Effects of Side-Chain and Electron Exchange Correlation on the Band Structure of Perylene Diimide Liquid Crystals: A Density Functional Study

The structural and electronic properties of perylene diimide liquid crystal PPEEB are studied using ab initio methods based on the density functional theory (I)FT). Using available experimental crystallographic data as a guide, we propose a detailed structural model for the packing of solid PPEEB. We find that due to the localized nature of the band edge wave function, theoretical approaches beyond the standard method, such as hybrid functional (PBE0), are required to correctly characterize the band structure of this material. Moreover, unlike previous assumptions, we observe the formation of hydrogen bonds between the side chains of different molecules, which leads to a dispersion of the energy levels. This result indicates that the side chains of the molecular crystal not only are responsible for its structural conformation but also can be used for tuning the electronic and optical properties of these materials.

The Schenberg data acquisition and analysis: results from its first commissioning run

The Mario Schenberg gravitational wave detector has started its commissioning phase at the Physics Institute of the University of Sao Paulo. We have collected almost 200 h of data from the instrument in order to check out its behavior and performance. We have also been developing a data acquisition system for it under a VXI System. Such a system is composed of an analog-to-digital converter and a GPS receiver for time synchronization. We have been building the software that controls and sets up the data acquisition. Here we present an overview of the Mario Schenberg detector and its data acquisition system, some results from the first commissioning run and solutions for some problems we have identified.

Spin-density functional for exchange anisotropic Heisenberg model

Ground-state energies for anti ferromagnetic Heisenberg models with exchange anisotropy are estimated by means of a local-spin approximation made in the context of the density functional theory. Correlation energy is obtained using the non-linear spin-wave theory for homogeneous systems from which the spin functional is built. Although applicable to chains of any size, the results are shown for small number of sites, to exhibit finite-size effects and allow comparison with exact-numerical data from direct diagonalization of small chains. (C) 2009 Elsevier B.V. All rights reserved.

Analysis of Agonist and Antagonist Effects on Thyroid Hormone Receptor Conformation by Hydrogen/Deuterium Exchange

Thyroid hormone receptors (TRs) are ligand-gated transcription factors with critical roles in development and metabolism. Although x-ray structures of TR ligand-binding domains (LBDs) with agonists are available, comparable structures without ligand (apo-TR) or with antagonists are not. It remains important to understand apo-LBD conformation and the way that it rearranges with ligands to develop better TR pharmaceuticals. In this study, we conducted hydrogen/deuterium exchange on TR LBDs with or without agonist (T(3)) or antagonist (NH(3)). Both ligands reduce deuterium incorporation into LBD amide hydrogens, implying tighter overall folding of the domain. As predicted, mass spectroscopic analysis of individual proteolytic peptides after hydrogen/deuterium exchange reveals that ligand increases the degree of solvent protection of regions close to the buried ligand-binding pocket. However, there is also extensive ligand protection of other regions, including the dimer surface at H10-H11, providing evidence for allosteric communication between the ligand-binding pocket and distant interaction surfaces. Surprisingly, C-terminal activation helix H12, which is known to alter position with ligand, remains relatively protected from solvent in all conditions suggesting that it is packed against the LBD irrespective of the presence or type of ligand. T(3), but not NH(3), increases accessibility of the upper part of H3-H5 to solvent, and we propose that TR H12 interacts with this region in apo-TR and that this interaction is blocked by T(3) but not NH(3.) We present data from site-directed mutagenesis experiments and molecular dynamics simulations that lend support to this structural model of apo-TR and its ligand-dependent conformational changes. (Molecular Endocrinology 25: 15-31, 2011)

Improving data perturbation testing techniques for Web services

The widespread use of service-oriented architectures (SOAs) and Web services in commercial software requires the adoption of development techniques to ensure the quality of Web services. Testing techniques and tools concern quality and play a critical role in accomplishing quality of SOA based systems. Existing techniques and tools for traditional systems are not appropriate to these new systems, making the development of Web services testing techniques and tools required. This article presents new testing techniques to automatically generate a set of test cases and data for Web services. The techniques presented here explore data perturbation of Web services messages upon data types, integrity and consistency. To support these techniques, a tool (GenAutoWS) was developed and applied to real problems. (C) 2010 Elsevier Inc. All rights reserved.

PACKMOL: A Package for Building Initial Configurations for Molecular Dynamics Simulations

Adequate initial configurations for molecular dynamics simulations consist of arrangements of molecules distributed in space in such a way to approximately represent the system`s overall structure. In order that the simulations are not disrupted by large van der Waals repulsive interactions, atoms from different molecules Must keep safe pairwise distances. Obtaining Such a molecular arrangement can be considered it packing problem: Each type molecule must satisfy spatial constraints related to the geometry of the system, and the distance between atoms of different molecules Must be greater than some specified tolerance. We have developed a code able to pack millions of atoms. grouped in arbitrarily complex molecules, inside a variety of three-dimensional regions. The regions may be intersections of spheres, ellipses, cylinders, planes, or boxes. The user must provide only the structure of one molecule of each type and the geometrical constraints that each type of molecule must satisfy. Building complex mixtures, interfaces, solvating biomolecules in water, other solvents, or mixtures of solvents, is straight forward. In addition. different atoms belonging to the same molecule may also be restricted to different spatial regions, in Such a way that more ordered molecular arrangements call be built, as micelles. lipid double-layers, etc. The packing time for state-of-the-art molecular dynamics systems varies front a few seconds to a few Minutes in a personal Computer. The input files are simple and Currently compatible with PDB, Tinker, Molden, or Moldy coordinate files. The package is distributed as free software and call be downloaded front http://www.ime.unicamp.br/similar to martinez/packmol/. (C) 2009 Wiley Periodicals. Inc. J Comput Chem 30: 2157-2164, 2009

Polymorphisms in genes involved in neurodevelopment may be associated with altered brain morphology in schizophrenia: Preliminary evidence

An abnormality in neurodevelopment is one of the most robust etiologic hypotheses in schizophrenia (SZ). There is also strong evidence that genetic factors may influence abnormal neurodevelopment in the disease. The present study evaluated in SZ patients, whose brain structural data had been obtained with magnetic resonance imaging (MRI), the possible association between structural brain measures, and 32 DNA polymorphisms,located in 30 genes related to neurogenesis and brain development. DNA was extracted from peripheral blood cells of 25 patients with schizophrenia, genotyping was performed using diverse procedures, and putative associations were evaluated by standard statistical methods (using the software Statistical Package for Social Sciences - SPSS) with a modified Bonferroni adjustment. For reelin (RELN), a protease that guides neurons in the developing brain and underlies neurotransmission and synaptic plasticity in adults, an association was found for a non-synonymous polymorphism (Va1997Leu) with left and right ventricular enlargement. A putative association was also found between protocadherin 12 (PCDH12), a cell adhesion molecule involved in axonal guidance and synaptic specificity, and cortical folding (asymmetry coefficient of gyrification index). Although our results are preliminary, due to the small number of individuals analyzed, such an approach could reveal new candidate genes implicated in anomalous neurodevelopment in schizophrenia. (c) 2007 Elsevier Ireland Ltd. All rights reserved.

Trade effects of exchange rate fluctuations: Evidence from Sweden

An overview of the theoretical literature for the last two decades suggests that there is no clear-cut relationship one can pin down between exchange rate volatility and trade flows. Analytical results are based on specific assumptions and only hold in certain cases. Especially, the impact of exchange rate volatility on export and import activity investigated separately leads also to dissimilar conclusions among countries studied. The general presumption is that an increase in exchange rate volatility will have an adverse effect on trade flows and consequently, the overall heath of the world economy. However, neither theoretical models nor empirical studies provide us with a definitive answer, leaving obtained results highly ambiguous and inconsistent (Baum and Caglayan, 2006). We purposed to empirically investigate trade effects of exchange rate fluctuations in Sweden from the perspective of export and import in this research. The data comprises period from January 1993 to December 2006, where export and import volumes are considered from the point of their determinants, including exchange rate volatility, which has been measured through EGARCH model. The results for the case of Sweden show that short run dynamics of volatility negatively associated with both export and import, whereas considered from the case of previous period volatility it exhibits positive relationship. These results are consistent with the most findings of prior studies, where the relationship remained ambiguous.

Integration av webbaserat analysprogram och kartprogram : Integration of web based analysis-software andmap-software

I takt med att GIS (Grafiska InformationsSystem) blir allt vanligare och mer användarvänligt har WM-data sett att kunder skulle ha intresse i att kunna koppla information från sin verksamhet till en kartbild. Detta för att lättare kunna ta till sig informationen om hur den geografiskt finns utspridd över ett område för att t.ex. ordna effektivare tranporter. WM-data, som det här arbetet är utfört åt, avser att ta fram en prototyp som sedan kan visas upp för att påvisa för kunder och andra intressenter att detta är möjligt att genomföra genom att skapa en integration mellan redan befintliga system. I det här arbetet har prototypen tagits fram med skogsindustrin och dess lager som inriktning. Befintliga program som integrationen ska skapas mellan är båda webbaserade och körs i en webbläsare. Analysprogrammet som ska användas heter Insikt och är utvecklat av företaget Trimma, kartprogrammet heter GIMS som är WM-datas egna program. Det ska vara möjligt att i Insikt analysera data och skapa en rapport. Den ska sedan skickas till GIMS där informationen skrivs ut på kartan på den plats som respektive information hör till. Det ska även gå att välja ut ett eller flera områden i kartan och skicka till Insikt för att analysera information från enbart de utvalda områdena. En prototyp med önskad funktionalitet har under arbetets gång tagits fram, men för att ha en säljbar produkt är en del arbeta kvar. Prototypen har visats för ett antal intresserade som tyckte det var intressant och tror att det är något som skulle kunna användas flitigt inom många områden.

Advanced Building Energy Data Visualization

Advanced Building Energy Data Visualization is a way to detect performance problems in commercialbuildings. By placing sensors in a building that collects data from example, air temperature and electricalpower, then makes it possible to calculate the data in Data Visualization software. This softwaregenerates visual diagrams so the building manager or building operator can see if for example thepower consumption is to high.A first step (before sensors are installed in a building) to see how the energy consumption is in abuilding can be to use a Benchmarking Tool. There is a number of Benchmarking Tools that is availablefor free on the Internet. Each tool have a bit different approach, but they all show how much energyconsumption there is in a building compared to other similar buildings.In this study a new web design for the benchmarking tool CalARCH has been developed. CalARCHis developed at the Berkeley Lab in Berkeley, California, USA. CalARCH uses data collected only frombuildings in California, and is only for comparing buildings in California with other similar buildingsin the state.Five different versions of the web site were made. Then a web survey was done to determine whichversion would be the best for CalARCH. The results showed that Version 5 and Version 3 was the best.Then a new version was made, based on these two versions. This study was made at the LawrenceBerkeley Laboratory.

Testing of combined heating systems for small houses: Improved procedures for whole system test methods : Deliverable 2.3

Dynamic system test methods for heating systems were developed and applied by the institutes SERC and SP from Sweden, INES from France and SPF from Switzerland already before the MacSheep project started. These test methods followed the same principle: a complete heating system – including heat generators, storage, control etc., is installed on the test rig; the test rig software and hardware simulates and emulates the heat load for space heating and domestic hot water of a single family house, while the unit under test has to act autonomously to cover the heat demand during a representative test cycle. Within the work package 2 of the MacSheep project these similar – but different – test methods were harmonized and improved. The work undertaken includes:  • Harmonization of the physical boundaries of the unit under test. • Harmonization of the boundary conditions of climate and load. • Definition of an approach to reach identical space heat load in combination with an autonomous control of the space heat distribution by the unit under test. • Derivation and validation of new six day and a twelve day test profiles for direct extrapolation of test results.   The new harmonized test method combines the advantages of the different methods that existed before the MacSheep project. The new method is a benchmark test, which means that the load for space heating and domestic hot water preparation will be identical for all tested systems, and that the result is representative for the performance of the system over a whole year. Thus, no modelling and simulation of the tested system is needed in order to obtain the benchmark results for a yearly cycle. The method is thus also applicable to products for which simulation models are not available yet. Some of the advantages of the new whole system test method and performance rating compared to the testing and energy rating of single components are:  • Interaction between the different components of a heating system, e.g. storage, solar collector circuit, heat pump, control, etc. are included and evaluated in this test. • Dynamic effects are included and influence the result just as they influence the annual performance in the field. • Heat losses are influencing the results in a more realistic way, since they are evaluated under "real installed" and representative part-load conditions rather than under single component steady state conditions.   The described method is also suited for the development process of new systems, where it replaces time-consuming and costly field testing with the advantage of a higher accuracy of the measured data (compared to the typically used measurement equipment in field tests) and identical, thus comparable boundary conditions. Thus, the method can be used for system optimization in the test bench under realistic operative conditions, i.e. under relevant operating environment in the lab.   This report describes the physical boundaries of the tested systems, as well as the test procedures and the requirements for both the unit under test and the test facility. The new six day and twelve day test profiles are also described as are the validation results.

Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.

Agent-Oriented Data Curation in Bioinformatics

The practitioners of bioinformatics require increasing sophistication from their software tools to take into account the particular characteristics that make their domain complex. For example, there is a great variation of experience of researchers, from novices who would like guidance from experts in the best resources to use to experts that wish to take greater management control of the tools used in their experiments. Also, the range of available, and conflicting, data formats is growing and there is a desire to automate the many trivial manual stages of in-silico experiments. Agent-oriented software development is one approach to tackling the design of complex applications. In this paper, we argue that, in fact, agent-oriented development is a particularly well-suited approach to developing bioinformatics tools that take into account the wider domain characteristics. To illustrate this, we design a data curation tool, which manages the format of experimental data, extend it to better account for the extra requirements placed by the domain characteristics, and show how the characteristics lead to a system well suited to an agent-oriented view.