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

A New Approach to the Prediction of Partition Coefficients in Water/Organic Interfaces

In the present work, a new approach for the determination of the partition coefficient in different interfaces based on the density function theory is proposed. Our results for log P(ow) considering a n-octanol/water interface for a large super cell for acetone -0.30 (-0.24) and methane 0.95 (0.78) are comparable with the experimental data given in parenthesis. We believe that these differences are mainly related to the absence of van der Walls interactions and the limited number of molecules considered in the super cell. The numerical deviations are smaller than that observed for interpolation based tools. As the proposed model is parameter free, it is not limited to the n-octanol/water interface.

Vanadium oxide-porphyrin nanocomposites as gas sensor interfaces for probing low water content in ethanol

Vanadium pentoxide xerogels (VXG) incorporating meso(3- and 4-pyridyl)porphyrin cobalt(III) species coordinated to four [Ru(bipy)(2)Cl](+) complexes were employed as gas sensing materials capable of detecting small amounts of water in commercial ethanol and fuel supplies. According to their X-ray diffraction data, the original VXG lamellar framework was maintained in the nanocomposite material, but the interlamellar distance increased from 11.7 to 15.2 angstrom, reflecting the intercalation of the porphyrin species into the vanadium pentoxide matrix. The films generated by direct deposition of the nanocomposite aqueous suspensions exhibited good electrical and electrochemical performance for application in resistive sensors. The analysis of water in ethanol and fuels was carried out successfully using an especially designed electric setup incorporating a laminar gas flow chamber and interdigitated gold electrodes coated with the nanocomposites. (C) 2010 Elsevier B.V. All rights reserved.

Supramolecular Approach to Gold Nanoparticle/Triruthenium Cluster Hybrid Materials and Interfaces

A systematic and comprehensive study of the interaction of citrate-stabilized gold nanoparticles with triruthenium cluster complexes of general formula [Ru(3)(CH(3)COO)(6)(L)](+) [L = 4-cyanopyridine (4-CNpy), 4,4`-bipyridine (4,4`-bpy) or 4,4`-bis(pyridyl)ethylene (bpe)] has been carried out. The cluster-nanoparticle interaction in solution and the construction of thin films of the hybrid materials were investigated in detail by electronic and surface plasmon resonance (SPR) spectroscopy, Raman scattering spectroscopy and scanning electron microscopy (SEM). Citrate-stabilized gold nanoparticles readily interacted with [Ru(3)O(CH(3)COO)(6)(L)(3)](+) complexes to generate functionalized nanoparticles that tend to aggregate according to rates and extents that depend on the bond strength defined by the characteristics of the cluster L ligands following the sequence bpe > 4,4`-bpy >> 4-CNpy. The formation of compact thin films of hybrid AuNP/[Ru(3)O(CH(3)COO)(6)(L)(3)](+) derivatives with L = bpe and 4,4`-bpy indicated that the stability/lability of AuNP-cluster bonds as well as their solubility are important parameters that influence the film contruction process. Fluorine-doped tin oxide electrodes modified with thin films of these nanomaterials exhibited similar electrocatalytic activity but much higher sensitivity than a conventional gold electrode in the oxidation of nitrite ion to nitrate depending on the bridging cluster complex, demonstrating the high potential for the development of amperometric sensors.

Power Management Controls

In an office building in the US the office equipment uses about 7% of the total electricity use. Eventhough this is a low number, there is still a reason to save more energy, especially since one third of theenergy savings are lost when power management is not enabled.The core in the project ”Power Management Controls” is to develop a voluntary standard, The UserInterface Standard, that manufacturers of office equipment can use as a reference when they developnew equipment and design new interfaces. The interface is an important part of the use of powermanagement and doing this should increase the use of power management and save more energy. Theinterfaces are ofter hidden or inconsistent and confusing, which makes it harder for the user tounderstand power management. A more consistent interface makes it easier for the user to understandthe meaning of an interface and power management itselfThe standard consists of six different parts, which describe what can be done to achieve a consistentinterface. The standard also describes the part of the project called Dynamic Behavior. This part isconcentrating on the interfaces and the behavior of the device over time, which is important for the userto understand.The purpose of this degree project is to study and participate in the project ”Power ManagementControls”, and to understand what is being done to save more energy.

A user guide to simple monitoring and sustainable operation of PV-diesel hybrid systems : Handbook for system users and operators

This report contains a suggestion for a simple monitoring and evaluation guideline for PV-diesel hybrid systems. It offers system users a way to better understand if their system is operated in a way that will make it last for a long time. It also gives suggestions on how to act if there are signs of unfavourable use or failure. The application of the guide requires little technical equipment, but daily manual measurements. For the most part, it can be managed by pen and paper, by people with no earlier experience of power systems.The guide is structured and expressed in a way that targets PV-diesel hybrid system users with no, or limited, earlier experience of power engineering. It is less detailed in terms of motivations for certain choices and limitations, but rich in details concerning calculations, evaluation procedures and maintenance routines. A more scientific description of the guide can be found in a related journal article.

User perspectives on the Swedish Maternal Health Care Register

Background: Established in 1999, the Swedish Maternal Health Care Register (MHCR) collects data on pregnancy, birth, and the postpartum period for most pregnant women in Sweden. Antenatal care (ANC) midwives manually enter data into the Web-application that is designed for MHCR. The aim of this study was to investigate midwives? experiences, opinions and use of the MHCR. Method: A national, cross-sectional, questionnaire survey, addressing all Swedish midwives working in ANC, was conducted January to March 2012. The questionnaire included demographic data, preformed statements with six response options ranging from zero to five (0 = totally disagree and 5 = totally agree), and opportunities to add information or further clarification in the form of free text comments. Parametric and non-parametric methods and logistic regression analyses were applied, and content analysis was used for free text comments. Results: The estimated response rate was 53.1%. Most participants were positive towards the Web-application and the included variables in the MHCR. Midwives exclusively engaged in patient-related work tasks perceived the register as burdensome (70.3%) and 44.2% questioned the benefit of the register. The corresponding figures for midwives also engaged in administrative supervision were 37.8% and 18.5%, respectively. Direct electronic transfer of data from the medical records to the MHCR was emphasised as significant future improvement. In addition, the midwives suggested that new variables of interest should be included in the MHCR ? e.g., infertility, outcomes of previous pregnancy and birth, and complications of the index pregnancy. Conclusions: In general, the MHCR was valued positively, although perceived as burdensome. Direct electronic transfer of data from the medical records to the MHCR is a prioritized issue to facilitate the working situation for midwives. Finally, the data suggest that the MHCR is an underused source for operational planning and quality assessment in local ANC centres.

Shared decision-making in mental health care : a user perspective on decisional needs in community-based services

BACKGROUND: Shared decision-making (SDM) is an emergent research topic in the field of mental health care and is considered to be a central component of a recovery-oriented system. Despite the evidence suggesting the benefits of this change in the power relationship between users and practitioners, the method has not been widely implemented in clinical practice. OBJECTIVE: The objective of this study was to investigate decisional and information needs among users with mental illness as a prerequisite for the development of a decision support tool aimed at supporting SDM in community-based mental health services in Sweden. METHODS: Three semi-structured focus group interviews were conducted with 22 adult users with mental illness. The transcribed interviews were analyzed using a directed content analysis. This method was used to develop an in-depth understanding of the decisional process as well as to validate and conceptually extend Elwyn et al.'s model of SDM. RESULTS: The model Elwyn et al. have created for SDM in somatic care fits well for mental health services, both in terms of process and content. However, the results also suggest an extension of the model because decisions related to mental illness are often complex and involve a number of life domains. Issues related to social context and individual recovery point to the need for a preparation phase focused on establishing cooperation and mutual understanding as well as a clear follow-up phase that allows for feedback and adjustments to the decision-making process. CONCLUSIONS AND IMPLICATIONS FOR PRACTICE: The current study contributes to a deeper understanding of decisional and information needs among users of community-based mental health services that may reduce barriers to participation in decision-making. The results also shed light on attitudinal, relationship-based, and cognitive factors that are important to consider in adapting SDM in the mental health system.

Agents and the Grid: Service Discovery

The Grid is a large-scale computer system that is capable of coordinating resources that are not subject to centralised control, whilst using standard, open, general-purpose protocols and interfaces, and delivering non-trivial qualities of service. In this chapter, we argue that Grid applications very strongly suggest the use of agent-based computing, and we review key uses of agent technologies in Grids: user agents, able to customize and personalise data; agent communication languages offering a generic and portable communication medium; and negotiation allowing multiple distributed entities to reach service level agreements. In the second part of the chapter, we focus on Grid service discovery, which we have identified as a prime candidate for use of agent technologies: we show that Grid-services need to be located via personalised, semantic-rich discovery processes, which must rely on the storage of arbitrary metadata about services that originates from both service providers and service users. We present UDDI-MT, an extension to the standard UDDI service directory approach that supports the storage of such metadata via a tunnelling technique that ties the metadata store to the original UDDI directory. The outcome is a flexible service registry which is compatible with existing standards and also provides metadata-enhanced service discovery.

Transparent Provenance Derivation for User Decisions

It is rare for data's history to include computational processes alone. Even when software generates data, users ultimately decide to execute software procedures, choose their configuration and inputs, reconfigure, halt and restart processes, and so on. Understanding the provenance of data thus involves understanding the reasoning of users behind these decisions, but demanding that users explicitly document decisions could be intrusive if implemented naively, and impractical in some cases. In this paper, therefore, we explore an approach to transparently deriving the provenance of user decisions at query time. The user reasoning is simulated, and if the result of the simulation matches the documented decision, the simulation is taken to approximate the actual reasoning. The plausibility of this approach requires that the simulation mirror human decision -making, so we adopt an automated process explicitly modelled on human psychology. The provenance of the decision is modelled in OPM, allowing it to be queried as part of a larger provenance graph, and an OPM profile is provided to allow consistent querying of provenance across user decisions.

Dynamically Adapting BDI Agent Architectures based on High-level User Specifications

Users are facing an increasing challenge of managing information and being available anytime anywhere, as the web exponentially grows. As a consequence, assisting them in their routine tasks has become a relevant issue to be addressed. In this paper, we introduce a software framework that supports the development of Personal Assistance Software (PAS). It relies on the idea of exposing a high level user model in order to increase user trust in the task delegation process as well as empowering them to manage it. The framework provides a synchronization mechanism that is responsible for dynamically adapting an underlying BDI agent-based running implementation in order to keep this high-level view of user customizations consistent with it.

Divining Rods and Lightning Fields: Interactions and Interfaces: A Studio Exhibition in Communication With Save the Bay

"Design proposals for an outdoor 'exhibit' on the Shores of Narragansett Bay".

Interfaces da comunicação mercadológica com o público infantil

Este trabalho tem o intuito de analisar a criança enquanto objeto e destinatário da comunicação mercadológica, enfatizando o trabalho da publicidade e efeitos da televisão. Utilizou-se como recurso metodológico a pesquisa bibliográfica e documental com delineamento exploratório. Os resultados apontam para a necessidade de se aprofundar o estudo da criança no contexto da comunicação mercadológica, mas mostra indícios de que somente com a participação de todos os segmentos sociais pode-se obter um sistema publicitário mais responsável e ético ao lidar com o público infantil.

Proposta de um modelo gráfico e navegacional básico para interfaces de aplicações educacionais baseado em validação experimental

O desenvolvimento de projetos de interfaces gráficas está apoiado em guias de recomendações. Estes guias apresentam regras genéricas aos projetos de Interfaces Homem Computador–IHC. Entretanto, aplicações particulares, como as educacionais, não encontram regras específicas que atendam as necessidades do usuário-alvo. Ainda, a análise comparativa entre guias disponíveis aponta contradições entre as recomendações genéricas com aquelas específicas aplicadas a um determinado ambiente. A necessidade de um modelo de referência para a construção de interfaces gráficas amigáveis ao usuário e a escassez e contradições de recomendações específicas às aplicações educacionais motivaram o trabalho de pesquisa prática junto aos usuáriosalvo. Para a identificação das recomendações sobre aspectos gráficos básicos e elementos de navegação necessários a uma efetiva interação com interfaces dedicadas a aplicações educacionais, foi desenvolvido um instrumento de pesquisa que permitiu a investigação das preferências relativas aos aspectos pesquisados junto ao público-alvo. Os dados coletados foram tratados estatisticamente e os resultados obtidos contrariam tanto critérios adotados em interfaces de sistemas de ensino disponíveis na Internet como algumas recomendações sobre os mesmos disponíveis na literatura. Os resultados obtidos apontam, também, para a preferência dos usuários por elementos de navegação que não são referidos nos guias de recomendações consultados. A análise dos resultados possibilitou a geração de um modelo básico que recomenda preferências sobre aspectos gráficos básicos, como aplicação de cores em fontes e fundos de tela, tipologia de fontes para textos e paginação, e também, sobre componentes de navegação, como posicionamento e preferência por tipo de recurso de navegação. O modelo proposto está fundamentado nas recomendações de Nielsen [NIE 00], o qual recomenda que as necessidades dos usuários na interatividade com a interface sejam identificadas junto a estes usuários. As recomendações apresentadas neste trabalho foram utilizadas, inicialmente, nos ambientes educacionais desenvolvidos dentro dos projetos Tapejara [TAP 00] e LaVia [LAV 00].