Bioconductor: open software development for computational biology and bioinformatics.

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples

A survey of simulation techniques in commerce and defence

Despite the developments in Modelling and Simulation (M&S) tools and techniques over the past years, there has been a gap in the M&S research and practice in healthcare on developing a toolkit to assist the modellers and simulation practitioners with selecting an appropriate set of techniques. This study is a preliminary step towards this goal. This paper presents some results from a systematic literature survey on applications of M&S in the commerce and defence domains that could inspire some improvements in the healthcare. Interim results show that in the commercial sector Discrete-Event Simulation (DES) has been the most widely used technique with System Dynamics (SD) in second place. However in the defence sector, SD has gained relatively more attention. SD has been found quite useful for qualitative and soft factors analysis. From both the surveys it becomes clear that there is a growing trend towards using hybrid M&S approaches

Charge separation: From the topology of molecular electronic transitions to the dye/semiconductor interfacial energetics and kinetics

Charge separation properties, that is the ability of a chromophore, or a chromophore/semiconductor interface, to separate charges upon light absorption, are crucial characteristics for an efficient photovoltaic device. Starting from this concept, we devote the first part of this book chapter to the topological analysis of molecular electronic transitions induced by photon capture. Such analysis can be either qualitative or quantitative, and is presented here in the framework of the reduced density matrix theory applied to single-reference, multiconfigurational excited states. The qualitative strategies are separated into density-based and wave function-based approaches, while the quantitative methods reported here for analysing the photoinduced charge transfer nature are either fragment-based, global or statistical. In the second part of this chapter we extend the analysis to dye-sensitized metal oxide surface models, discussing interfacial charge separation, energetics and electron injection kinetics from the dye excited state to the semiconductor conduction band states

Hierarchical modeling for an industrial implementation of a Digital Twin for electrical drives

Digital twins have become popular for their ability to monitor and optimize a process or a machine, ideally through its complete life cycle using simulations and sensor data. In this paper, we focus on the challenge of accurate and real-time simulations for digital twins in the context of electrical machines. To build such a digital twin involves not only computational models for the electromagnetic aspects, but also mechanical and thermal effects need to be taken into account. We address mathematical tools that can be employed to carry out the required simulations based on physical laws as well as surrogate or data-driven models. One of those tools is a model hierarchy of very fine to very coarse models as well as reduced order models for obtaining real-time simulations. The required software tools to carry out simulations in the digital twin are also discussed. The simulation models are implemented in a pipeline that allows for the automatic modeling of new machines and the automatic configuration of new digital twins. Finally, the overall implemented digital twin is tested and implemented in a physical demonstrator

Visualizing simulated electrical fields from electroencephalography and transcranial electric brain stimulation: a comparative evaluation

pre-printElectrical activity of neuronal populations is a crucial aspect of brain activity. This activity is not measured directly but recorded as electrical potential changes using head surface electrodes (electroencephalogram - EEG). Head surface electrodes can also be deployed to inject electrical currents in order to modulate brain activity (transcranial electric stimulation techniques) for therapeutic and neuroscientific purposes. In electroencephalography and noninvasive electric brain stimulation, electrical fields mediate between electrical signal sources and regions of interest (ROI). These fields can be very complicated in structure, and are influenced in a complex way by the conductivity profile of the human head. Visualization techniques play a central role to grasp the nature of those fields because such techniques allow for an effective conveyance of complex data and enable quick qualitative and quantitative assessments. The examination of volume conduction effects of particular head model parameterizations (e.g., skull thickness and layering), of brain anomalies (e.g., holes in the skull, tumors), location and extent of active brain areas (e.g., high concentrations of current densities) and around current injecting electrodes can be investigated using visualization. Here, we evaluate a number of widely used visualization techniques, based on either the potential distribution or on the current-flow. In particular, we focus on the extractability of quantitative and qualitative information from the obtained images, their effective integration of anatomical context information, and their interaction. We present illustrative examples from clinically and neuroscientifically relevant cases and discuss the pros and cons of the various visualization techniques

The Joint Center for Energy Storage Research: A New Paradigm for Battery Research and Development

The Joint Center for Energy Storage Research (JCESR) seeks transformational change in transportation and the electricity grid driven by next generation high performance, low cost electricity storage. To pursue this transformative vision JCESR introduces a new paradigm for battery research: integrating discovery science, battery design, research prototyping and manufacturing collaboration in a single highly interactive organization. This new paradigm will accelerate the pace of discovery and innovation and reduce the time from conceptualization to commercialization. JCESR applies its new paradigm exclusively to beyond-lithium-ion batteries, a vast, rich and largely unexplored frontier. This review presents JCESR's motivation, vision, mission, intended outcomes or legacies and first year accomplishments.Comment: 17 pages, 14 figures, 96 reference