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

Formation of out of plane oxime metallacycles in [Cu(2)] and [Cu(4)] complexes

The reaction Of Cu(ClO(4))(2)center dot 6H(2)O with dimethylglyoxime (H(2)dmg) in a 1:1 mole ratio in aqueous methanol at room temperature affords the dinuclear complex [Cu(2)(mu-Hdmg)(4)] (1). Reaction of 1 with [Cu(bpy)(H(2)O)(2)](ClO(4))(2) (bpy = 2,2`-bipyridine) in a 1:1 mole ratio in aqueous methanol at room temperature yields the tetranuclear complex [Cu(2)(mu-HdMg)(2)(mu-dMg)(2)(bpy)(2)(H(2)O)(2)](ClO(4))(2) (2). The direct reaction of Cu(ClO(4))(2)center dot 6H(2)O with H(2)dmg and bpy in a 2:21 mole ratio in aqueous methanol at room temperature also yields 2 quantitatively. The complexes 1 and 2 were structurally characterized by X-ray crystallography. Unlike the binding in Ni/Co-dmg, two different types of N-O bridging modes during the oxime based metallacycle formation and stacking of square planar units have been identified in these complexes. The neutral dinuclear complex 1 has CuN(4)O coordination spheres and complex 2 consists of a dicationic [Cu(2)(mu-HdMg)(2)(mu-dMg)(2)(bpy)(2)(H(2)O)(2)](2+) unit and two uncoordinated ClO(4)(-) anions having CuN(4)O and CuN(2)O(3) coordination spheres. The two copper(II) ions are at a distance of 3.846(8) angstrom in 1 for the trans out of plane link and at 3.419(10) and 3.684(10) angstrom in 2 for the trans out of plane and cis in plane arrangements, respectively. The average Cu-N(oxime) distances are 1.953 and 1.935 angstrom, respectively. The average basal and apical Cu-N(oxime) distances are 1.945, 2.295 and 2.429 angstrom. The UV-Vis spectra of 2 is similar to the spectrum of the reaction mixture of 1 and [Cu(bpy)(H(2)O)(2)](2+). Variable temperature magnetic properties measurement shows that the interaction between the paramagnetic copper centers in complex I is antiferromagnetic in nature. The EPR spectra of frozen solution of the complexes at 77 K consist of axially symmetric fine-structure transitions (Delta M(S) = 1) and half-field signals (Delta M(S) = 2) at ca. 1600 G, suggesting the presence of appreciable Cu-Cu interactions. (C) 2009 Elsevier Ltd. All rights reserved.

Cellulose swelling by aprotic and protic solvents: What are the similarities and differences?

The swelling of microcrystalline, native and mercerized cotton and eucalyptus celluloses by 16 aprotic solvents was investigated. The number of moles of solvent/anhydroglucose unit, nSw, correlates well with solvent molar volume, basicity and dipolarity/polarizability. Swelling is sensitive to cellulose crystallite size, surface area and the presence of its chains in parallel or anti-parallel arrangements. Use of solvatochromic parameters is a superior alternative to the use of other descriptors, such as Hildebrand`s solubility parameters and Gutmann`s donor numbers. The calculated nSw for 28 protic and aprotic solvents correlated well with their experimental counterparts, although hydrogen bond donation by the solvent was not included.

Cellulose swelling by protic solvents: which properties of the biopolymer and the solvent matter?

The question posed in the title has been addressed by studying the swelling of celluloses at 20 C by twenty protic solvents, including water; linear- and branched-chain aliphatic alcohols; unsaturated aliphatic alcohols, and alkoxyalcohols. The biopolymers investigated included microcrystalline cellulose, MC, native and never-dried mercerized cotton cellulose, cotton and M-cotton, and native and never-dried mercerized eucalyptus cellulose, eucalyptus and M-eucalyptus, respectively. In most cases, better correlations with the physico-chemical properties of the solvents were obtained when the swelling was expressed as number of moles of solvent/anhydroglucose unit, nSw, rather than as % increase in sample weight. The descriptors employed in these correlations included, where available, Hildebrand`s solubility parameters, Gutmann`s acceptor and donor numbers, solvent molar volume, V(S), as well as solvatochromic parameters. The latter, employed for the first time for correlating the swelling of biopolymers, included empirical solvent polarity, E(T)(30), solvent ""acidity"", alpha(S), ""basicity"", beta(S), and dipolarity/polarizability, pi(S)*, respectively. Small regression coefficients and large sums of the squares of the residues were obtained when values of nSw were correlated with two solvent parameters. Much better correlations were obtained with three solvent parameters. The most statistically significant descriptor in the correlation equation depends on the cellulose, being pi(S)* for MC, cotton, and eucalyptus, and V(S) for M-cotton and M-eucalyptus. The best correlations were obtained with the same set of four parameters for all celluloses, namely, solvent pKa (or alpha(S)) beta(S), pi(S)*, and V(S), respectively. These results indicate that the supra-molecular structure of the biopolymer, in particular the average sizes of crystallites and micro-pores, and the presence of its chains in parallel (cellulose I) or anti-parallel (cellulose II) arrangements control its swelling. At least for the present biopolymer/solvent systems, use of solvatochromic parameters is a superior alternative to Hildebrand`s solubility parameters and/or Gutmann`s acceptor and donor numbers. The relevance of these results to the accessibility of the hydroxyl groups of cellulose, hence to its reactivity, is briefly discussed.

The influence of perhydroazepine and piperidine as further ancillary ligands on Ru-PPh(3)-based catalysts for ROMP of norbornene and norbornadiene

Polynorbornadiene and polynorbornene were synthesized via ring opening metathesis polymerization (ROMP) with [RuCl(2)(PPh(3))(2)(amine)] as catalyst precursors, amine = piperidine (1) or perhydroazepine (2) in the presence of 5 mu L of ethyl diazoacetate (EDA) ([monomer]/[Ru] = 5000; 40 degrees C with 1; 25 degrees C with 2). The effects of the solvent volume (2-8 mL of CHCl(3)) reaction time (5-120 min) and atmosphere type (argon and air) on the yields were investigated to observe the behavior of the two different precursors. Quantitative yields were obtained for 60 or 120 min regardless of the starting volumes, either in argon or air, with both Ru species. However, low yields were obtained for short times (5-30 min) when the reactions are performed with large volumes (6-8 mL). In argon, the yields were larger with 2, associated to a faster propagation reaction controlled by the Ru active species. In air, the yields were larger with 1, associated to a higher resistance to O(2) of the starting and propagating Ru species. The different activities between 1 and 2 are discussed considering the steric hindrance and electronic characteristics of the amines such as ancillary ligands and their arrangements with PPh(3) and Cl(-) ions in the metal centers. (c) 2009 Elsevier B.V. All rights reserved.

Sociologin, hybriderna och den sociala verkligheten : exemplet kärnavfall

Sociology, hybrids and social reality: the case of nuclear waste The continuing technological transformation of nature means that sociology’s traditional vision of a sharp divide between nature and society is becoming ever harder to defend. Starting from Bruno Latour’s critique of modernity, and Nikolas Rose’s explorations of political power beyond the state, this article presents a framework for analysing the expanding wealth of hybrids of nature and society surrounding us today, and the problems of government they pose. These hybrids confront us with the need to rethink sociology’s conception of ‘the social’. With Latour’s help, the interplay of nature and society can be understood as subject to technical mediation, opening the way for studies of the varying arrangements through which different configurations of nature and society are produced. Rather than alternative social constructions of nature, what sociologists should be at pains to analyse and question are different programmes and strategies for bringing together natural and social forces in durable combinations. In the article, the geological disposal of nuclear waste serves as a useful example for exploring the fruitfulness of the analytical framework put forward. This complex undertaking constitutes just one component in a larger field of technoscientific endeavour that has irrevocably transformed nature while simultaneously re-making society. Addressing this case, we seek to reveal the promise of a sociology that does not bound ‘the social’ in advance, but rather makes the co-production of technology and society one of its most important objects of study.

Demokrati eller presidentdiktatur? : Konstitutionella vägval i postkommunistiska länder

While authoritarian presidents prevail under heavily president-oriented constitutions throughout the post-Soviet region, democracy along parliamentary lines triumphs in Central Europe. This article discusses the constitutional pattern among the post-communist countries on the basis of two general questions: First, how can we explain why strong presidential constitutions dominate throughout the post-Soviet region whereas constrained presidencies and governments anchored in parliament have become the prevailing option in Central Europe? Second, and interlinked with the first question, why have so many post-communist countries (in the post-Soviet region as well as in Central Europe) chosen neither parliamentarism nor presidentialism, but instead semi-presidential arrangements whereby a directly elected president is provided with considerable powers and coexists with a prime minister? The analysis indicates that both historical-institutional and actor-oriented factors are relevant here. Key factors have been regime transition, pre-communist era constitutions and leaders, as well as short-term economic and political considerations. With differing strengths and in partly different ways, these factors seem to have affected the actors’ preferences and final constitutional compromises.

"Jag slåss med rosa handskar, men de är fan inte fluffiga" : En kvalitativ studie om verksamheten Pink Gloves Boxing

Syftet med denna studie var att undersöka vilken betydelse verksamheten Pink Gloves Boxing haft för enskilda deltagares psykosociala livssituation, som öppenvårdsinsats i Borlänge kommun. Dessutom har syftet varit att undersöka vilka komponenter i verksamheten som bidragit till en eventuell förändring avseende psykosocial livssituation. Då studien ämnat fånga deltagares subjektiva upplevelser av Pink Gloves Boxing har det empiriska materialet insamlats genom semistrukturerade intervjuer med sex deltagare. Genom en tematisk analys av det insamlade materialet framkom centrala teman och subteman, vilka utgjort grunden i studiens resultatdel. För att analysera resultatet har en teoretisk tolkningsram tillämpats, vilken innefattat teorier om empowerment och genus. Samtliga informanter pekar på bättre fysik och ökad psykisk hälsa, av sitt deltagande i verksamheten. Stresshantering, aggressionskontroll och grupptillhörighet är exempel på förtjänster av ett deltagande, som informanterna framhållit. Gynnande komponenter som framträder i verksamheten är tränarnas roll, gruppen, träningsformen och verksamhetens upplägg, som exempelvis endast kvinnliga deltagare och gruppsamtal.

Design and use of mobile technology in distance language education : Matching learning practices with technologies-in-practice

This thesis focuses on the adaptation of formal education to people’s technology- use patterns, theirtechnology-in-practice, where the ubiquitous use of mobile technologies is central. The research question is: How can language learning practices occuring in informal learning environments be effectively integrated with formal education through the use of mobile technology? The study investigates the technical, pedagogical, social and cultural challenges involved in a design science approach. The thesis consists of four studies. The first study systematises MALL (mobile-assisted language learning) research. The second investigates Swedish and Chinese students’ attitudes towards the use of mobile technology in education. The third examines students’ use of technology in an online language course, with a specific focus on their learning practices in informal learning contexts and their understanding of how this use guides their learning. Based on the findings, a specifically designed MALL application was built and used in two courses. Study four analyses the app use in terms of students’ perceived level of self-regulation and structuration. The studies show that technology itself plays a very important role in reshaping peoples’ attitudes and that new learning methods are coconstructed in a sociotechnical system. Technology’s influence on student practices is equally strong across borders. Students’ established technologies-in-practice guide the ways they approach learning. Hence, designing effective online distance education involves three interrelated elements: technology, information, and social arrangements. This thesis contributes to mobile learning research by offering empirically and theoretically grounded insights that shift the focus from technology design to design of information systems.

Unlicensed personnel administering medications to older persons living at home : a challenge for social and care services

BACKGROUND: Administration of medication to care recipients is delegated to home-care assistants working in the municipal social care, alongside responsibility for providing personal assistance for older people. Home-care assistants have practical administration skills, but lack formal medical knowledge. AIM: The aim of this study was to explore how home-care assistants perceive administration of medication to older people living at home, as delegated to them in the context of social care. METHODS: Four focus groups consisting of 19 home-care assistants were conducted. Data were analysed using qualitative content analysis. RESULTS: According to home-care assistants, health and social care depends on delegation arrangements to function effectively, but in the first place it relieves a burden for district nurses. Even when the delegation had expired, administration of medication continued, placing the statutes of regulation in a subordinate position. There was low awareness among home-care assistants about the content of the statutes of delegation. Accepting delegation to administer medications has become an implicit prerequisite for social care work in the municipality. CONCLUSIONS: Accepting the delegation to administer medication was inevitable and routine. In practice, the regulating statute is made subordinate and consequently patient safety can be threatened. The organisation of health and social care relies on the delegation arrangement to meet the needs of a growing number of older home-care recipients. IMPLICATIONS FOR PRACTICE: This is a crucial task which management within both the healthcare professions and municipal social care needs to address, to bridge the gap between statutes and practice, to create arenas for mutual collaboration in the care recipients' best interest and to ensure patient safety.

A simplified heat pump model for use in solar plus heat pump system simulation studies

Solar plus heat pump systems are often very complex in design, with sometimes special heat pump arrangements and control. Therefore detailed heat pump models can give very slow system simulations and still not so accurate results compared to real heat pump performance in a system. The idea here is to start from a standard measured performance map of test points for a heat pump according to EN 14825 and then determine characteristic parameters for a simplified correlation based model of the heat pump. By plotting heat pump test data in different ways including power input and output form and not only as COP, a simplified relation could be seen. By using the same methodology as in the EN 12975 QDT part in the collector test standard it could be shown that a very simple model could describe the heat pump test data very accurately, by identifying 4 parameters in the correlation equation found. © 2012 The Authors.

Simulation model using meta heuristic algorithms for achieving optimal arrangement of storage bins in a sawmill yard

Bin planning (arrangements) is a key factor in the timber industry. Improper planning of the storage bins may lead to inefficient transportation of resources, which threaten the overall efficiency and thereby limit the profit margins of sawmills. To address this challenge, a simulation model has been developed. However, as numerous alternatives are available for arranging bins, simulating all possibilities will take an enormous amount of time and it is computationally infeasible. A discrete-event simulation model incorporating meta-heuristic algorithms has therefore been investigated in this study. Preliminary investigations indicate that the results achieved by GA based simulation model are promising and better than the other meta-heuristic algorithm. Further, a sensitivity analysis has been done on the GA based optimal arrangement which contributes to gaining insights and knowledge about the real system that ultimately leads to improved and enhanced efficiency in sawmill yards. It is expected that the results achieved in the work will support timber industries in making optimal decisions with respect to arrangement of storage bins in a sawmill yard.

Religion and Subjective Well-Being Among China’s Elderly Population

Evidence from developed and developing countries alike demonstrates a strongly positive relationship between religiosity and happiness, particularly for women and particularly among the elderly. Using survey data from the oldest old in China, we find a strong negative relationship between religious participation and subjective well-being in a rich multivariate logistic framework that controls for demographics, health and disabilities, living arrangements and marital status, wealth and income, lifestyle and social networks, and location. In contrast to other studies, we also find that religion has a larger effect on subjective well-being on men than women.

Rawls and Health Care

John Rawls’s A Theory of Justice (1971), his first major work articulating his theory of justice as fairness, was immediately recognized as a fundamental contribution to political philosophy in the twentieth century. Working within the tradition established by previous philosophers such as Kant and Locke, Rawls employed the contract theory approach. Taking it to a higher order of abstraction, he sought to determine not what the structure of social organization would be, but what the principles which governed social institutions would be under a hypothetical contracting situation. Rawls uses this contract theory approach to construct a society in which the morally irrelevant contingencies of nature and social arrangements are mitigated by principles of justice which govern the basic institutions of society. A common observation has been that Rawls left out any discussion of health care and how it might fit into his conception of a just society. Several philosophers have articulated expansions of the theory to account for health care. In the chapters that follow I will continue this tradition and consider how justice as fairness might be expanded to account for just health care allocation. In doing so, I hope to answer a particularly strong critique of the theory brought up by Amartya Sen and Martha Nussbaum, and to argue for a broadened conception of health care which takes into account the complex causal relationship between society and human health.