Metamodel-based formalization of DEVS atomic models

The Discrete-Event System Specification (DEVS) formalism is a modeling formalism based on systems theory that provides a general methodology for hierarchical construction of reusable models in a modular way. When concrete DEVS models are developed using programming languages, it is difficult to ensure they conform to their formal model. Hence, building an implementation of formal models in a way that ensures DEVS formalism correctness is not easy. In this paper, we improve the interplay of abstraction (i.e., formal specification) and concreteness (i.e., programming code implementation) in advancing the theory and practice of DEVS using a specific-designed metamodel. The main contribution is a novel conceptualization of classic DEVS with ports founded on existing approaches but that also includes new improved elements related to the definition of atomic models. That is, our metamodel includes all the concepts and relationships needed to define the formal specification of DEVS atomic models. This allows us to define instances of our conceptualization that comply with the DEVS formal specification. To instantiate our metamodel, we propose a computer-aided environment that has been developed using the Eclipse Modeling Project. As an example, we show how our metamodel can be used to define the classic “switch” model. As a conclusion, we discuss how the final metamodel can be used to support interoperability with DEVS simulation tools.

Cryo-EM Map–Based Model Validation Using the False Discovery Rate Approach

Significant technological developments and increasing scientific interest in cryogenic electron microscopy (cryo-EM) has resulted in a rapid increase in the amount of data generated by these experiments and the derived atomic models. Robust measures for the validation of 3D reconstructions and atomic models are essential for appropriate interpretation of the data. The resolution of data and availability of software tools that work across a range of resolutions often limit the quality of derived models. Hence, the final atomic model is often incomplete or contains regions where atomic positions are less reliable or incorrectly built. Extensive manual pruning and local adjustments or rebuilding are usually required to address these issues. The presented research introduces a software tool for the validation of the backbone trace of atomic models built in the cryo-EM density maps. In this study, we use the false discovery rate analysis, which can be used to segregate molecular signals from the background. Each atomic position in the model can be associated with an FDR backbone validation score, which can be used to identify potential mistraced residues. We demonstrate that the proposed validation score is complementary to existing validation metrics and is useful especially in cases where the model is built in the maps having varying local resolution. We also discuss the application of the score for automated pruning of atomic models built ab-initio during the iterative model building process in Buccaneer. We have implemented this score in the CCP-EM software suite.

Protein identification from electron cryomicroscopy maps by automated model building and side-chain matching

Using single-particle electron cryo-microscopy (cryo-EM), it is possible to obtain multiple reconstructions showing the 3D structures of proteins imaged as a mixture. Here, it is shown that automatic map interpretation based on such reconstructions can be used to create atomic models of proteins as well as to match the proteins to the correct sequences and thereby to identify them. This procedure was tested using two proteins previously identified from a mixture at resolutions of 3.2 Å, as well as using 91 deposited maps with resolutions between 2 and 4.5 Å. The approach is found to be highly effective for maps obtained at resolutions of 3.5 Å and better, and to have some utility at resolutions as low as 4 Å.

Examining Learning of Atomic Level Ideas About Precipitation Reactions with a Resources Framework

One particular challenge in chemistry learning is developing students’ atomic level understanding of chemical processes. It is necessary to help students learn how to critique atomic models rather than accept...