation on wound healing dynamics in mice treated with steroidal and non-steroidal anti-inflammatory agents. Male albino mice, 28-32 g, were randomized into 6 groups of 6 animals each: control (C), He-Ne laser (L), dexamethasone (D), D + L, celecoxib (X), and X + L. D and X were injected im at doses of 5 and 22 mg/kg, respectively, 24 h before the experiment. A 1-cm long surgical wound was made with a scalpel on the abdomens of the mice. Animals from groups L, D + L and X + L were exposed to 4 J (cm²)-1 day-1 of He-Ne laser for 12 s and were sacrificed on days 1, 2, or 3 after the procedure, when skin samples were taken for histological examination. A significant increase of collagen synthesis was observed in group L compared with C (168 ± 20 vs 63 ± 8 mm²). The basal cellularity values on day 1 were: C = 763 ± 47, L = 1116 ± 85, D = 376 ± 24, D + L = 698 ± 31, X = 453 ± 29, X + L = 639 ± 32 U/mm². These data show that application of L increases while D and X decrease the inflammatory cellularity compared with C. They also show that L restores the diminished cellularity induced by the anti-inflammatory drugs. We suggest that He-Ne laser promotes collagen formation and restores the baseline cellularity after pharmacological inhibition, indicating new perspectives for laser therapy aiming to increase the healing process when anti-inflammatory drugs are used.

Dynamics of immunosuppression in hamsters with experimental visceral leishmaniasis

Immunosuppression has been reported to occur during active visceral leishmaniasis and some factors such as the cytokine profile may be involved in this process. In the mouse model of cutaneous leishmaniasis using Leishmania (Leishmania) major, the Th1 response is related to protection while the Th2 response is related to disease progression. However, in hamsters, which are considered to be an excellent model for the study of visceral leishmaniasis, this dichotomy is not observed. Using outbred 45- to 60-day-old (140 to 150 g) male hamsters infected intraperitoneally with 2 x 10(7) L. (L.) chagasi amastigotes, we evaluated the immune response of spleen cells and the production of cytokines. We used 3 to 7 hamsters per group evaluated. We detected a preserved response to concanavalin A measured by index of proliferation during all periods of infection studied, while a proliferative response to Leishmania antigen was detected only at 48 and 72 h post-infection. Messenger RNA from cytokines type 1 (IL-2, TNF-α, IFN-γ) and type 2 (IL-4, IL-10 and TGF-β) detected by reverse transcriptase polymerase chain reaction and produced by spleen cells showed no qualitative difference between control non-infected hamsters and infected hamsters during any period of infection evaluated. Cytokines were measured by the DNA band intensity on agarose gel using the Image Lab 1D L340 software with no differences observed. In conclusion, the present results showed an antigen-dependent immunosuppression in hamsters with active visceral leishmaniasis that was not related to the cytokine profile.

Dynamics of chest wall volume regulation during constant work rate exercise in patients with chronic obstructive pulmonary disease

This study evaluated the dynamic behavior of total and compartmental chest wall volumes [(V CW) = rib cage (V RC) + abdomen (V AB)] as measured breath-by-breath by optoelectronic plethysmography during constant-load exercise in patients with stable chronic obstructive pulmonary disease. Thirty males (GOLD stages II-III) underwent a cardiopulmonary exercise test to the limit of tolerance (Tlim) at 75% of peak work rate on an electronically braked cycle ergometer. Exercise-induced dynamic hyperinflation was considered to be present when end-expiratory (EE) V CW increased in relation to resting values. There was a noticeable heterogeneity in the patterns of V CW regulation as EEV CW increased non-linearly in 17/30 "hyperinflators" and decreased in 13/30 "non-hyperinflators" (P < 0.05). EEV AB decreased slightly in 8 of the "hyperinflators", thereby reducing and slowing the rate of increase in end-inspiratory (EI) V CW (P < 0.05). In contrast, decreases in EEV CW in the "non-hyperinflators" were due to the combination of stable EEV RC with marked reductions in EEV AB. These patients showed lower EIV CW and end-exercise dyspnea scores but longer Tlim than their counterparts (P < 0.05). Dyspnea increased and Tlim decreased non-linearly with a faster rate of increase in EIV CW regardless of the presence or absence of dynamic hyperinflation (P < 0.001). However, no significant between-group differences were observed in metabolic, pulmonary gas exchange and cardiovascular responses to exercise. Chest wall volumes are continuously regulated during exercise in order to postpone (or even avoid) their migration to higher operating volumes in patients with COPD, a dynamic process that is strongly dependent on the behavior of the abdominal compartment.

Structural dynamics in the global pulp and paper industry

The pulp and paper industry is currently facing broad structural changes due to global shifts in demand and supply. These changes have significant impacts on national economies worldwide. Planted forests (especially eucalyptus) and recovered paper have quickly increased their importance as raw material for paper and paperboard production. Although advances in information and communication technologies could reduce the demand for communication papers, and the growth of paper consumption has indeed flattened in developed economies, particularly in North America and Western Europe, the consumption is increasing on a global scale. Moreover, the focal point of production and consumption is moving from the Western world to the rapidly growing markets of Southeast Asia. This study analyzes how the so-called megatrends (globalization, technological development, and increasing environmental awareness) affect the pulp and paper industry’s external environment, and seeks reliable ways to incorporate the impact of the megatrends on the models concerning the demand, trade, and use of paper and pulp. The study expands current research in several directions and points of view, for example, by applying and incorporating several quantitative methods and different models. As a result, the thesis makes a significant contribution to better understand and measure the impacts of structural changes on the pulp and paper industry. It also provides some managerial and policy implications.

Non-Markovian dynamics in quantum optical dephasing channels

Quantum computation and quantum communication are two of the most promising future applications of quantum mechanics. Since the information carriers used in both of them are essentially open quantum systems it is necessary to understand both quantum information theory and the theory of open quantum systems in order to investigate realistic implementations of such quantum technologies. In this thesis we consider the theory of open quantum systems from a quantum information theory perspective. The thesis is divided into two parts: review of the literature and original research. In the review of literature we present some important definitions and known results of open quantum systems and quantum information theory. We present the definitions of trace distance, two channel capacities and superdense coding capacity and give a reasoning why they can be used to represent the transmission efficiency of a communication channel. We also show derivations of some properties useful to link completely positive and trace preserving maps to trace distance and channel capacities. With the help of these properties we construct three measures of non-Markovianity and explain why they detect non-Markovianity. In the original research part of the thesis we study the non-Markovian dynamics in an experimentally realized quantum optical set-up. For general one-qubit dephasing channels we calculate the explicit forms of the two channel capacities and the superdense coding capacity. For the general two-qubit dephasing channel with uncorrelated local noises we calculate the explicit forms of the quantum capacity and the mutual information of a four-letter encoding. By using the dynamics in the experimental implementation as a set of specific dephasing channels we also calculate and compare the measures in one- and two-qubit dephasing channels and study the options of manipulating the environment to achieve revivals and higher transmission rates in superdense coding protocol with dephasing noise. Kvanttilaskenta ja kvanttikommunikaatio ovat kaksi puhutuimmista tulevaisuuden kvanttimekaniikan käytännön sovelluksista. Koska molemmissa näistä informaatio koodataan systeemeihin, jotka ovat oleellisesti avoimia kvanttisysteemejä, sekä kvantti-informaatioteorian, että avointen kvanttisysteemien tuntemus on välttämätöntä. Tässä tutkielmassa käsittelemme avointen kvanttisysteemien teoriaa kvantti-informaatioteorian näkökulmasta. Tutkielma on jaettu kahteen osioon: kirjallisuuskatsaukseen ja omaan tutkimukseen. Kirjallisuuskatsauksessa esitämme joitakin avointen kvanttisysteemien ja kvantti-informaatioteorian tärkeitä määritelmiä ja tunnettuja tuloksia. Esitämme jälkietäisyyden, kahden kanavakapasiteetin ja superdense coding -kapasiteetin määritelmät ja esitämme perustelun sille, miksi niitä voidaan käyttää kuvaamaan kommunikointikanavan lähetystehokkuutta. Näytämme myös todistukset kahdelle ominaisuudelle, jotka liittävät täyspositiiviset ja jäljensäilyttävät kuvaukset jälkietäisyyteen ja kanavakapasiteetteihin. Näiden ominaisuuksien avulla konstruoimme kolme epä-Markovisuusmittaa ja perustelemme, miksi ne havaitsevat dynamiikan epä-Markovisuutta. Oman tutkimuksen osiossa tutkimme epä-Markovista dynamiikkaa kokeellisesti toteutetussa kvanttioptisessa mittausjärjestelyssä. Yleisen yhden qubitin dephasing-kanavan tapauksessa laskemme molempien kanavakapasiteettien ja superdense coding -kapasiteetin eksplisiittiset muodot. Yleisen kahden qubitin korreloimattomien ympäristöjen dephasing-kanavan tapauksessa laskemme yhteisen informaation lausekkeen nelikirjaimisessa koodauksessa ja kvanttikanavakapasiteetin. Käyttämällä kokeellisen mittajärjestelyn dynamiikkoja esimerkki dephasing-kanavina me myös laskemme konstruoitujen epä-Markovisuusmittojen arvot ja vertailemme niitä yksi- ja kaksi-qubitti-dephasing-kanavissa. Lisäksi käyttäen kokeellisia esimerkkikanavia tutkimme, kuinka ympäristöä manipuloimalla superdense coding –skeemassa voidaan saada yhteinen informaatio ajoittain kasvamaan tai saavuttaa kaikenkaikkiaan korkeampi lähetystehokkuus.

Determining vehicle drivetrain dynamics using system identification

Target of this book is to propose an approach for modelling drivetrain dynamics in order to design further a vibration control system of a hybrid bus. In this thesis two approaches are examined and compared. First model is obtained by theoretical means: drivetrain is represented as a system of rotating masses, which motion is described with differential equations. Second model is obtained using system identification method: mathematical description of the dynamic behavior of a system is formed based on measured input (torque) and output (speed) data. Then two models are compared and an optimal approach is suggested.

Using Computational Fluid-Dynamics (CFD) for the evaluation of beer pasteurization: effect of orientation of cans

In-package pasteurization is the most used method for beer microbiological stabilization. The search for safer and better quality food has created a need to better understand the processes involved in producing it. However, little is known about the temperature and velocity profiles during the thermal processes of liquid foods in commercial packaging, which results in over-dimensioned processes to guarantee safety, decreasing the sensorial and nutritional characteristics of the product and increasing process costs. Simulations using Computational Fluid-Dynamics (CFD) have been used by various authors to evaluate those processes. The objective of the present paper was to evaluate the effect of packaging orientation in the pasteurization of beer in a commercial aluminum can using CFD. A heating process was simulated at 60 ºC up to 15 PUs (a conventional beer process, in which 1 Pasteurization Unit (PU) is equivalent to 1minute at 60 ºC). The temperature profile and convection current velocity along the process and the variation of the PUs were evaluated in relation to time considering the cans in the conventional, inverted, and horizontal positions. The temperature and velocity profiles were similar to those presented in the literature. The package position did not result in process improvement.

Computational fluid dynamics evaluation of liquid food thermal process in a brick shaped package

Food processes must ensure safety and high-quality products for a growing demand consumer creating the need for better knowledge of its unit operations. The Computational Fluid Dynamics (CFD) has been widely used for better understanding the food thermal processes, and it is one of the safest and most frequently used methods for food preservation. However, there is no single study in the literature describing thermal process of liquid foods in a brick shaped package. The present study evaluated such process and the influence of its orientation on the process lethality. It demonstrated the potential of using CFD to evaluate thermal processes of liquid foods and the importance of rheological characterization and convection in thermal processing of liquid foods. It also showed that packaging orientation does not result in different sterilization values during thermal process of the evaluated fluids in the brick shaped package.

Dynamics of gas levels inside packages containing minimally processed Pera orange

The purpose of this study was to evaluate the changes in concentrations of O2 and CO2 inside packages of minimally processed Pera orange. Previously selected oranges that were washed, sanitized, and chilled were peeled using hydrothermal treatment (immersion of fruits in water at 50 °C for 8 minutes). The peeled oranges were then packed in five different plastic packages under passive and active modified atmosphere (5% O2 + 10% CO2 + 85% N2). The fruits were stored at 6 °C and 12 °C. The package headspace gas composition was evaluated for twelve days at 6 °C and nine days at 12 °C. The polypropylene film (32 µm) promoted modified atmosphere similar to that initially injected (5% O2 + 10% CO2 + 85% N2) at 6 °C and 12 °C. With regard to the atmosphere modification system, the injection of a gas mixture anticipated achieving an equilibrium atmosphere inside the packages at 12 °C. At 6 °C, the gas composition inside the packages was kept close to that of the injection, but the equilibrium was not verified.

Analysis of Phase Separator Design Criteria Using Computational Fluid Dynamics

Gravitational phase separation is a common unit operation found in most large-scale chemical processes. The need for phase separation can arise e.g. from product purification or protection of downstream equipment. In gravitational phase separation, the phases separate without the application of an external force. This is achieved in vessels where the flow velocity is lowered substantially compared to pipe flow. If the velocity is low enough, the denser phase settles towards the bottom of the vessel while the lighter phase rises. To find optimal configurations for gravitational phase separator vessels, several different geometrical and internal design features were evaluated based on simulations using OpenFOAM computational fluid dynamics (CFD) software. The studied features included inlet distributors, vessel dimensions, demister configurations and gas phase outlet configurations. Simulations were conducted as single phase steady state calculations. For comparison, additional simulations were performed as dynamic single and two-phase calculations. The steady state single phase calculations provided indications on preferred configurations for most above mentioned features. The results of the dynamic simulations supported the utilization of the computationally faster steady state model as a practical engineering tool. However, the two-phase model provides more truthful results especially with flows where a single phase does not determine the flow characteristics.

Effect of incorporation of nutraceutical capsule waste of safflower oil in the mechanical characteristics of corn starch films

Abstract Biodegradable films blends made of safflower oil nutraceutical capsules waste corn starch (20:4, 30:4, 40:4 and 50:4) were prepared. The objective of this study was to evaluate the influence of addition of different concentrations of safflower oil nutraceutical capsule waste in the mechanical properties (tensile strength, elongation at break, Young’s modulus) and thickness of corn starch films. A decrease in tensile strength and Young’s modulus and an increase in elongation at break were observed with the increase in the content of the nutraceutical capsule waste. The results showed that the blends of safflower oil capsules waste-corn starch films demonstrated promising characteristics to form biodegradable films with different mechanical characteristics.