Insights into mechanism kinematics for protein motion simulation

Background: The high demanding computational requirements necessary to carry out protein motion simulations make it difficult to obtain information related to protein motion. On the one hand, molecular dynamics simulation requires huge computational resources to achieve satisfactory motion simulations. On the other hand, less accurate procedures such as interpolation methods, do not generate realistic morphs from the kinematic point of view. Analyzing a protein's movement is very similar to serial robots; thus, it is possible to treat the protein chain as a serial mechanism composed of rotational degrees of freedom. Recently, based on this hypothesis, new methodologies have arisen, based on mechanism and robot kinematics, to simulate protein motion. Probabilistic roadmap method, which discretizes the protein configurational space against a scoring function, or the kinetostatic compliance method that minimizes the torques that appear in bonds, aim to simulate protein motion with a reduced computational cost. Results: In this paper a new viewpoint for protein motion simulation, based on mechanism kinematics is presented. The paper describes a set of methodologies, combining different techniques such as structure normalization normalization processes, simulation algorithms and secondary structure detection procedures. The combination of all these procedures allows to obtain kinematic morphs of proteins achieving a very good computational cost-error rate, while maintaining the biological meaning of the obtained structures and the kinematic viability of the obtained motion. Conclusions: The procedure presented in this paper, implements different modules to perform the simulation of the conformational change suffered by a protein when exerting its function. The combination of a main simulation procedure assisted by a secondary structure process, and a side chain orientation strategy, allows to obtain a fast and reliable simulations of protein motion.

RESTful Discovery and Eventing for Service Provisioning in Assisted Living Environments

Service provisioning in assisted living environments faces distinct challenges due to the heterogeneity of networks, access technology, and sensing/actuation devices in such an environment. Existing solutions, such as SOAP-based web services, can interconnect heterogeneous devices and services, and can be published, discovered and invoked dynamically. However, it is considered heavier than what is required in the smart environment-like context and hence suffers from performance degradation. Alternatively, REpresentational State Transfer (REST) has gained much attention from the community and is considered as a lighter and cleaner technology compared to the SOAP-based web services. Since it is simple to publish and use a RESTful web service, more and more service providers are moving toward REST-based solutions, which promote a resource-centric conceptualization as opposed to a service-centric conceptualization. Despite such benefits of REST, the dynamic discovery and eventing of RESTful services are yet considered a major hurdle to utilization of the full potential of REST-based approaches. In this paper, we address this issue, by providing a RESTful discovery and eventing specification and demonstrate it in an assisted living healthcare scenario. We envisage that through this approach, the service provisioning in ambient assisted living or other smart environment settings will be more efficient, timely, and less resource-intensive.

Advanced techniques for diagnostics and control applied to particle accelerators

201 p.