Toward the atomistic simulation of T cell epitopes automated construction of MHC:peptide structures for free energy calculations

Epitopes mediated by T cells lie at the heart of the adaptive immune response and form the essential nucleus of anti-tumour peptide or epitope-based vaccines. Antigenic T cell epitopes are mediated by major histocompatibility complex (MHC) molecules, which present them to T cell receptors. Calculating the affinity between a given MHC molecule and an antigenic peptide using experimental approaches is both difficult and time consuming, thus various computational methods have been developed for this purpose. A server has been developed to allow a structural approach to the problem by generating specific MHC:peptide complex structures and providing configuration files to run molecular modelling simulations upon them. A system has been produced which allows the automated construction of MHC:peptide structure files and the corresponding configuration files required to execute a molecular dynamics simulation using NAMD. The system has been made available through a web-based front end and stand-alone scripts. Previous attempts at structural prediction of MHC:peptide affinity have been limited due to the paucity of structures and the computational expense in running large scale molecular dynamics simulations. The MHCsim server (http://igrid-ext.cryst.bbk.ac.uk/MHCsim) allows the user to rapidly generate any desired MHC:peptide complex and will facilitate molecular modelling simulation of MHC complexes on an unprecedented scale.

Quality-driven resource utilization methods for video streaming in wireless communication networks

This research is focused on the optimisation of resource utilisation in wireless mobile networks with the consideration of the users’ experienced quality of video streaming services. The study specifically considers the new generation of mobile communication networks, i.e. 4G-LTE, as the main research context. The background study provides an overview of the main properties of the relevant technologies investigated. These include video streaming protocols and networks, video service quality assessment methods, the infrastructure and related functionalities of LTE, and resource allocation algorithms in mobile communication systems. A mathematical model based on an objective and no-reference quality assessment metric for video streaming, namely Pause Intensity, is developed in this work for the evaluation of the continuity of streaming services. The analytical model is verified by extensive simulation and subjective testing on the joint impairment effects of the pause duration and pause frequency. Various types of the video contents and different levels of the impairments have been used in the process of validation tests. It has been shown that Pause Intensity is closely correlated with the subjective quality measurement in terms of the Mean Opinion Score and this correlation property is content independent. Based on the Pause Intensity metric, an optimised resource allocation approach is proposed for the given user requirements, communication system specifications and network performances. This approach concerns both system efficiency and fairness when establishing appropriate resource allocation algorithms, together with the consideration of the correlation between the required and allocated data rates per user. Pause Intensity plays a key role here, representing the required level of Quality of Experience (QoE) to ensure the best balance between system efficiency and fairness. The 3GPP Long Term Evolution (LTE) system is used as the main application environment where the proposed research framework is examined and the results are compared with existing scheduling methods on the achievable fairness, efficiency and correlation. Adaptive video streaming technologies are also investigated and combined with our initiatives on determining the distribution of QoE performance across the network. The resulting scheduling process is controlled through the prioritization of users by considering their perceived quality for the services received. Meanwhile, a trade-off between fairness and efficiency is maintained through an online adjustment of the scheduler’s parameters. Furthermore, Pause Intensity is applied to act as a regulator to realise the rate adaptation function during the end user’s playback of the adaptive streaming service. The adaptive rates under various channel conditions and the shape of the QoE distribution amongst the users for different scheduling policies have been demonstrated in the context of LTE. Finally, the work for interworking between mobile communication system at the macro-cell level and the different deployments of WiFi technologies throughout the macro-cell is presented. A QoEdriven approach is proposed to analyse the offloading mechanism of the user’s data (e.g. video traffic) while the new rate distribution algorithm reshapes the network capacity across the macrocell. The scheduling policy derived is used to regulate the performance of the resource allocation across the fair-efficient spectrum. The associated offloading mechanism can properly control the number of the users within the coverages of the macro-cell base station and each of the WiFi access points involved. The performance of the non-seamless and user-controlled mobile traffic offloading (through the mobile WiFi devices) has been evaluated and compared with that of the standard operator-controlled WiFi hotspots.

Simulation of surface EMG for the analysis of muscle activity during whole body vibratory stimulation

This study aims to reproduce the effect of motor-unit synchronization on surface EMG recordings during vibratory stimulation to highlight vibration evoked muscle activity. The authors intended to evaluate, through numerical simulations, the changes in surface EMG spectrum in muscles undergoing whole body vibration stimulation. In some specific bands, in fact, vibration induced motion artifacts are also typically present. In addition, authors meant to compare the simulated EMGs with respect to real recordings in order to discriminate the effect of synchronization of motor units discharges with vibration frequencies from motion artifacts. Computations were performed using a model derived from previous studies and modified to consider the effect of vibratory stimulus, the motor unit synchronization and the endplates-electrodes relative position on the EMG signal. Results revealed that, in particular conditions, synchronization of MUs' discharge generates visible peaks at stimulation frequency and its harmonics. However, only a part of the total power of surface EMGs might be enclosed within artifacts related bands (±1. Hz centered at the stimulation frequency and its superior harmonics) even in case of strong synchronization of motor units discharges with the vibratory stimulus. © 2013 Elsevier Ireland Ltd.

Formal methods @ runtime

Heuristics, simulation, artificial intelligence techniques and combinations thereof have all been employed in the attempt to make computer systems adaptive, context-aware, reconfigurable and self-managing. This paper complements such efforts by exploring the possibility to achieve runtime adaptiveness using mathematically-based techniques from the area of formal methods. It is argued that formal methods @ runtime represents a feasible approach, and promising preliminary results are summarised to support this viewpoint. The survey of existing approaches to employing formal methods at runtime is accompanied by a discussion of their challenges and of the future research required to overcome them. © 2011 Springer-Verlag.