Thermodynamic concepts in adaptive resolution simulations

This thesis work is devoted to the conceptual and technical development of the Adaptive Resolution Scheme (AdResS), a molecular dynamics method that allows the simulation of a system with different levels of resolution simultaneously. The simulation domain is divided into high and low resolution zones and a transition region that links them, through which molecules can freely diffuse.rnThe first issue of this work regards the thermodynamic consistency of the method, which is tested and verified in a model liquid of tetrahedral molecules. The results allow the introduction of the concept of the Thermodynamic Force, an external field able to correct spurious density fluctuations present in the transition region in usual AdResS simulations.rnThe AdResS is also applied to a system where two different representations with the same degree of resolution are confronted. This simple test extends the method from an Adaptive Resolution Scheme to an Adaptive Representation Scheme, providing a way of coupling different force fields based on thermodynamic consistency arguments. The Thermodynamic Force is successfully applied to the example described in this work as well.rnAn alternative approach of deducing the Thermodynamic Force from pressure consistency considerations allows the interpretation of AdResS as a first step towards a molecular dynamics simulation in the Grand Canonical ensemble. Additionally, such a definition leads to a practical way of determining the Thermodynamic Force, tested in the well studied tetrahedral liquid. The effects of AdResS and this correction on the atomistic domain are analyzed by inspecting the local distribution of velocities, radial distribution functions, pressure and particle number fluctuation. Their comparison with analogous results coming from purely atomistic simulations shows good agreement, which is greatly improved under the effect of the external field.rnA further step in the development of AdResS, necessary for several applications in biophysics and material science, consists of its application to multicomponent systems. To this aim, the high-resolution representation of a model binary mixture is confronted with its coarse-grained representation systematically parametrized. The Thermodynamic Force, whose development requires a more delicate treatment, also gives satisfactory results.rnFinally, AdResS is tested in systems including two-body bonded forces, through the simulation of a model polymer allowed to adaptively change its representation. It is shown that the distribution functions that characterize the polymer structure are in practice not affected by the change of resolution.rnThe technical details of the implementation of AdResS in the ESPResSo package conclude this thesis work.Diese Arbeit befasst sich mit den konzeptionellen und technischen Entwicklung des "Adaptive Resolution Scheme" (AdResS), einer Methode der Molekulardynamik, welche die gleichzeitige Simulation eines System in unterschiedlichen Auflösungen, ermöglicht. Die Simulationsdomäne teiltsich in einen Bereich mit höherer und einen Bereich mit geringerer Auflösung.rnGekoppelt sind sie durch einen Übergangsbereich, indem die Moleküle frei diffundieren können.rnDer erste Teil der Dissertation ist auf die thermodynamische Konsistenz der Methode fokussiert, die an einem flüssigen Modell aus tetraedrischen Molekülen getestet und verifiziert wurde. Die Ergebnisse erlauben die Einführung des Konzepts der Thermodynamischen Kraft, bei dem ein externes Feld unphysikalische Dichtefluktuationen im Übergangsbereich, die in üblichen AdResS Simulationen auftreten, korrigiert. AdResS wird auch auf ein System angewandt, bei dem sich zwei unterschiedliche Darstellungen mit identischem Auflösungsniveau gegenüberstehen. Dieser einfache Test erweitert die Anwendbarkeit der Methode von einem Schema mit adaptiver Auflösung zu einem Schema mit adaptiver Darstellung, in dem unterschiedliche Kraftfelder, die auf thermodynamischen Konsistenzargumenten basieren, gekoppelt werden können. Die Methode der Thermodynamischen Kraft wurde in dem hier dargestellten Beispiel erfolgreich angewandt.rnEin alternativer, auf konstantem Druck basierender Ansatz für die Deduktion der Thermodynamischen Kraft, ermöglicht die Interpretation des AdResS als ersten Schritt hin zu einer molekulardynamischen Simulation im gross kanonischen Ensemble. Ausserdem hilft eine solche Definition die Thermodynamisches Kraft, die in der bekannten tetraedrischen Flüssigkeit getestet wird, einfacher zu bestimmen. Die Effekte von AdResS und deren Korrektur im atomistische Bereich der Simulation wurden durch die Untersuchung der lokalen Verteilung der Geschwindigkeiten, Radialverteilungsfunktionen, Druck und Schwankung der Partikelanzahl, analysiert. Deren Vergleich mit analogen Ergebnissen aus rein atomistichen Simulationen zeigt eine gute Übereinstimmung, die unter dem Einfluss des externen Feldes noch gesteigert wird.rnEin weiterer Schritt in der Entwicklung des AdResS, der für verschiedene Anwendungen in der Biophysik und Materialkunde nötig ist, setzt seine Anwendung zu Multikomponentensystemen voraus. In dieser Hinsicht wird die Darstellung in höherer Auflösung eines binären Mischungsmodells gegen seine vergröberte (coarse-grained) Darstellung systematisch parametrisiert. Dabei bringt die Methode der Thermodynamischen Kraft zufriedenstellende Ergebnisse, auch wenn ihre Entwicklung eine noch feinere Bearbeitung benötigt.rnSchliess lich wurde das AdResS in Systemen mit zweikörper-gebundenen Kräften durch die Simulation von einem Modellpolymer, dem es erlaubt ist, seine Darstellung adaptiv zu verändern, getestet. Es wird gezeigt, dass die Verteilung der Funktionen, die die Polymerstruktur charakterisieren, in der Praxis durch eine Veränderung der Auflösung nicht beeinflusst wird.rnDie Erläuterung der technischen Details für die Ausführung von AdResS im ESPResSo Softwarepaket bildet den letzten Teil dieser Dissertation

Using a Gridded Global Dataset to Characterize Regional Hydroclimate in Central Chile

Central Chile is facing dramatic projections of climate change, with a consensus for declining precipitation, negatively affecting hydropower generation and irrigated agriculture. Rising from sea level to 6000 m within a distance of 200 km, precipitation characterization is difficult because of a lack of long-term observations, especially at higher elevations. For understanding current mean and extreme conditions and recent hydroclimatological change, as well as to provide a baseline for downscaling climate model projections, a temporally and spatially complete dataset of daily meteorology is essential. The authors use a gridded global daily meteorological dataset at 0.25° resolution for the period 1948–2008, adjusted by monthly precipitation observations interpolated to the same grid using a cokriging method with elevation as a covariate. For validation, daily statistics of the adjusted gridded precipitation are compared to station observations. For further validation, a hydrology model is driven with the gridded 0.25° meteorology and streamflow statistics are compared with observed flow. The high elevation precipitation is validated by comparing the simulated snow extent to Moderate Resolution Imaging Spectroradiometer (MODIS) images. Results show that the daily meteorology with the adjusted precipitation can accurately capture the statistical properties of extreme events as well as the sequence of wet and dry events, with hydrological model results displaying reasonable agreement with observed streamflow and snow extent. This demonstrates the successful use of a global gridded data product in a relatively data-sparse region to capture hydroclimatological characteristics and extremes

Emerging materials for transition: A taxonomy proposal from a design perspective

In response to environmental challenges, design promotes emerging materials connected with the circular economy and environmental sustainability. However, there is confusion about their definition and contribution to sustainable design and production, showing a gap in their classification. This article proposes a taxonomy as a helpful tool to consolidate and unify terminology, definitions and general understanding of these emerging materials. An analysis of 31 real-world case studies helped outline the taxonomic proposal to formalise knowledge, fostering clarity in classifying and identifying them. The taxonomy aims to organise emerging materials, generate reflections, and encourage their responsible development, diffusion, and adoption

Emerging materials fostering interdisciplinary collaboration in Materials Design

Materials Design is a recognized emerging and growing area in design practice and research that converges different fields and approaches to addressing a holistic perspective of materials in and for design. Therefore, it incorporates knowledge from various disciplines, like engineering and science. Direct interdisciplinary collaboration between engineers, scientists, artists and designers can benefit projects whose purpose is to bring innovation regarding materials and design. We assume this interdisciplinarity is a crucial practice for developing the emerging field of Materials Design with a sustainable and circular perspective. This article conveys the findings of an empirical collection of case studies on emerging materials and product design. The results demonstrate the sustainability and circularity orientations they present and different disciplinary cooperation to generate innovative outcomes. The authors examined ten European enterprises that present products driven by emerging materials from alternative sources to support the statement. The paper identifies and reflects on the importance and value of collaboration. It aims to disseminate knowledge about the field of Materials Design and intends to highlight that interdisciplinary collaboration in this area can be favourable for achieving a sustainable paradigm and more responsible production and consumption patterns

Variation in fine-scale genetic structure and local dispersal patterns between peripheral populations of a South American passerine bird

Indexación: Scopus.The distribution of suitable habitat influences natal and breeding dispersal at small spatial scales, resulting in strong microgeographic genetic structure. Although environmental variation can promote interpopulation differences in dispersal behavior and local spatial patterns, the effects of distinct ecological conditions on within-species variation in dispersal strategies and in fine-scale genetic structure remain poorly understood. We studied local dispersal and fine-scale genetic structure in the thorn-tailed rayadito (Aphrastura spinicauda), a South American bird that breeds along a wide latitudinal gradient. We combine capture-mark-recapture data from eight breeding seasons and molecular genetics to compare two peripheral populations with contrasting environments in Chile: Navarino Island, a continuous and low density habitat, and Fray Jorge National Park, a fragmented, densely populated and more stressful environment. Natal dispersal showed no sex bias in Navarino but was female-biased in the more dense population in Fray Jorge. In the latter, male movements were restricted, and some birds seemed to skip breeding in their first year, suggesting habitat saturation. Breeding dispersal was limited in both populations, with males being more philopatric than females. Spatial genetic autocorrelation analyzes using 13 polymorphic microsatellite loci confirmed the observed dispersal patterns: a fine-scale genetic structure was only detectable for males in Fray Jorge for distances up to 450 m. Furthermore, two-dimensional autocorrelation analyzes and estimates of genetic relatedness indicated that related males tended to be spatially clustered in this population. Our study shows evidence for context-dependent variation in natal dispersal and corresponding local genetic structure in peripheral populations of this bird. It seems likely that the costs of dispersal are higher in the fragmented and higher density environment in Fray Jorge, particularly for males. The observed differences in microgeographic genetic structure for rayaditos might reflect the genetic consequences of population-specific responses to contrasting environmental pressures near the range limits of its distribution.http://onlinelibrary.wiley.com/doi/10.1002/ece3.3342/epd

Перспективы развития биотехнологий

В статье затронуты проблемы демографического кризиса. Рассмотрены вопросы развития биотехнологий, а так же существующие виды биотехнологий. Более глубоко рассмотрен такой вид биотехнологии как биомедицина, представлены существующие наработки ученых в этой сфере. При изучении был сделан вывод, что развитие биотехнологии, в честности биомедицины приведет к повышению продолжительности жизни, а вследствие решения демографической проблемы.The article touches upon the problems of the demographic crisis. The questions of development of biotechnologies, as well as existing types of biotechnologies are considered. Deeply considered this kind of biotechnology as biomedicine, presents the existing developments of scientists in this field. The study concluded that the development of biotechnology, in the honesty of biomedicine, will lead to an increase in life expectancy, and as a result of solving the demographic problem

Consideraciones generales acerca del uso de la laringe eléctrica en la reeducación logopédica de un laringectomizado

The aim of this paper is to spread the use of the electrolarynx as one of the methods used within the context of voice therapygiven to a person who has lost the larynx and therefore the ability to communicate orally, with the role of the voice pathologyspecialist being decisive the in improving the quality of life for cancer patientsEl objetivo del presente artículo es difundir el uso de la laringe eléctrica como uno de los métodos usados dentro del contexto dela reeducación logopédica a la que va a ser sometido a la persona que ha perdido la laringe y por ende la capacidad paracomunicarse oralmente. Siendo el rol de la especialista en patología vocal determinante para mejorar la calidad de vida delpaciente oncológic

Efficient Path Planning in Narrow Passages via Closed-Form Minkowski Operations

Path planning has long been one of the major research areas in robotics, with PRM and RRT being two of the most effective classes of path planners. Though generally very efficient, these sampling-based planners can become computationally expensive in the important case of "narrow passages". This paper develops a path planning paradigm specifically formulated for narrow passage problems. The core is based on planning for rigid-body robots encapsulated by unions of ellipsoids. The environmental features are enclosed geometrically using convex differentiable surfaces (e.g., superquadrics). The main benefit of doing this is that configuration-space obstacles can be parameterized explicitly in closed form, thereby allowing prior knowledge to be used to avoid sampling infeasible configurations. Then, by characterizing a tight volume bound for multiple ellipsoids, robot transitions involving rotations are guaranteed to be collision-free without traditional collision detection. Furthermore, combining the stochastic sampling strategy, the proposed planning framework can be extended to solving higher dimensional problems in which the robot has a moving base and articulated appendages. Benchmark results show that, remarkably, the proposed framework outperforms the popular sampling-based planners in terms of computational time and success rate in finding a path through narrow corridors and in higher dimensional configuration spaces

A structural model of cooking fuel choices in developing countries

Access to cleaning cooking fuels and stoves is an important indicator of well-being, as this enables several improvements in quality of life. In many developing countries, a big proportion of the population still depends on biomass for cooking, and the adoption of clean cooking fuels is still limited. Here, we propose a structural model to estimate household demand and choices for cooking fuel using micro-datasets from nationally representative surveys for a subset of developing countries. We test the model by estimating the demand response to simulated changes in fuel prices and income. We find that the model provides a close approximation to the observed patterns in the data from the surveys. We also find that as long as incomes rise and the relative difference between the prices of biomass and cleaner fuels decreases, households will transition to cleaner cooking fuels. We discuss potential applications of the method for constructing and analyzing future scenarios of cooking energy transitions