Mechanical unfolding and refolding pathways of ubiquitin

Mechanical unfolding and refolding of ubiquitin are studied by Monte Carlo simulations of a Go model with binary variables. The exponential dependence of the time constants on the force is verified, and folding and unfolding lengths are computed, with good agreement with experimental results. Furthermore, the model exhibits intermediate kinetic states, as observed in experiments. Unfolding and refolding pathways and intermediate states, obtained by tracing single secondary structure elements, are consistent with simulations of previous all-atom models and with the experimentally observed step sizes

Model Transformations in MT

Model transformations are recognised as a vital aspect of Model Driven Development,but current approaches cover only a small part of the possible spectrum. In this paper I present the MT model transformation which shows how a QVT-like language can be extended with novel pattern matching constructs, how tracing information can be automatically constructed and visualized, and how the transformed model is pruned of extraneous elements. As MT is implemented as a DSL within the Converge language, this paper also demonstrates how a general purpose language can be embedded in a model transformation language, and how DSL development can aid experimentation and exploration of new parts of the model transformation spectrum

Mixing Formal and Informal Model Elements for Tracing Requirements

Tracing between informal requirements and formal models is challenging. A method for such tracing should permit to deal efficiently with changes to both the requirements and the model. A particular challenge is posed by the persisting interplay of formal and informal elements. In this paper, we describe an incremental approach to requirements validation and systems modelling. Formal modelling facilitates a high degree of automation: it serves for validation and traceability. The foundation for our approach are requirements that are structured according to the WRSPM reference model. We provide a system for traceability with a state-based formal method that supports refinement. We do not require all specification elements to be modelled formally and support incremental incorporation of new specification elements into the formal model. Refinement is used to deal with larger amounts of requirements in a structured way. We provide a small example using Problem Frames and Event-B to demonstrate our approach

Metamodel for Tracing Concerns across the Life Cycle

Several aspect-oriented approaches have been proposed to specify aspects at different phases in the software life cycle. Aspects can appear within a phase, be refined or mapped to other aspects in later phases, or even disappear.\ud Tracing aspects is necessary to support understandability and maintainability of software systems. Although several approaches have been introduced to address traceability of aspects, two important limitations can be observed. First, tracing is not yet tackled for the entire life cycle. Second, the traceability model that is applied usually refers to elements of specific aspect languages, thereby limiting the reusability of the adopted traceability model.We propose the concern traceability metamodel (CTM) that enables traceability of concerns throughout the life cycle, and which is independent from the aspect languages that are used. CTM can be enhanced to provide additional properties for tracing, and be instantiated to define\ud customized traceability models with respect to the required aspect languages. We have implemented CTM in the tool M-Trace, that uses XML-based representations of the models and XQuery queries to represent tracing information. CTM and M-Trace are illustrated for a Concurrent Versioning System to trace aspects from the requirements level to architecture design level and the implementation

Cryo-EM map interpretation and protein model-building using iterative map segmentation.

A procedure for building protein chains into maps produced by single-particle electron cryo-microscopy (cryo-EM) is described. The procedure is similar to the way an experienced structural biologist might analyze a map, focusing first on secondary structure elements such as helices and sheets, then varying the contour level to identify connections between these elements. Since the high density in a map typically follows the main-chain of the protein, the main-chain connection between secondary structure elements can often be identified as the unbranched path between them with the highest minimum value along the path. This chain-tracing procedure is then combined with finding side-chain positions based on the presence of density extending away from the main path of the chain, allowing generation of a Cα model. The Cα model is converted to an all-atom model and is refined against the map. We show that this procedure is as effective as other existing methods for interpretation of cryo-EM maps and that it is considerably faster and produces models with fewer chain breaks than our previous methods that were based on approaches developed for crystallographic maps

Physical modeling of echelle spectrographs: the CARMENES case study

We have developed a generic physical modeling scheme for high resolution spectroscopy based on simple optical principles. This model predicts the position of centroids for a given set of spectral features with high accuracy. It considers off-plane grating equations and rotations of the different optical elements in order to properly account for tilts in the spectral lines and order curvature. In this way any astronomical spectrograph can be modeled and controlled without the need of commercial ray tracing software. The computations are based on direct ray tracing applying exact corrections to certain surfaces types. This allows us to compute the position on the detector of any spectral feature with high reliability. The parameters of this model, which describe the physical properties of the spectrograph, are continuously optimized to ensure the best possible fit to the observed spectral line positions. We present the physical modeling of CARMENES as a case study. We show that our results are in agreement with commercial ray tracing software. The model prediction matches the observations at a pixel size level, providing an efficient tool in the design, construction and data reduction of high resolution spectrographs. © 2018 SPIE

A line-of-sight optimised MIMO architecture for outdoor environments

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The historical and recent evolution in the Sudanic and Sub-Sudanic Savannah of NE-Nigeria: geographical, linguistic and anthropological aspects

The search for persistent elements in nature and culture, which comprises language as a constitutive part, is a prerequisite for the definition of any change which is the aim of our common project. When analysing the process of transformation by a number of disciplines we expect to discover significant features of this alteration and the forces dominating it. The current highly complex present linguistic situation in the western and south-western fringe of the Chad Basin will be reconstructed from the historical migrations undertaken by the various linguistic groups from Lake Chad (mainly Chadic languages) to their present settlements. The six authors, the linguists Dr. Dimitr Ibriszimov, Dr. Doris Löhr, Christopher Mtaku, the ethno-musicologist Dr. Raimund Vogels, and the historian Ibrahim Maina Waziri integrated the results of their studies into one paper towards a systemic approach by tracing back the common roots of the languages, the customs and the music of those peoples and give an outline of their tradition concerning their movements. A basic dual model of migration will be put forward