Computational structure‐based drug design: Predicting target flexibility

The role of molecular modeling in drug design has experienced a significant revamp in the last decade. The increase in computational resources and molecular models, along with software developments, is finally introducing a competitive advantage in early phases of drug discovery. Medium and small companies with strong focus on computational chemistry are being created, some of them having introduced important leads in drug design pipelines. An important source for this success is the extraordinary development of faster and more efficient techniques for describing flexibility in three‐dimensional structural molecular modeling. At different levels, from docking techniques to atomistic molecular dynamics, conformational sampling between receptor and drug results in improved predictions, such as screening enrichment, discovery of transient cavities, etc. In this review article we perform an extensive analysis of these modeling techniques, dividing them into high and low throughput, and emphasizing in their application to drug design studies. We finalize the review with a section describing our Monte Carlo method, PELE, recently highlighted as an outstanding advance in an international blind competition and industrial benchmarks.We acknowledge the BSC-CRG-IRB Joint Research Program in Computational Biology. This work was supported by a grant from the Spanish Government CTQ2016-79138-R.J.I. acknowledges support from SVP-2014-068797, awarded by the Spanish Government.Peer ReviewedPostprint (author's final draft

An Adaptive Design Methodology for Reduction of Product Development Risk

Embedded systems interaction with environment inherently complicates understanding of requirements and their correct implementation. However, product uncertainty is highest during early stages of development. Design verification is an essential step in the development of any system, especially for Embedded System. This paper introduces a novel adaptive design methodology, which incorporates step-wise prototyping and verification. With each adaptive step product-realization level is enhanced while decreasing the level of product uncertainty, thereby reducing the overall costs. The back-bone of this frame-work is the development of Domain Specific Operational (DOP) Model and the associated Verification Instrumentation for Test and Evaluation, developed based on the DOP model. Together they generate functionally valid test-sequence for carrying out prototype evaluation. With the help of a case study 'Multimode Detection Subsystem' the application of this method is sketched. The design methodologies can be compared by defining and computing a generic performance criterion like Average design-cycle Risk. For the case study, by computing Average design-cycle Risk, it is shown that the adaptive method reduces the product development risk for a small increase in the total design cycle time.Comment: 21 pages, 9 figure

Optimisation of Mobile Communication Networks - OMCO NET

The mini conference “Optimisation of Mobile Communication Networks” focuses on advanced methods for search and optimisation applied to wireless communication networks. It is sponsored by Research & Enterprise Fund Southampton Solent University. The conference strives to widen knowledge on advanced search methods capable of optimisation of wireless communications networks. The aim is to provide a forum for exchange of recent knowledge, new ideas and trends in this progressive and challenging area. The conference will popularise new successful approaches on resolving hard tasks such as minimisation of transmit power, cooperative and optimal routing

A methodology for exploring emergence in learning communities

Learning communities are becoming increasingly complex in nature, often being used to drive multiple agendas. For example, there is an increasing move to develop learning cities which seek to draw on synergies to both improve citizen learning and skills as well as economic regeneration. Such synergy-driven learning communities, of which the learning cities are but one example, seek to utilise interaction to develop 'emergent products', be it at the individual level or the system-wide level, which could not be produced in isolation. Successfully enabling emergence is critical to their success. Designing for specific types of emergence is however difficult given the intrinsic unpredictability of complex systems. Insight into the intrinsic characteristics of these synergy-driven learning communities and how their interaction leads to emergence over time is required. This paper reports on the methodology developed to explore these highly complex learning communities. The approach adopted was to combine exploratory case studies which established the intrinsic characteristics of the learning communities with an exploration of emergence guided by a meta-level conceptual framework of emergence. This was augmented by secondary data to aid triangulation and provide rigour. As well as discussing the rationale for the adopted approach, implementation issues and the rich information set obtained are discussed using specific case examples. Findings from the investigations led to recommendations regarding future development of appropriate methods for seeding and managing such complex learning communities. The meta level framework means the approach may be readily adapted to other complex social system

Formal and Informal Methods for Multi-Core Design Space Exploration

We propose a tool-supported methodology for design-space exploration for embedded systems. It provides means to define high-level models of applications and multi-processor architectures and evaluate the performance of different deployment (mapping, scheduling) strategies while taking uncertainty into account. We argue that this extension of the scope of formal verification is important for the viability of the domain.Comment: In Proceedings QAPL 2014, arXiv:1406.156

Meeting the design challenges of nano-CMOS electronics: an introduction to an upcoming EPSRC pilot project

The years of ‘happy scaling’ are over and the fundamental challenges that the semiconductor industry faces, at both technology and device level, will impinge deeply upon the design of future integrated circuits and systems. This paper provides an introduction to these challenges and gives an overview of the Grid infrastructure that will be developed as part of a recently funded EPSRC pilot project to address them, and we hope, which will revolutionise the electronics design industry