Stereochemical Analysis of Higher α,α-Dialkylglycine Containing Peptides. Characterization of Local Helical Conformations at Dipropylglycine Residues and Observation of a Novel Hydrated Multiple β-Turn Structure in Crystals of a Glycine Rich Peptide

The peptide Boc-Gly-Dpg-Gly-Gly-Dpg-Gly-NHMe (1) has been synthesized to examine the conformational preferences of Dpg residues in the context of a poor helix promoting sequence. Single crystals of 1 were obtained in the space group P21/c with a = 13.716(2) Å, b = 12.960(2) Å, c = 22.266(4) Å, and β = 98.05(1)°; R = 6.3% for 3660 data with |Fo| > 4σ. The molecular conformation in crystals revealed that the Gly(1)-Dpg(2) segment adopts φ, ψ values distorted from those expected for an ideal type II‘ β-turn (φGly(1) = +72.0°, ψGly(1) = −166.0°; φDpg(2) = −54.0°, ψDpg(2) = −46.0°) with an inserted water molecule between Boc-CO and Gly(3)NH. The Gly(3)-Gly(4) segment adopts φ, ψ values which lie broadly in the right handed helical region (φGly(3) = −78.0°, ψGly(3) = −9.0°; φGly(4) = −80.0°, ψGly(4) = −18.0°). There is a chiral reversal at Dpg(5) which takes up φ, ψ values in the left handed helical region. The Dpg(5)-Gly(6) segment closely resembles an ideal type I‘ β-turn (φDpg(5) = +56.0°, ψDpg(5) = +32.0°; φGly(6) = +85.0°, ψGly(6) = −3.0°). Molecules of both chiral senses are found in the centrosymmetric crystal. The C-terminus forms a hydrated Schellman motif, with water insertion into the potential 6 → 1 hydrogen bond between Gly(1)CO and Gly(6)NH. NMR studies in CDCl3 suggest substantial retention of the multiple turn conformation observed in crystals. In solution the observed NOEs support local helical conformation at the two Dpg residues.

Local structure in LaMnO3 and CaMnO3 perovskites: A quantitative structural refinement of mn K-edge XANES data

Hole-doped perovskites such as La1-xCaxMnO3 present special magnetic and magnetotransport properties, and it is commonly accepted that the local atomic structure around Mn ions plays a crucial role in determining these peculiar features. Therefore experimental techniques directly probing the local atomic structure, like x-ray absorption spectroscopy (XAS), have been widely exploited to deeply understand the physics of these compounds. Quantitative XAS analysis usually concerns the extended region [extended x-ray absorption fine structure (EXAFS)] of the absorption spectra. The near-edge region [x-ray absorption near-edge spectroscopy (XANES)] of XAS spectra can provide detailed complementary information on the electronic structure and local atomic topology around the absorber. However, the complexity of the XANES analysis usually prevents a quantitative understanding of the data. This work exploits the recently developed MXAN code to achieve a quantitative structural refinement of the Mn K-edge XANES of LaMnO3 and CaMnO3 compounds; they are the end compounds of the doped manganite series LaxCa1-xMnO3. The results derived from the EXAFS and XANES analyses are in good agreement, demonstrating that a quantitative picture of the local structure can be obtained from XANES in these crystalline compounds. Moreover, the quantitative XANES analysis provides topological information not directly achievable from EXAFS data analysis. This work demonstrates that combining the analysis of extended and near-edge regions of Mn K-edge XAS spectra could provide a complete and accurate description of Mn local atomic environment in these compounds.

Local structure of Sr(2)FeMoxW1-xO(6) double perovskites studied by EXAFS

Sr2FeMoO6 double perovskits display low field MR at a relatively high temperature and unusual ferromagnetic properties. These compounds depicts metal to insulator transition increasing x above x(c) similar to 0.25. A comparative analysis of the near edge regions (XANES) suggests that iron is Fe3+ in the metallic range. Checking the end compounds, we found that the doped samples can be viewn as inhomogeneous distributions of the end compounds. This could help to distinguish between the two scenarios proposed to explain the metal to insulator transition. Moreover, the local atomic structure of Sr2FeMoxW1-xO6 as a function of composition (0 <= x <= 1) has been investigated by Extended X-ray absorption spectroscopy (EXAFS) a the Fe, Mo, Sr K-edges andW L-III-edge.

The 5-Methyl Group in Thymine Dynamically Influences the Structure of A-Tracts in DNA at the Local and Global Level

DNA sequences containing a stretch of several A:T basepairs without a 5'-TA-3' step are known as A-tracts and have been the subject of extensive investigation because of their unique structural features such as a narrow minor groove and their crucial role in several biological processes. One of the aspects under investigation has been the influence of the 5-methyl group of thymine on the properties of A-tracts. Detailed molecular dynamics simulation studies of the sequences d(CGCAAAUUUGCG) and d(CGCAAATTTGCG) indicate that the presence of the 5-methyl group in thymine increases the frequency of a narrow minor groove conformation, which could facilitate its specific recognition by proteins, and reduce its susceptibility to cleavage by DNase I. The bias toward a wider minor groove in the absence of the thymine 5-methyl group is a static structural feature. Our results also indicate that the presence of the thymine 5-methyl group is necessary for calibrating the backbone conformation and the basepair and dinucleotide step geometry of the core A-tract as well as the flanking CA/TG and the neighboring GC/GC steps, as observed in free and protein-bound DNA. As a consequence, it also fine-tunes the curvature of the longer DNA fragment in which the A-tract is embedded.

Global processes, local strategies : migration of educated Dominicans.

The aim of this thesis is to examine migration of educated Dominicans in light of global processes. Current global developments have resulted in increasingly global movements of people, yet people tend to come from certain places in large numbers rather than others. At the same time, international migration is increasingly selective, which shows in the disproportional number of educated migrants. This study discovers individual and societal motivations that explain why young educated Dominicans decide to migrate and return. The theoretical framework of this thesis underlines that migration is a dynamic process rooted in other global developments. Migratory movements should be seen as a result of interacting macro- and microstructures, which are linked by a number of intermediate mechanisms, meso-structures. The way individuals perceive opportunity structures concretises the way global developments mediate to the micro-level. The case of the Dominican Republic shows that there is a diversity of local responses to the world system, as Dominicans have produced their own unique historical responses to global changes. The thesis explains that Dominican migration is importantly conditioned by socioeconomic and educational background. Migration is more accessible for the educated middle class, because of the availability of better resources. Educated migrants also seem less likely to rely on networks to organize their migrations. The role of networks in migration differs by socioeconomic background on the one hand, and by the specific connections each individual has to current and previous migrants on the other hand. The personal and cultural values of the migrant are also pivotal. The central argument of this thesis is that a veritable culture of migration has evolved in the Dominican Republic. The actual economic, political and social circumstances have led many Dominicans to believe that there are better opportunities elsewhere. The globalisation of certain expectations on the one hand, and the development of the specifically Dominican feeling of ‘externalism’ on the other, have for their part given rise to the Dominican culture of migration. The study also suggests that the current Dominican development model encourages migration. Besides global structures, local structures are found to ve pivotal in determining how global processes are materialised in a specific place. The research for this thesis was conducted by using qualitative methodology. The focus of this thesis was on thematic interviews that reveal the subject’s point of view and give a fuller understanding of migration and mobility of the educated. The data was mainly collected during a field research phase in Santo Domingo, the Dominican Republic in December 2009 and January 2010. The principal material consists of ten thematic interviews held with educated Dominican current or former migrants. Four expert interviews, relevant empirical data, theoretical literature and newspaper articles were also comprehensively used.

Governance theory as a framework for empirical research : a case study on local environmental policy-making in Helsinki, Finland

Governance has been one of the most popular buzzwords in recent political science. As with any term shared by numerous fields of research, as well as everyday language, governance is encumbered by a jungle of definitions and applications. This work elaborates on the concept of network governance. Network governance refers to complex policy-making situations, where a variety of public and private actors collaborate in order to produce and define policy. Governance is processes of autonomous, self-organizing networks of organizations exchanging information and deliberating. Network governance is a theoretical concept that corresponds to an empirical phenomenon. Often, this phenomenon is used to descirbe a historical development: governance is often used to describe changes in political processes of Western societies since the 1980s. In this work, empirical governance networks are used as an organizing framework, and the concepts of autonomy, self-organization and network structure are developed as tools for empirical analysis of any complex decision-making process. This work develops this framework and explores the governance networks in the case of environmental policy-making in the City of Helsinki, Finland. The crafting of a local ecological sustainability programme required support and knowledge from all sectors of administration, a number of entrepreneurs and companies and the inhabitants of Helsinki. The policy process relied explicitly on networking, with public and private actors collaborating to design policy instruments. Communication between individual organizations led to the development of network structures and patterns. This research analyses these patterns and their effects on policy choice, by applying the methods of social network analysis. A variety of social network analysis methods are used to uncover different features of the networked process. Links between individual network positions, network subgroup structures and macro-level network patterns are compared to the types of organizations involved and final policy instruments chosen. By using governance concepts to depict a policy process, the work aims to assess whether they contribute to models of policy-making. The conclusion is that the governance literature sheds light on events that would otherwise go unnoticed, or whose conceptualization would remain atheoretical. The framework of network governance should be in the toolkit of the policy analyst.

A new method of producing local enhancement of buoyancy in liquid flows

We describe here a novel method of generating large volumetric heating in a liquid. The method uses the principle of ohmic heating of the liquid, rendered electrically conducting by suitable additives if necessary. Electrolysis is prevented by the use of high frequency alternating voltage and chemically treated electrodes. The technique is demonstrated by producing substantial heating in an initially neutral jet of water. Simple flow visualisation studies, made by adding dye to the jet, show marked changes in the growth and development of the jet with heat addition.

HARMONY: a server for the assessment of protein structures

Protein structure validation is an important step in computational modeling and structure determination. Stereochemical assessment of protein structures examine internal parameters such as bond lengths and Ramachandran (phi, psi) angles. Gross structure prediction methods such as inverse folding procedure and structure determination especially at low resolution can sometimes give rise to models that are incorrect due to assignment of misfolds or mistracing of electron density maps. Such errors are not reflected as strain in internal parameters. HARMONY is a procedure that examines the compatibility between the sequence and the structure of a protein by assigning scores to individual residues and their amino acid exchange patterns after considering their local environments. Local environments are described by the backbone conformation, solvent accessibility and hydrogen bonding patterns. We are now providing HARMONY through a web server such that users can submit their protein structure files and, if required, the alignment of homologous sequences. Scores are mapped on the structure for subsequent examination that is useful to also recognize regions of possible local errors in protein structures. HARMONY server is located at http://caps.ncbs.res.in/harmony/

Theoretical foundations for multiple rendezvous of glowworm-inspired mobile agents with variable local-decision domains

We present the theoretical foundations for the multiple rendezvous problem involving design of local control strategies that enable groups of visibility-limited mobile agents to split into subgroups, exhibit simultaneous taxis behavior towards, and eventually rendezvous at, multiple unknown locations of interest. The theoretical results are proved under certain restricted set of assumptions. The algorithm used to solve the above problem is based on a glowworm swarm optimization (GSO) technique, developed earlier, that finds multiple optima of multimodal objective functions. The significant difference between our work and most earlier approaches to agreement problems is the use of a virtual local-decision domain by the agents in order to compute their movements. The range of the virtual domain is adaptive in nature and is bounded above by the maximum sensor/visibility range of the agent. We introduce a new decision domain update rule that enhances the rate of convergence by a factor of approximately two. We use some illustrative simulations to support the algorithmic correctness and theoretical findings of the paper.