The octet rule in chemical space: Generating virtual molecules

We present a generator of virtual molecules that selects valid chemistry on the basis of the octet rule. Also, we introduce a mesomer group key that allows a fast detection of duplicates in the generated structures. Compared to existing approaches, our model is simpler and faster, generates new chemistry and avoids invalid chemistry. Its versatility is illustrated by the correct generation of molecules containing third-row elements and a surprisingly adept handling of complex boron chemistry. Without any empirical parameters, our model is designed to be valid also in unexplored regions of chemical space. One first unexpected finding is the high prevalence of dipolar structures among generated molecules.Comment: 24 pages, 10 figure

En-route: on enabling resource usage testing for autonomous driving frameworks

Software resource usage testing, including execution time bounds and memory, is a mandatory validation step during the integration of safety-related real-time systems. However, the inherent complexity of Autonomous Driving (AD) systems challenges current practice for resource usage testing. This paper exposes the difficulties to perform resource usage testing for AD frameworks by analyzing a complex and critical module of an AD framework, and provides some guidelines and practical evidence on how resource usage testing can be effectively performed, thus enabling end users to validate their safety-related real-time AD frameworks.This work has been partially supported by the Spanish Ministry of Economy and Competitiveness (MINECO) under grant TIN2015-65316-P, the UP2DATE European Union’s Horizon 2020 (H2020) research and innovation programme under grant agreement No 871465, and the HiPEAC Network of Excellence. MINECO partially supported Jaume Abella under Ramon y Cajal postdoctoral fellowship (RYC-2013-14717) and Leonidas Kosmidis under Juan de la Cierva-Formación postdoctoral fellowship (FJCI-2017-34095)Peer ReviewedPostprint (author's final draft

Quantifying biogenic bias in screening libraries.

In lead discovery, libraries of 10(6) molecules are screened for biological activity. Given the over 10(60) drug-like molecules thought possible, such screens might never succeed. The fact that they do, even occasionally, implies a biased selection of library molecules. We have developed a method to quantify the bias in screening libraries toward biogenic molecules. With this approach, we consider what is missing from screening libraries and how they can be optimized

Systematic Literature Review: Current Products, Topic, and Implementation of Graph Database

Planning, developing, and updating software cannot be separated from the role of the database. From various types of databases, graph databases are considered to have various advantages over their predecessor, relational databases. Graph databases then become the latest trend in the software and data science industry, apart from the development of graph theory itself. The proliferation of research on GDB in the last decade raises questions about what topics are associated with GDB, what industries use GDB in its data processing, what the GDB models are, and what types of GDB have been used most frequently by users in the last few years. This article aims to answer these questions through a Literature Review, which is carried out by determining objectives, determining the limits of review coverage, determining inclusion and exclusion criteria for data retrieval, data extraction, and quality assessment. Based on a review of 60 studies, several research topics related to GDB are Semantic Web, Big Data, and Parallel computing. A total of 19 (30%) studies used Neo4j as their database. Apart from Social Networks, the industries that implement GDB the most are the Transportation sector, Scientific Article Networks, and general sectors such as Enterprise Data, Biological data, and History data. This Literature Review concludes that research on the topic of the Graph Database is still developing in the future. This is shown by the breadth of application and the variety of new derivatives of GDB products offered by researchers to address existing problems

D2D-Based Grouped Random Access to Mitigate Mobile Access Congestion in 5G Sensor Networks

The Fifth Generation (5G) wireless service of sensor networks involves significant challenges when dealing with the coordination of ever-increasing number of devices accessing shared resources. This has drawn major interest from the research community as many existing works focus on the radio access network congestion control to efficiently manage resources in the context of device-to-device (D2D) interaction in huge sensor networks. In this context, this paper pioneers a study on the impact of D2D link reliability in group-assisted random access protocols, by shedding the light on beneficial performance and potential limitations of approaches of this kind against tunable parameters such as group size, number of sensors and reliability of D2D links. Additionally, we leverage on the association with a Geolocation Database (GDB) capability to assist the grouping decisions by drawing parallels with recent regulatory-driven initiatives around GDBs and arguing benefits of the suggested proposal. Finally, the proposed method is approved to significantly reduce the delay over random access channels, by means of an exhaustive simulation campaign.Comment: First submission to IEEE Communications Magazine on Oct.28.2017. Accepted on Aug.18.2019. This is the camera-ready versio

Holistic debugging - enabling instruction set simulation for software quality assurance

We present holistic debugging, a novel method for observing execution of complex and distributed software. It builds on an instruction set simulator, which provides reproducible experiments and non-intrusive probing of state in a distributed system. Instruction set simulators, however, only provide low-level information, so a holistic debugger contains a translation framework that maps this information to higher abstraction level observation tools, such as source code debuggers. We have created Nornir, a proof-of-concept holistic debugger, built on the simulator Simics. For each observed process in the simulated system, Nornir creates an abstraction translation stack, with virtual machine translators that map machine-level storage contents (e.g. physical memory, registers) provided by Simics, to application-level data (e.g. virtual memory contents) by parsing the data structures of operating systems and virtual machines. Nornir includes a modified version of the GNU debugger (GDB), which supports non-intrusive symbolic debugging of distributed applications. Nornir's main interface is a debugger shepherd, a programmable interface that controls multiple debuggers, and allows users to coherently inspect the entire state of heterogeneous, distributed applications. It provides a robust observation platform for construction of new observation tools

"Gray" BCS condensate of excitons and internal Josephson effect

It has been recently suggested that the Bose-Einstein condensate formed by excitons in the dilute limit must be dark, i.e., not coupled to photons. Here, we show that, under a density increase, the dark exciton condensate must acquire a bright component due to carrier exchange in which dark excitons turn bright. This however requires a density larger than a threshold which seems to fall in the forbidden region of the phase separation between a dilute exciton gas and a dense electron-hole plasma. The BCS-like condensation which is likely to take place on the dense side, must then have a dark and a bright component - which makes it "gray". It should be possible to induce an internal Josephson effect between these two coherent components, with oscillations of the photoluminescence as a strong proof of the existence for this "gray" BCS-like exciton condensate.Comment: 4 pages, typo correcte