Dynamical and structural properties of dendrimer macromolecules

This work is devoted to the study of the dynamical and structural properties of dendrimers. Different approaches were used: analytical theory, computer simulation results and experimental NMR studies. The theory of the relaxation spectrum of dendrimer macromolecules was developed. Relaxation processes which are manifest in the local orientational mobility of dendrimer macromolecules were established and studied in detail. Theoretical results and conclusions were used for experimental studies of carbosilane dendimers.

The Structural Basis for inorganic Pyrophosphatase Catalysis and Regulation

Inorganic pyrophosphatases (PPases) are essential enzymes for every living cell. PPases provide the necessary thermodynamic pull for many biosynthetic reactions by hydrolyzing pyrophosphate. There are two types of PPases: integral membrane-bound and soluble enzymes. The latter type is divided into two non-homologous protein families, I and II. Family I PPases are present in all kingdoms of life, whereas family II PPases are only found in prokaryotes, including archae. Family I PPases, particularly that from Saccharomyces cerevisiae, are among the most extensively characterized phosphoryl transfer enzymes. In the present study, we have solved the structures of wild-type and seven active site variants of S. cerevisiae PPase bound to its natural metal cofactor, magnesium ion. These structures have facilitated derivation of the complete enzyme reaction scheme for PPase, fulfilling structures of all the reaction intermediates. The main focus in this study was on a novel subfamily of family II PPases (CBSPPase) containing a large insert formed by two CBS domains and a DRTGG domain within the catalytic domain. The CBS domain (named after cystathionine beta-synthase in which it was initially identified) usually occurs as tandem pairs with two or four copies in many proteins in all kingdoms of life. The structure formed by a pair of CBS domains is also known as a Bateman domain. CBS domains function as regulatory units, with adenylate ligands as the main effectors. The DRTGG domain (designated based on its most conserved residues) occurs less frequently and only in prokaryotes. Often, the domain co-exists with CBS domains, but its function remains unknown. The key objective of the current study was to explore the structural rearrangements in the CBS domains induced by regulatory adenylate ligands and their functional consequences. Two CBS-PPases were investigated, one from Clostridium perfringens (cpCBS-PPase) containing both CBS and DRTGG domains in its regulatory region and the other from Moorella thermoacetica (mt CBS-PPase) lacking the DRTGG domain. We additionally constructed a separate regulatory region of cpCBS-PPase (cpCBS). Both full-length enzymes and cpCBS formed homodimers. Two structures of the regulatory region of cpCBS-PPase complexed with the inhibitor, AMP, and activator, diadenosine tetraphosphate, were solved. The structures were significantly different, providing information on the structural pathway from bound adenylates to the interface between the regulatory and catalytic parts. To our knowledge, these are the first reported structures of a regulated CBS enzyme, which reveal large conformational changes upon regulator binding. The activator-bound structure was more open, consistent with the different thermostabilities of the activator- and inhibitor-bound forms of cpCBS-PPase. The results of the functional studies on wild-type and variant CBS-PPases provide support for inferences made on the basis of structural analyses. Moreover, these findings indicate that CBS-PPase activity is highly sensitive to adenine nucleotide distribution between AMP, ADP and ATP, and hence to the energy level of the cell. CBS-PPase activity is markedly inhibited at low energy levels, allowing PPi energy to be used for cell survival instead of being converted into heat.

Environmental inFluences on the Adoption of Open Innovation: Analysis of Structural, Institutional and Cultural Impacts

The concept of open innovation has recently gained widespread attention, and is particularly relevant now as many firms endeavouring to implement open innovation, face different sets of challenges associated with managing it. Prior research on open innovation has focused on the internal processes dealing with open innovation implementation and the organizational changes, already taking place or yet required in companies order to succeed in the global open innovation market. Despite the intensive research on open innovation, the question of what influences its adoption by companies in different contexts has not received much attention in studies. To fill this gap, this thesis contribute to the discussion on open innovation influencing factors by bringing in the perspective of environmental impacts, i.e. gathering data on possible sources of external influences, classifying them and testing their systemic impact through conceptual system dynamics simulation model. The insights from data collection and conceptualization in modelling are used to answer the question of how the external environment affects the adoption of open innovation. The thesis research is presented through five research papers reflecting the method triangulation based study (conducted at initial stage as case study, later as quantitative analysis and finally as system dynamics simulation). This multitude of methods was used to collect the possible external influence factors and to assess their impact (on positive/negative scale rather than numerical). The results obtained throughout the thesis research bring valuable insights into understanding of open innovation influencing factors inside a firm’s operating environment, point out the balance required in the system for successful open innovation performance and discover the existence of tipping point of open innovation success when driven by market dynamics and structures. The practical implications on how firms and policy-makers can leverage environment for their potential benefits are offered in the conclusions.

Structural aspects and floristic similarity among tropical dry forest fragments with different management histories in northern Minas Gerais, Brazil

In order to produce useful knowledge to the initiatives of protection and management of forest fragments, more specifically for tropical dry forests which suffer with frequent anthropic activities, and due to the lack of specific studies, this article aimed describe the structure and the floristic similarity among three areas of dry forest with different management histories. The study was developed in Capitão Enéas municipality, Northern Minas Gerais, Brazil, where three fragments were evaluated, being one in regeneration for 30 years, another submitted to occasional fire and the third with selective cut in small scale. The sampling was developed through the point quarter method considering all the alive phanerophyte individuals with circumference at breast height (CBH) > 15 cm. In the three fragments, 512 individuals, distributed in 60 species, 47 genera, and 23 families were sampled. The most representative families were Fabaceae (26), Anacardiaceae (4), Bignoniaceae (3) and Combretaceae (3). However, fourteen families were represented by only one species. Only eight species were common to all fragments - Myracrodruon urundeuva standed out with 26.9% of all sampled individuals - while a great number of species were exclusive of each fragment. The floristic and structural differences between the fragments are possibly related to the history and intensity of management in each area besides the topography variations and the presence or absence of limestone outcrops. These results show the importance of each fragment, indicating that the loss of anyone would cause negative impacts on the regional flora and consequently to the associated biodiversity.

Conventional and novel cardiovascular risk factors in young Finns and their associations with structural and functional vascular changes of subclinical atherosclerosis. The Cardiovascular Risk in Young Finns Study

Background: Atherosclerosis begins in early life progressing from asymptomatic to symptomatic as we age. Although substantial progress has been made in identifying the determinants of atherosclerosis in middle to older age adults at increased cardiovascular risk, there is lack of data examining determinants and prediction of atherosclerosis in young adults. Aims: The current study was designed to investigate levels of cardiovascular risk factors in young adults, subclinical measures of atherosclerosis, and prediction of subclinical arterial changes with conventional risk factor measures and novel metabolic profiling of serum samples. Subjects and Methods: This thesis utilised data from the follow-ups performed in 2001 and 2007 in the Cardiovascular Risk in Young Finns study, a Finnish population-based prospective cohort study that examined 2,204 subjects who were aged 30-45 years in 2007. Subclinical atherosclerosis was studied using noninvasive ultrasound measurements of carotid intima-media thickness (IMT), carotid arterial distensibility (CDist) and brachial flow-mediated dilation (FMD). Measurements included conventional risk factors and metabolic profiling using highthroughput nuclear magnetic resonance (NMR) methods that provided data on 42 lipid markers and 16 circulating metabolites. Results: Trends in lipids were favourable between 2001 and 2007, whereas waist circumference, fasting glucose, and blood pressure levels increased. To study the stability of noninvasive ultrasound markers, 6-year tracking (the likelihood to maintain the original fractile over time) in 6 years was examined. IMT tracked more strongly than CDist and FMD. Cardiovascular risk scores (Framingham, SCORE, Finrisk, Reynolds and PROCAM) predicted subclinical atherosclerosis equally. Lipoprotein subclass testing did not improve the prediction of subclinical atherosclerosis over and above conventional risk factors. However, circulating metabolites improved risk stratification. Tyrosine and docosahexaenoic acid were found to be novel biomarkers of high IMT. Conclusions: Prediction of cardiovascular risk in young Finnish adults can be performed with any of the existing risk scores. The addition of metabonomics to risk stratification improves prediction of subclinical changes and enables more accurate targeting of prevention at an early stage.

DPS-Like Peroxide Resistance Protein: Structural and Functional Studies on a Versatile Nanocontainer

Oxidative stress is a constant threat to almost all organisms. It damages a number of biomolecules and leads to the disruption of many crucial cellular functions. It is caused by reactive oxygen species (ROS), such as hydrogen peroxide (H2O₂), superoxide (•O₂ -), and hydroxyl radical (•OH). The most harmful of these compounds is •OH, which is only formed in cells in the presence of redox-cycling transition metals, such as iron and copper. Bacteria have developed a number of mechanisms to cope with ROS. One of the most widespread means employed by bacteria is the DNA-binding proteins from starved cells (Dps). Dps proteins protect the cells by binding and oxidizing Fe2+, thus greatly reducing the production of •OH. The oxidized iron is stored inside the protein as an iron core. In addition, Dps proteins bind directly to DNA forming a protective coating that shields DNA from harmful agents. Moreover, Dps proteins have been found to elicit other protective functions in cells and to participate in bacterial virulence. Dps proteins are of special importance to Streptococci owing to the lack of catalase in this genus of bacteria.This study was focused on structural and functional characterization of streptococcal Dpslike peroxide resistance (Dpr) proteins. Initially, crystal structures of Streptococcus pyogenes Dpr were determined. The data confirmed the presence of a di-metal ferroxidase center (FOC) in Dpr proteins and revealed the presence of a novel N-terminal helix as well as a surface metal-binding site. The crystal structures of Streptococcus suis Dpr complexed with transition metals demonstrated the metal specificity of the FOC. Solution binding studies also indicated the presence of a di-metal FOC. These results suggested a possible role for Dpr in the detoxification of various metals. Iron was found to mineralize inside the protein as ferrihydrite based on X-ray absorption spectroscopy data. The iron core was found to exhibit clear superparamagnetic behaviour using magnetic and Mössbauer measurements. The results from this study are expected to further increase our understanding on the binding, oxidation, and mineralization of iron and other metals in Dpr proteins. In particular, the structural and magnetic properties of the iron core can form a basis for potential new applications in nanotechnology. From the streptococcal viewpoint, the results would help in understanding better the complicated picture of bacterial pathogenesis. Dpr proteins may also provide a novel target for drug design due to their tight involvement in bacterial virulence.

STRUCTURAL LEAF CHANGES IN TREES AROUND A SUBWAY AIR DUCT

ABSTRACTWhile a number of papers have shown that subway systems have an impact on the air quality through the release of particulate matters, no information about the impact of such particles on tree attributes is available. Tree leaves from three different species from the exit side of a subway station in Rio de Janeiro, Brazil, were more asymmetrical than leaves from the entrance side. This leaves also presenting changes in leaves cuticle and chlorophyll content.

PHYTOSOCIOLOGY AND STRUCTURAL CHARACTERIZATION OF WOODY REGENERATION FROM A REFORESTATION WITH NATIVE SPECIES IN SOUTHEASTERN BRAZIL

ABSTRACT In Brazil, specifically in São Paulo State, there are guidelines based on the high diversity of tropical forests that instructs the restoration projects in the state (current SMA 32/2014). The main goal of this study was verify the importance and effectiveness of the high diversity of arboreal species originated from a reforestation, and its influence in a woody regenerating composition. We developed a phytosociologic study in a woody regenerating stratum of a nine year old reforestation at a Private Reserve of Natural Heritage (RPPN), in Mogi-Guaçu, São Paulo State. All specimens with height > 30 cm and Diameter at Breast Height (DBH) < 5 cm were evaluated. The woody regenerating diversity was smaller than the overstory diversity and the species composition was similar to the overstory. The Simpson index (1-D) was 0.85, Shannon index (H') was 2.46 and the Pielou index (J') was 0.60. The zoochoric dispersion syndrome was major among the species. Our results suggest that the use of high diversity of native seedlings in a reforestation leads to high diversity of species in woody regeneration stratum, after one decade of planting.

Numerical evaluation of the modulus of longitudinal elasticity in structural round timber elements of the Eucalyptus genus

Currently, the standards that deal with the determination of the properties of rigidity and strength for structural round timber elements do not take in consideration in their calculations and mathematical models the influence of the existing irregularities in the geometry of these elements. This study has as objective to determine the effective value of the modulus of longitudinal elasticity for structural round timber pieces of the Eucalyptus citriodora genus by a technique of optimization allied to the Inverse Analysis Method, to the Finite Element Method and the Least Square Method.

The position effect of structural Eucalyptus round timber on the flexural modulus of elasticity

Round timber has great use in civil construction, performing the function of beams, columns, foundations, poles for power distribution among others, with the advantage of not being processed, such as lumber. The structural design of round timber requires determining the elastic properties, mainly the modulus of elasticity. The Brazilian standards responsible for the stiffness and strength determination of round timber are in effect for over twenty years with no technical review. Round timber, for generally present an axis with non-zero curvature according to the position of the element in the bending test, may exhibit different values of modulus of elasticity. This study aims to analyze the position effect of Eucalyptus grandis round timber on the flexural modulus of elasticity. The three-point bending test was evaluated in two different positions based on the longitudinal rotation of the round timber element. The results revealed that at least two different positions of the round timber element are desired to obtain significant modulus of elasticity.

Alternative methodology for calculating the modulus of elasticity of wooden beams of structural dimensions

This study aims to present an alternative calculation methodology based on the Least Squares Method for determining the modulus of elasticity in bending wooden beams of structural dimensions. The equations developed require knowledge of three or five points measured in displacements along the piece, allowing greater reliability on the response variable, using the statistical bending test at three points and non-destructively, resulting from imposition of measures from small displacements L/300 and L/200, the largest being stipulated by the Brazilian norm NBR 7190:1997. The woods tested were Angico, Cumaru, Garapa and Jatoba. Besides obtaining the modulus of elasticity through the alternative methodology proposed, these were also obtained employing the Brazilian norm NBR 7190:1997, adapted to the condition of non-destructive testing (small displacements) and for pieces of structural dimensions. The results of the modulus of elasticity of the four species of wood according to both calculation approaches used proved to be equivalent, implying the good approximation provided by the methodology of calculation adapted from the Brazilian norm.

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.

Simulation of structural stress history based on dynamic analysis

Modern machine structures are often fabricated by welding. From a fatigue point of view, the structural details and especially, the welded details are the most prone to fatigue damage and failure. Design against fatigue requires information on the fatigue resistance of a structure’s critical details and the stress loads that act on each detail. Even though, dynamic simulation of flexible bodies is already current method for analyzing structures, obtaining the stress history of a structural detail during dynamic simulation is a challenging task; especially when the detail has a complex geometry. In particular, analyzing the stress history of every structural detail within a single finite element model can be overwhelming since the amount of nodal degrees of freedom needed in the model may require an impractical amount of computational effort. The purpose of computer simulation is to reduce amount of prototypes and speed up the product development process. Also, to take operator influence into account, real time models, i.e. simplified and computationally efficient models are required. This in turn, requires stress computation to be efficient if it will be performed during dynamic simulation. The research looks back at the theoretical background of multibody dynamic simulation and finite element method to find suitable parts to form a new approach for efficient stress calculation. This study proposes that, the problem of stress calculation during dynamic simulation can be greatly simplified by using a combination of floating frame of reference formulation with modal superposition and a sub-modeling approach. In practice, the proposed approach can be used to efficiently generate the relevant fatigue assessment stress history for a structural detail during or after dynamic simulation. In this work numerical examples are presented to demonstrate the proposed approach in practice. The results show that approach is applicable and can be used as proposed.

Structural and operational optimisation : applications in energy systems

In this work mathematical programming models for structural and operational optimisation of energy systems are developed and applied to a selection of energy technology problems. The studied cases are taken from industrial processes and from large regional energy distribution systems. The models are based on Mixed Integer Linear Programming (MILP), Mixed Integer Non-Linear Programming (MINLP) and on a hybrid approach of a combination of Non-Linear Programming (NLP) and Genetic Algorithms (GA). The optimisation of the structure and operation of energy systems in urban regions is treated in the work. Firstly, distributed energy systems (DES) with different energy conversion units and annual variations of consumer heating and electricity demands are considered. Secondly, district cooling systems (DCS) with cooling demands for a large number of consumers are studied, with respect to a long term planning perspective regarding to given predictions of the consumer cooling demand development in a region. The work comprises also the development of applications for heat recovery systems (HRS), where paper machine dryer section HRS is taken as an illustrative example. The heat sources in these systems are moist air streams. Models are developed for different types of equipment price functions. The approach is based on partitioning of the overall temperature range of the system into a number of temperature intervals in order to take into account the strong nonlinearities due to condensation in the heat recovery exchangers. The influence of parameter variations on the solutions of heat recovery systems is analysed firstly by varying cost factors and secondly by varying process parameters. Point-optimal solutions by a fixed parameter approach are compared to robust solutions with given parameter variation ranges. In the work enhanced utilisation of excess heat in heat recovery systems with impingement drying, electricity generation with low grade excess heat and the use of absorption heat transformers to elevate a stream temperature above the excess heat temperature are also studied.