Evaluating boundary dependent errors in QM/MM simulations.

Hybrid quantum mechanics/molecular mechanics (QM/MM) simulations provide a powerful tool for studying chemical reactions, especially in complex biochemical systems. In most works to date, the quantum region is kept fixed throughout the simulation and is defined in an ad hoc way based on chemical intuition and available computational resources. The simulation errors associated with a given choice of the quantum region are, however, rarely assessed in a systematic manner. Here we study the dependence of two relevant quantities on the QM region size: the force error at the center of the QM region and the free energy of a proton transfer reaction. Taking lysozyme as our model system, we find that in an apolar region the average force error rapidly decreases with increasing QM region size. In contrast, the average force error at the polar active site is considerably higher, exhibits large oscillations and decreases more slowly, and may not fall below acceptable limits even for a quantum region radius of 9.0 A. Although computation of free energies could only be afforded until 6.0 A, results were found to change considerably within these limits. These errors demonstrate that the results of QM/MM calculations are heavily affected by the definition of the QM region (not only its size), and a convergence test is proposed to be a part of setting up QM/MM simulations.

In Bello, Pax: a responsabilidade penal dos brasileiros em Operações de Paz

Esta Tese analisa a possibilidade de responsabilização penal dos brasileiros que têm participado de operações de paz capitaneadas ou delegadas pela Organização das Nações Unidas. Além de apresentar como se procede esta responsabilização no ambiente nacional, também analisa a possibilidade de sua responsabilização internacional diante da evolução que esta tem constatado desde o final do período conhecido como guerra-fria. Para tanto, parte de uma contextualização histórica da evolução e modificação das operações de paz, mostrando como o Brasil também modificou sua inserção nesta questão, em especial depois de 1990. Decorrente desse relevante aumento de responsabilidades e numérico de brasileiros engajados nestas operações apresenta como a fundamentação doutrinária legal e normativa também sofreu significativas mudanças nas últimas décadas. A partir deste ponto, fazendo uso de metodologia analítico-descritiva, apresenta as qualificações jurídicas admitidas, análise dos principais documentos internacionais que abordam a responsabilização penal dos integrantes de operações de paz e como se processa a relação entre estes documentos e o ordenamento jurídico brasileiro. Procura analisar como se processa, no ambiente interno, a jurisdição e competência para julgamento destas questões. Apresenta como o direito internacional tem sido influenciado pelo crescimento do direito internacional penal e como este pode se manifestar diante de integrantes de operações de paz, fazendo, inclusive, uma abordagem de como outras cortes internacionais têm se manifestado sobre a questão. Parte de decisões de direito interno de outros países, mostra a contribuição que os tribunais Ad Hoc instituídos pela ONU trouxeram para culminar na análise da possibilidade (ou não) de responsabilização destes integrantes pelo Tribunal Penal Internacional, ou mesmo, por terceiros Estados fazendo uso da Jurisdição Universal. Assim, a tese demonstra que efetivamente o Brasil dispõe de meios para exercer sua plena jurisdição perante seus nacionais envolvidos nestas operações internacionais, no entanto, a fim de garantir maior adensamento de juridicidade e sustentação legal, aponta possíveis soluções como contribuição para dirimir eventuais ponderações internas e internacionais.

Lehen Hezkuntzan autoezagutza fisikoa, emozionala eta soziala lantzeko proposamen didaktiko baten diseinua eta esku-hartzea

[eus] Autoezagutza ez akademikoa pertsonaren garapenaren pilare funtsezkoenetariko bat kontsideratzen da. Aldaketaren bat eragiteko asmoz, Lehen Hezkuntzako hirugarren mailako neska eta mutilei zuzenduta dauden ekintza batzuk diseinatu eta praktikan jarri dira. Adin honetako neska eta mutilak, haien nortasuna eta batez ere autoezagutzaren garapenaren erdian aurkitzen dira. Horregatik, “ad hoc” diseinatu diren pretest eta postest baten bitartez, ekintza hauek espero ziren aldaketak sorrarazi dituzten ebaluatu da.

Etymological notes on Aleut (III). With methodological notes on (Eskimo-Aleut) historical linguistics

[EN] The goal of this contribution is twofold: on the one hand, to review two relatively recent contributions in the field of Eskimo-Aleut historical linguistics in which it is proposed that Eskimo-Aleut languages are related genealogically to Wakashan (Holst 2004) and?/or Nostratic (Krougly-Enke 2008). These contributions can be characterized by saying that their authors have taken little care to be diligent and responsible in the application of the comparative method, and that their familiarity with the languages involved is insufficient. Eskimo-Aleut languages belong to a very exclusive group of language families that have been (and still are) used, sometimes compulsively, in the business of so-called “long-range comparisons”. Those carrying out such studies are very often unaware of the most basic facts regarding the philological and linguistic traditions of those languages, as a result of what mountains of very low quality works with almost no-relevancy for the specialist grow every year to the desperation of the scientific community, whose attitude toward them ranges from the most profound indifference to the toughest (and most explicit) critical tone. Since Basque also belongs to this group of “compare-with-everything-you-come- across” languages, it is my intention to provide the Basque readership with a sort of “pedagogical case” to show that little known languages, far from underrepresented in the field, already have a very long tradition in historical and comparative linguistics, i.e. nobody can approach them without previous acquaintance with the materials. Studies dealing with the methodological inappropriateness of the Moscow School’s Nostratic hypothesis or the incorrectness of many of the proposed new taxonomic Amerindian subfamilies (several of them involving the aforementioned Wakashan languages), that is to say, the frameworks on which Krougly-Enke and Holst work, respectively, are plenty (i.a. Campbell 1997: 260-329, Campbell & Poser 2008: 234-96), therefore there is no reason to insist once more on the very same point. This is the reason why I will not discuss per se Eskimo-Aleut–Wakashan or Eskimo-Aleut–Nostratic. On the contrary, I will focus attention upon very concrete aspects of Krougly-Enke and Holst´s proposals, i.e. when they work on “less ambitious” problems, for example, dealing with the minutiae of internal facts or analyzing certain words from the sole perspective of Eskimo-Aleut materials (in other words, those cases in which even they do not invoke the ad hoc help of Nostratic stuff). I will try to explain why some of their proposals are wrong, demonstrate where the problem lies, and fix it if possible. In doing so, I will propose new etymologies in an attempt at showing how we may proceed. The main difference between this and handbook examples lies in the reality of what we are doing: this is a pure etymological exercise from beginning to end. I will try to throw a bit of light on a couple of problematic questions regarding Aleut historical phonology, demonstrating how much work should be done at the lowest level of the Eskimo-Aleut pyramid; it is technically impossible to reach the peak of the pyramid without having completed the base. As far as Aleut is regarded, I will mainly profit not only from the use of the traditional philological analysis of Aleut (and, eventually, of Eskimo) materials, but also of diachronic typology, bringing into discussion what in my opinion seems useful, and in some cases I think decisive, parallels. It is worth noting that this paper makes up yet another part of a series of exploratory works dealing with etymological aspects of the reconstruction of Proto-Eskimo-Aleut, with special emphasis on Aleut (vid. i.a. Alonso de la Fuente 2006/2007, 2008a, 2008b, 2010a), whose main goal is to become the solid basis for an etymological dictionary of the Aleut language, currently in progress.

On the Stability and Equilibrium Points of Multistaged SI (n) R Epidemic Models

This paper relies on the concept of next generation matrix defined ad hoc for a new proposed extended SEIR model referred to as SI(n)R-model to study its stability. The model includes n successive stages of infectious subpopulations, each one acting at the exposed subpopulation of the next infectious stage in a cascade global disposal where each infectious population acts as the exposed subpopulation of the next infectious stage. The model also has internal delays which characterize the time intervals of the coupling of the susceptible dynamics with the infectious populations of the various cascade infectious stages. Since the susceptible subpopulation is common, and then unique, to all the infectious stages, its coupled dynamic action on each of those stages is modeled with an increasing delay as the infectious stage index increases from 1 to n. The physical interpretation of the model is that the dynamics of the disease exhibits different stages in which the infectivity and the mortality rates vary as the individual numbers go through the process of recovery, each stage with a characteristic average time.

Evolution of the tectogene concept, 1930-1965

The tectogene, or crustal downbuckle, was proposed in the early 1930s by F.A. Vening Meinesz to explain the unexpected belts of negative gravity anomalies in island arcs. He attributed the isostatic imbalance to a deep sialic root resulting from the action of subcrustal convection currents. Vening Meinesz's model was initially corroborated experimentally by P.H. Kuenen, but additional experiments by D.T. Griggs and geological analysis by H.H. Hess in the late 1930s led to substantial revision in detail. As modified, the tectogene provided a plausible model for the evolution of island arcs into alpine mountain belts for another two decades. Additional revisions became necessary in the early 1950s to accommodate the unexpected absence of sialic crust in the Caribbean and the marginal seas of the western Pacific. By 1960 the cherished analogy between island arcs and alpine mountain belts had collapsed under the weight of the detailed field investigations by Hess and his students in the Caribbean region. Hess then incorporated a highly modified form of the tectogene into his sea-floor spreading hypothesis. Ironically, this final incarnation of the concept preserved some of the weaker aspects of the 1930s original, such as the ad hoc explanation for the regular geometry of island arcs.

Vítimas e monstros: a construção do tipo "abuso sexual infantil" em laudos psicológicos no Judiciário.

Abuso sexual infantil é tomado na acepção do construcionismo social, como tipo classificatório, e com uma abordagem histórica. As fortes cargas moral e emocional da categoria são sublinhadas, assim como a noção de carreira moral da criança abusada e de abusador. A psicologia é um dos campos e disciplinas que construiu a categoria e a molda diariamente em suas práticas, teorizações e inclusão em instituições sociais e políticas. A dissertação busca analisar esta moldagem numa amostra de laudos psicológicos relativos a acusações de abuso sexual, constantes de processos de Varas de Família e Varas Criminais no Judiciário do Rio de Janeiro. Os laudos analisados são de autoria de psicólogos do quadro do Tribunal de Justiça do Estado do Rio de Janeiro (TJ-RJ), de psicólogos nomeados ad hoc, de instituições de atendimento a vítimas de violência sexual e de consultórios particulares. Como complementação, são analisadas entrevistas feitas com cinco psicólogos do quadro do TJ-RJ sobre laudos em acusações de abuso sexual infantil e sobre a categoria, afirmando a presença permanente desta, apesar de não mais como um boom (ocorrido no início dos anos 2000), em processos de guarda e visitação de filhos e criminais. A análise constatou a presença de duas posturas da psicologia, a das Varas de Família, que trabalha com a correlação litígio-falsa acusação de abuso sexual- alienação parental, em visão determinista, e a das Varas Criminais, marcada pela exclusão da avaliação do homem acusado e por fortes preconcepções, apoiadas na psicologia do abuso sexual, sobre a amplitude dos abusos sexuais e o testemunho da criança vítima e dos acusadores. Noções controversas de manuais clássicos da psicologia do abuso sexual, da psiquiatria e do senso comum sobre vitimização, sequelas, síndromes, pedofilia estão presentes nos laudos, assim como, mais raramente, o reconhecimento da sexualidade infantil e adolescente. O homem pode aparecer como um pai vitimizado ou um monstro moralmente desqualificado.

Application of a laminar flamelet model to confined explosion hazards

The majority of computational studies of confined explosion hazards apply simple and inaccurate combustion models, requiring ad hoc corrections to obtain realistic flame shapes and often predicting an order of magnitude error in the overpressures. This work describes the application of a laminar flamelet model to a series of two-dimensional test cases. The model is computationally efficient applying an algebraic expression to calculate the flame surface area, an empirical correlation for the laminar flame speed and a novel unstructured, solution adaptive numerical grid system which allows important features of the solution to be resolved close to the flame. Accurate flame shapes are predicted, the correct burning rate is predicted near the walls, and an improvement in the predicted overpressures is obtained. However, in these fully turbulent calculations the overpressures are still too high and the flame arrival times too low, indicating the need for a model for the early laminar burning phase. Due to the computational expense, it is unrealistic to model a laminar flame in the complex geometries involved and therefore a pragmatic approach is employed which constrains the flame to propagate at the laminar flame speed. Transition to turbulent burning occurs at a specified turbulent Reynolds number. With the laminar phase model included, the predicted flame arrival times increase significantly, but are still too low. However, this has no significant effect on the overpressures, which are predicted accurately for a baffled channel test case where rapid transition occurs once the flame reaches the first pair of baffles. In a channel with obstacles on the centreline, transition is more gradual and the accuracy of the predicted overpressures is reduced. However, although the accuracy is still less than desirable in some cases, it is much better than the order of magnitude error previously expected.

An analysis of the cooperative mechano-sensitive feedback between intracellular signaling, focal adhesion development, and stress fiber contractility

Cells communicate with their external environment via focal adhesions and generate activation signals that in turn trigger the activity of the intracellular contractile machinery. These signals can be triggered by mechanical loading that gives rise to a cooperative feedback loop among signaling, focal adhesion formation, and cytoskeletal contractility, which in turn equilibrates with the applied mechanical loads. We devise a signaling model that couples stress fiber contractility and mechano-sensitive focal adhesion models to complete this above mentioned feedback loop. The signaling model is based on a biochemical pathway where IP3 molecules are generated when focal adhesions grow. These IP3 molecules diffuse through the cytosol leading to the opening of ion channels that disgorge Ca2+ from the endoplasmic reticulum leading to the activation of the actin/myosin contractile machinery. A simple numerical example is presented where a one-dimensional cell adhered to a rigid substrate is pulled at one end, and the evolution of the stress fiber activation signal, stress fiber concentrations, and focal adhesion distributions are investigated. We demonstrate that while it is sufficient to approximate the activation signal as spatially uniform due to the rapid diffusion of the IP3 through the cytosol, the level of the activation signal is sensitive to the rate of application of the mechanical loads. This suggests that ad hoc signaling models may not be able to capture the mechanical response of cells to a wide range of mechanical loading events. © 2011 American Society of Mechanical Engineers.

Decision tree-based context clustering based on cross validation and hierarchical priors

The standard, ad-hoc stopping criteria used in decision tree-based context clustering are known to be sub-optimal and require parameters to be tuned. This paper proposes a new approach for decision tree-based context clustering based on cross validation and hierarchical priors. Combination of cross validation and hierarchical priors within decision tree-based context clustering offers better model selection and more robust parameter estimation than conventional approaches, with no tuning parameters. Experimental results on HMM-based speech synthesis show that the proposed approach achieved significant improvements in naturalness of synthesized speech over the conventional approaches. © 2011 IEEE.

Prices need no preferences: social trends determine decisions in experimental markets for pain relief.

OBJECTIVE: A standard view in health economics is that, although there is no market that determines the "prices" for health states, people can nonetheless associate health states with monetary values (or other scales, such as quality adjusted life year [QALYs] and disability adjusted life year [DALYs]). Such valuations can be used to shape health policy, and a major research challenge is to elicit such values from people; creating experimental "markets" for health states is a theoretically attractive way to address this. We explore the possibility that this framework may be fundamentally flawed-because there may not be any stable values to be revealed. Instead, perhaps people construct ad hoc values, influenced by contextual factors, such as the observed decisions of others. METHOD: The participants bid to buy relief from equally painful electrical shocks to the leg and arm in an experimental health market based on an interactive second-price auction. Thirty subjects were randomly assigned to two experimental conditions where the bids by "others" were manipulated to follow increasing or decreasing price trends for one, but not the other, pain. After the auction, a preference test asked the participants to choose which pain they prefer to experience for a longer duration. RESULTS: Players remained indifferent between the two pain-types throughout the auction. However, their bids were differentially attracted toward what others bid for each pain, with overbidding during decreasing prices and underbidding during increasing prices. CONCLUSION: Health preferences are dissociated from market prices, which are strongly referenced to others' choices. This suggests that the price of health care in a free-market has the capacity to become critically detached from people's underlying preferences.

Antiwindup design for induction motor control in the field weakening domain

Operation of induction machines in the high-speed and/or high-torque range requires field-weakening to comply with voltage and current physical limitations. This paper presents an anti-windup approach to this problem: rather than developing an ad-hoc field weakening strategy in the high-speed region, we equip an unconstrained vector-control design with an anti-windup module that automatically adjusts the current and flux set-points so that voltage and current constraints are satisfied at every operating point. The anti-windup module includes a feedforward modification of the set point aimed at maximizing the available torque in steady-state and a feedback modification of the controller based on an internal model-based antiwindup scheme. This paper includes a complete stability analysis of the proposed solution and presents encouraging experimental results on an industrial drive. © 2012 IEEE.

Assessing boost-assist options for turbocharged engines using 1-D engine simulation and model predictive control

Delivering acceptable low end torque and good transient response is a significant challenge for all turbocharged engines. As downsized gasoline engines and Diesel engines make up a larger and larger proportion of the light-duty engines entering the market, the issue takes on greater significance. Several schemes have been proposed to improve torque response in highly boosted engines, including the use of electrical assist turbochargers and compressed air assist. In this paper we examine these methods with respect to their effectiveness in improving transient response and their relative performance along with some of the practical considerations for real world application. Results shown in this paper are from 1-D simulations using the Ricardo WAVE software package. The simulation model is based on a production light-duty Diesel engine modified to allow the introduction of compressed air at various points in the air-path as well as direct torque application to the turbocharger shaft (such as might be available from an electrical assist turbocharger). Whilst the 1-D simulation software provides a suitable environment for investigating the various boost assistance options, the overall air path performance also depends upon the control system. The introduction of boost assistance complicates the control in two significant ways: the system may run into constraints (such as compressor surge) that are not encountered in normal operation and the assistance introduces an additional control input. Production engine controllers are usually based on gain-scheduled PID control and extensive calibration. For this study, the non-linear nature of the engine together with the multiple configurations considered and the slower than real-time execution of 1-D models makes such an approach time consuming. Moreover, an ad-hoc approach would leave some doubt as to the fairness of comparisons between the different boost-assist options. Model Predictive Control has been shown to offer a convenient approach to controlling the 1-D simulations in a close to optimal manner for a typical Diesel VGT-EGR air path configuration. We show that the same technique can be applied to all the considered assistance methods with only modest calibration effort required. Copyright © 2012 SAE International.

Model based control for closed loop testing of 1-D engine simulation models

1-D engine simulation models are widely used for the analysis and verification of air-path design concepts and prediction of the resulting engine transient response. The latter often requires closed loop control over the model to ensure operation within physical limits and tracking of reference signals. For this purpose, a particular implementation of Model Predictive Control (MPC) based on a corresponding Mean Value Engine Model (MVEM) is reported here. The MVEM is linearised on-line at each operating point to allow for the formulation of quadratic programming (QP) problems, which are solved as the part of the proposed MPC algorithm. The MPC output is used to control a 1-D engine model. The closed loop performance of such a system is benchmarked against the solution of a related optimal control problem (OCP). As an example this study is focused on the transient response of a light-duty car Diesel engine. For the cases examined the proposed controller implementation gives a more systematic procedure than other ad-hoc approaches that require considerable tuning effort. © 2012 IFAC.

Climb-enabled discrete dislocation plasticity

A small strain two-dimensional discrete dislocation plasticity framework coupled to vacancy diffusion is developed wherein the motion of edge dislocations is by a combination of glide and climb. The dislocations are modelled as line defects in a linear elastic medium and the mechanical boundary value problem is solved by the superposition of the infinite medium elastic fields of the dislocations and a complimentary non-singular solution that enforces the boundary conditions. Similarly, the climbing dislocations are modelled as line sources/sinks of vacancies and the vacancy diffusion boundary value problem is also solved by a superposition of the fields of the line sources/sinks in an infinite medium and a complementary non-singular solution that enforces the boundary conditions. The vacancy concentration field along with the stress field provides the climb rate of the dislocations. Other short-range interactions of the dislocations are incorporated via a set of constitutive rules. We first employ this formulation to investigate the climb of a single edge dislocation in an infinite medium and illustrate the existence of diffusion-limited and sink-limited climb regimes. Next, results are presented for the pure bending and uniaxial tension of single crystals oriented for single slip. These calculations show that plasticity size effects are reduced when dislocation climb is permitted. Finally, we contrast predictions of this coupled framework with an ad hoc model in which dislocation climb is modelled by a drag-type relation based on a quasi steady-state solution. © 2013 Elsevier Ltd. All rights reserved.