Practical computational toolkits for dendrimers and dendrons structure design

Dendrimers and dendrons offer an excellent platform for developing novel drug delivery systems and medicines. The rational design and further development of these repetitively branched systems are restricted by difficulties in scalable synthesis and structural determination, which can be overcome by judicious use of molecular modelling and molecular simulations. A major difficulty to utilise in silico studies to design dendrimers lies in the laborious generation of their structures. Current modelling tools utilise automated assembly of simpler dendrimers or the inefficient manual assembly of monomer precursors to generate more complicated dendrimer structures. Herein we describe two novel graphical user interface (GUI) toolkits written in Python that provide an improved degree of automation for rapid assembly of dendrimers and generation of their 2D and 3D structures. Our first toolkit uses the RDkit library, SMILES nomenclature of monomers and SMARTS reaction nomenclature to generate SMILES and mol files of dendrimers without 3D coordinates. These files are used for simple graphical representations and storing their structures in databases. The second toolkit assembles complex topology dendrimers from monomers to construct 3D dendrimer structures to be used as starting points for simulation using existing and widely available software and force fields. Both tools were validated for ease-of-use to prototype dendrimer structure and the second toolkit was especially relevant for dendrimers of high complexity and size.Peer reviewe

Realising the open virtual commissioning of modular automation systems

To address the challenges in the automotive industry posed by the need to rapidly manufacture more product variants, and the resultant need for more adaptable production systems, radical changes are now required in the way in which such systems are developed and implemented. In this context, two enabling approaches for achieving more agile manufacturing, namely modular automation systems and virtual commissioning, are briefly reviewed in this contribution. Ongoing research conducted at Loughborough University which aims to provide a modular approach to automation systems design coupled with a virtual engineering toolset for the (re)configuration of such manufacturing automation systems is reported. The problems faced in the virtual commissioning of modular automation systems are outlined. AutomationML - an emerging neutral data format which has potential to address integration problems is discussed. The paper proposes and illustrates a collaborative framework in which AutomationML is adopted for the data exchange and data representation of related models to enable efficient open virtual prototype construction and virtual commissioning of modular automation systems. A case study is provided to show how to create the data model based on AutomationML for describing a modular automation system

Two intracellular and cell type-specific bacterial symbionts in the placozoan Trichoplax H2

Placozoa is an enigmatic phylum of simple, microscopic, marine metazoans(1,2). Although intracellular bacteria have been found in all members of this phylum, almost nothing is known about their identity, location and interactions with their host(3-6). We used metagenomic and metatranscriptomic sequencing of single host individuals, plus metaproteomic and imaging analyses, to show that the placozoan Trichoplax sp. H2 lives in symbiosis with two intracellular bacteria. One symbiont forms an undescribed genus in the Midichloriaceae (Rickettsiales)(7,8) and has a genomic repertoire similar to that of rickettsial parasites(9,10), but does not seem to express key genes for energy parasitism. Correlative image analyses and three-dimensional electron tomography revealed that this symbiont resides in the rough endoplasmic reticulum of its host's internal fibre cells. The second symbiont belongs to the Margulisbacteria, a phylum without cultured representatives and not known to form intracellular associations(11-13). This symbiont lives in the ventral epithelial cells of Trichoplax, probably metabolizes algal lipids digested by its host and has the capacity to supplement the placozoan's nutrition. Our study shows that one of the simplest animals has evolved highly specific and intimate associations with symbiotic, intracellular bacteria and highlights that symbioses can provide access to otherwise elusive microbial dark matter

A Model-Driven Engineering Approach for ROS using Ontological Semantics

This paper presents a novel ontology-driven software engineering approach for the development of industrial robotics control software. It introduces the ReApp architecture that synthesizes model-driven engineering with semantic technologies to facilitate the development and reuse of ROS-based components and applications. In ReApp, we show how different ontological classification systems for hardware, software, and capabilities help developers in discovering suitable software components for their tasks and in applying them correctly. The proposed model-driven tooling enables developers to work at higher abstraction levels and fosters automatic code generation. It is underpinned by ontologies to minimize discontinuities in the development workflow, with an integrated development environment presenting a seamless interface to the user. First results show the viability and synergy of the selected approach when searching for or developing software with reuse in mind.Comment: Presented at DSLRob 2015 (arXiv:1601.00877), Stefan Zander, Georg Heppner, Georg Neugschwandtner, Ramez Awad, Marc Essinger and Nadia Ahmed: A Model-Driven Engineering Approach for ROS using Ontological Semantic