Distributed all-atom simulations of intrinsically unstructured proteins

The Computational Biophysics Group at the Universitat Pompeu Fabra (GRIB-UPF) hosts two unique computational resources dedicated to the execution of large scale molecular dynamics (MD) simulations: (a) the ACMD molecular-dynamics software, used on standard personal computers with graphical processing units (GPUs); and (b) the GPUGRID. net computing network, supported by users distributed worldwide that volunteer GPUs for biomedical research. We leveraged these resources and developed studies, protocols and open-source software to elucidate energetics and pathways of a number of biomolecular systems, with a special focus on flexible proteins with many degrees of freedom. First, we characterized ion permeation through the bactericidal model protein Gramicidin A conducting one of the largest studies to date with the steered MD biasing methodology. Next, we addressed an open problem in structural biology, the determination of drug-protein association kinetics; we reconstructed the binding free energy, association, and dissaciociation rates of a drug like model system through a spatial decomposition and a Makov-chain analysis. The work was published in the Proceedings of the National Academy of Sciences and become one of the few landmark papers elucidating a ligand-binding pathway. Furthermore, we investigated the unstructured Kinase Inducible Domain (KID), a 28-peptide central to signalling and transcriptional response; the kinetics of this challenging system was modelled with a Markovian approach in collaboration with Frank Noe’s group at the Freie University of Berlin. The impact of the funding includes three peer-reviewed publication on high-impact journals; three more papers under review; four MD analysis components, released as open-source software; MD protocols; didactic material, and code for the hosting group.

A systolic array for linear MIMO detection based on an all-swap lattice reduction algorithm

A systolic array to implement lattice-reduction-aided lineardetection is proposed for a MIMO receiver. The lattice reductionalgorithm and the ensuing linear detections are operated in the same array, which can be hardware-efficient. All-swap lattice reduction algorithm (ASLR) is considered for the systolic design.ASLR is a variant of the LLL algorithm, which processes all lattice basis vectors within one iteration. Lattice-reduction-aided linear detection based on ASLR and LLL algorithms have very similarbit-error-rate performance, while ASLR is more time efficient inthe systolic array, especially for systems with a large number ofantennas.

Putting health in all policies: The National Institute for Welfare Enhancement

Welfare is a rather vague term whose meaning depends on ideology, values andjudgments. Material resources are just means to enhance people s well-being, butgrowth of the Gross Domestic Production is still the standard measure of thesuccess of a society. Fortunately, recent advances in measuring social performanceinclude health, education and other social outcomes. Because what we measureaffects what we do it is hoped that social policies will change. The movementHealth in all policies and its associated Health Impact Assessment methodologywill contribute to it. The task consists of designing transversal policies thatconsider health and other welfare goals, the short term and long-term implicationsand intergenerational redistributions of resources. As long as marginalproductivity on health outside the healthcare system is higher than inside it,efficiency needs cross-sectoral policies. And fairness needs them even more,because in order to reduce social inequalities in health, a wide social and politicalresponse is needed.Unless we reduce the well-documented inefficiencies in our current health caresystems the welfare states will fail to consolidate and the overall economic wellbeingcould be in serious trouble. In this article we sketched some policy solutionssuch as pricing according to net benefits of innovation and public encouragementof radical innovation besides the small type incremental and market-ledinnovation. We proposed an independent agency, the National Institute forWelfare Enhancement to guarantee long term fair and efficient social policies inwhich health plays a central role.

Strategies for an integrated distribution problem

The problems arising in the logistics of commercial distribution are complexand involve several players and decision levels. One important decision isrelated with the design of the routes to distribute the products, in anefficient and inexpensive way.This article explores three different distribution strategies: the firststrategy corresponds to the classical vehicle routing problem; the second isa master route strategy with daily adaptations and the third is a strategythat takes into account the cross-functional planning through amulti-objective model with two objectives. All strategies are analyzed ina multi-period scenario. A metaheuristic based on the Iteratetd Local Search,is used to solve the models related with each strategy. A computationalexperiment is performed to evaluate the three strategies with respect to thetwo objectives. The cross functional planning strategy leads to solutions thatput in practice the coordination between functional areas and better meetbusiness objectives.

Driver scheduling problem modelling

The Drivers Scheduling Problem (DSP) consists of selecting a set of duties for vehicle drivers, for example buses, trains, plane or boat drivers or pilots, for the transportation of passengers or goods. This is a complex problem because it involves several constraints related to labour and company rules and can also present different evaluation criteria and objectives. Being able to develop an adequate model for this problem that can represent the real problem as close as possible is an important research area.The main objective of this research work is to present new mathematical models to the DSP problem that represent all the complexity of the drivers scheduling problem, and also demonstrate that the solutions of these models can be easily implemented in real situations. This issue has been recognized by several authors and as important problem in Public Transportation. The most well-known and general formulation for the DSP is a Set Partition/Set Covering Model (SPP/SCP). However, to a large extend these models simplify some of the specific business aspects and issues of real problems. This makes it difficult to use these models as automatic planning systems because the schedules obtained must be modified manually to be implemented in real situations. Based on extensive passenger transportation experience in bus companies in Portugal, we propose new alternative models to formulate the DSP problem. These models are also based on Set Partitioning/Covering Models; however, they take into account the bus operator issues and the perspective opinions and environment of the user.We follow the steps of the Operations Research Methodology which consist of: Identify the Problem; Understand the System; Formulate a Mathematical Model; Verify the Model; Select the Best Alternative; Present the Results of theAnalysis and Implement and Evaluate. All the processes are done with close participation and involvement of the final users from different transportation companies. The planner s opinion and main criticisms are used to improve the proposed model in a continuous enrichment process. The final objective is to have a model that can be incorporated into an information system to be used as an automatic tool to produce driver schedules. Therefore, the criteria for evaluating the models is the capacity to generate real and useful schedules that can be implemented without many manual adjustments or modifications. We have considered the following as measures of the quality of the model: simplicity, solution quality and applicability. We tested the alternative models with a set of real data obtained from several different transportation companies and analyzed the optimal schedules obtained with respect to the applicability of the solution to the real situation. To do this, the schedules were analyzed by the planners to determine their quality and applicability. The main result of this work is the proposition of new mathematical models for the DSP that better represent the realities of the passenger transportation operators and lead to better schedules that can be implemented directly in real situations.

State and industry in the 1940s: The Spanish automobile industry

The decade of the 1940s was one of the darkest periods in the country's history, with years of famine, repression, general misery, and impoverishment of all aspects of national life ranging from culture to the economy. During those years plans were made to establish a Spanish motor industry once the Civil War had come to an end in 1939. It seemed a propitious moment for private enterprise and various foreign motor companies presented proposals for manufacturing their entire vehicle range, from cars to trucks. However, the government plans were for a State monopoly, a policy which meant that any private projects which did not contemplate the regime taking management decisions were rejected out of hand. From 1941 onwards, any new initiative was required to meet the plans set by INI. The main argument running through this paper is that one can only understand the development of the modern Spanish motor industry if one grasps the haggling between motor companies and government regarding market entry and the impact of the regime's autarchic policies in the 1940s.

MSISpIC: A Probabilistic Scan Matching Algorithm Using a Mechanical Scanned Imaging Sonar

This paper compares two well known scan matching algorithms: the MbICP and the pIC. As a result of the study, it is proposed the MSISpIC, a probabilistic scan matching algorithm for the localization of an Autonomous Underwater Vehicle (AUV). The technique uses range scans gathered with a Mechanical Scanning Imaging Sonar (MSIS), and the robot displacement estimated through dead-reckoning with the help of a Doppler Velocity Log (DVL) and a Motion Reference Unit (MRU). The proposed method is an extension of the pIC algorithm. Its major contribution consists in: 1) using an EKF to estimate the local path traveled by the robot while grabbing the scan as well as its uncertainty and 2) proposing a method to group into a unique scan, with a convenient uncertainty model, all the data grabbed along the path described by the robot. The algorithm has been tested on an AUV guided along a 600m path within a marina environment with satisfactory results

Vehicle de guiat automàtic (AGV)

Aquest projecte documenta la simulació d'un AGV (vehicle de guiat automàtic). Mitjançant un robot educatiu programat en Basic Stamp es simula un entorn d'anàlisi clínic a on el robot gestiona de forma automàtica les estacions d'anàlisi d'una hipotètica mostra de sang.

Implantación de la ISO 14001 en una planta de tratamiento de vehículos fuera de uso (VFU)

Nos hemos propuesto implantar la ISO 14001 en un centro autorizado de tratamiento de vehículos fuera de uso, denominado Recycling Gandía, S.L., con el fin de que dicho centro pueda obtener una ventaja competitiva, respecto de otros centros ubicados próximamente, dada la fuerte competencia existente. Con la implantación de un Sistema de Gestión Medioambiental y más concretamente la ISO 14001, se puede conseguir una mejora de la imagen de la empresa, un ahorro de costes, se pueden mejorar las relaciones con la Administración e incluso con las entidades financieras, se puede contribuir a la motivación de los trabajadores, se asegura el cumplimiento de la legislación ambiental. La actividad que nos ocupa, se dedica a la recepción y descontaminación de vehículos al final de su vida útil, reutilizando piezas o componentes de recambio., Los objetivos del presente trabajo van a ser fundamentalmente, el implantar el Manual de Gestión Ambiental en la planta de tratamiento de vehículos fuera de uso y el describir todos los procedimientos genéricos a seguir. Como conclusiones de este trabajo, tendremos las auditorías con las no conformidades detectadas, así como el compromiso adquirido en todos los niveles y departamentos de la empresa, lo cual se traducirá en una mejor satisfacción de los clientes y por tanto un aumento en el número de vehículos a tratar.

Using the HEGY Procedure When Not All Roots Are Present

Empirical studies have shown little evidence to support the presence of all unit roots present in the $^{\Delta_4}$ filter in quarterly seasonal time series. This paper analyses the performance of the Hylleberg, Engle, Granger and Yoo (1990) (HEGY) procedure when the roots under the null are not all present. We exploit the Vector of Quarters representation and cointegration relationship between the quarters when factors $(1-L),(1+L),\bigg(1+L^2\bigg),\bigg(1-L^2\bigg) y \bigg(1+L+L^2+L^3\bigg)$ are a source of nonstationarity in a process in order to obtain the distribution of tests of the HEGY procedure when the underlying processes have a root at the zero, Nyquist frequency, two complex conjugates of frequency $^{\pi/2}$ and two combinations of the previous cases. We show both theoretically and through a Monte-Carlo analysis that the t-ratios $^{t_{{\hat\pi}_1}}$ and $^{t_{{\hat\pi}_2}}$ and the F-type tests used in the HEGY procedure have the same distribution as under the null of a seasonal random walk when the root(s) is/are present, although this is not the case for the t-ratio tests associated with unit roots at frequency $^{\pi/2}$.

Using the HEGY Procedure When Not All Roots Are Present

Empirical studies have shown little evidence to support the presence of all unit roots present in the $^{\Delta_4}$ filter in quarterly seasonal time series. This paper analyses the performance of the Hylleberg, Engle, Granger and Yoo (1990) (HEGY) procedure when the roots under the null are not all present. We exploit the Vector of Quarters representation and cointegration relationship between the quarters when factors $(1-L),(1+L),\bigg(1+L^2\bigg),\bigg(1-L^2\bigg) y \bigg(1+L+L^2+L^3\bigg)$ are a source of nonstationarity in a process in order to obtain the distribution of tests of the HEGY procedure when the underlying processes have a root at the zero, Nyquist frequency, two complex conjugates of frequency $^{\pi/2}$ and two combinations of the previous cases. We show both theoretically and through a Monte-Carlo analysis that the t-ratios $^{t_{{\hat\pi}_1}}$ and $^{t_{{\hat\pi}_2}}$ and the F-type tests used in the HEGY procedure have the same distribution as under the null of a seasonal random walk when the root(s) is/are present, although this is not the case for the t-ratio tests associated with unit roots at frequency $^{\pi/2}$.

All assignment games with the same core have the same nucleolus

There exist coalitional games with transferable utility which have the same core but different nucleoli. We show that this cannot happen in the case of assignment games. Whenever two assignment games have the same core, their nucleoli also coincide. To show this, we prove that the nucleolus of an assignment game coincides with that of its buyer-seller exact representative