Visualising and controlling the flow in biomolecular systems at and between multiple scales:from atoms to hydrodynamics at different locations in time and space

A novel framework for modelling biomolecular systems at multiple scales in space and time simultaneously is described. The atomistic molecular dynamics representation is smoothly connected with a statistical continuum hydrodynamics description. The system behaves correctly at the limits of pure molecular dynamics (hydrodynamics) and at the intermediate regimes when the atoms move partly as atomistic particles, and at the same time follow the hydrodynamic flows. The corresponding contributions are controlled by a parameter, which is defined as an arbitrary function of space and time, thus, allowing an effective separation of the atomistic 'core' and continuum 'environment'. To fill the scale gap between the atomistic and the continuum representations our special purpose computer for molecular dynamics, MDGRAPE-4, as well as GPU-based computing were used for developing the framework. These hardware developments also include interactive molecular dynamics simulations that allow intervention of the modelling through force-feedback devices.

Localized waves in optical systems with periodic dispersion and nonlinearity management

We overview our recent developments in the theory of dispersion-managed (DM) solitons within the context of optical applications. First, we present a class of localized solutions with a period multiple to that of the standard DM soliton in the nonlinear Schrödinger equation with periodic variations of the dispersion. In the framework of a reduced ordinary differential equation-based model, we discuss the key features of these structures, such as a smaller energy compared to traditional DM solitons with the same temporal width. Next, we present new results on dissipative DM solitons, which occur in the context of mode-locked lasers. By means of numerical simulations and a reduced variational model of the complex Ginzburg-Landau equation, we analyze the influence of the different dissipative processes that take place in a laser.

It's good to be different:diversity, heterogeneity, and dynamics in collective systems

We identify two different forms of diversity present in engineered collective systems, namely heterogeneity (genotypic/phenotypic diversity) and dynamics (temporal diversity). Three qualitatively different case studies are analysed, and it is shown that both forms of diversity can be beneficial in very different problem and application domains. Behavioural diversity is shown to be motivated by input diversity and this observation is used to present recommendations for designers of collective systems.

Dimensioning RS codes for mitigation of phase noise induced cycle slips in DQPSK systems

We present a semi-analytical method for dimensioning Reed-Solomon codes for coherent DQPSK systems with laser phase noise and cycle slips. We evaluate the accuracy of our method for a 28 Gbaud system using numerical simulations.

Novel BCH code design for mitigation of phase noise induced cycle slips in DQPSK systems

We show that by proper code design, phase noise induced cycle slips causing an error floor can be mitigated for 28 Gbaud DQPSK systems. Performance of BCH codes are investigated in terms of required overhead. © 2014 OSA.

A new scheduling method for enhanced quality of experience in LTE systems

In this paper a new approach to the resource allocation and scheduling mechanism that reflects the effect of user's Quality of Experience is presented. The proposed scheduling algorithm is examined in the context of 3GPP Long Term Evolution (LTE) system. Pause Intensity (PI) as an objective and no-reference quality assessment metric is employed to represent user's satisfaction in the scheduler of eNodeB. PI is in fact a measurement of discontinuity in the service. The performance of the scheduling method proposed is compared with two extreme cases: maxCI and Round Robin scheduling schemes which correspond to the efficiency and fairness oriented mechanisms, respectively. Our work reveals that the proposed method is able to perform between fairness and efficiency requirements, in favor of higher satisfaction for the users to the desired level. © VDE VERLAG GMBH.

An incentivized auction based group-selling approach for demand response management in V2G systems

Vehicle-to-Grid (V2G) system with efficient Demand Response Management (DRM) is critical to solve the problem of supplying electricity by utilizing surplus electricity available at EVs. An incentivilized DRM approach is studied to reduce the system cost and maintain the system stability. EVs are motivated with dynamic pricing determined by the group-selling based auction. In the proposed approach, a number of aggregators sit on the first level auction responsible to communicate with a group of EVs. EVs as bidders consider Quality of Energy (QoE) requirements and report interests and decisions on the bidding process coordinated by the associated aggregator. Auction winners are determined based on the bidding prices and the amount of electricity sold by the EV bidders. We investigate the impact of the proposed mechanism on the system performance with maximum feedback power constraints of aggregators. The designed mechanism is proven to have essential economic properties. Simulation results indicate the proposed mechanism can reduce the system cost and offer EVs significant incentives to participate in the V2G DRM operation.

Polarisation phenomena in mode locked fibre lasers and fibre Raman amplifiers griffon tutorial

For a fibre Raman amplifier with randomly varying birefringence, we provide insight on the validity of previously explored multi-scale techniques leading to polarisation pulling of the signal state of polarisation to the pump state of polarisation. Unlike previous study, we demonstrate that in addition to polarisation pulling a new random birefringence-mediated phenomenon that goes beyond existing multi-scale techniques can boost resonance-like gain fluctuations similar to the Stochastic Anti-Resonance. For mode locked fibre lasers we report on fast and slow polarisation dynamics of fundamental, bound state, and multipulsing vector solitons along with stretched pulses. We demonstrate that tuning cavity anisotropy and birefringence along with parameters of an injected signal with randomly varying state of polarisation provides access to the variety of vector waveforms previously unexplored.

Noise-induced standing waves in oscillatory systems with time-delayed feedback

In oscillatory reaction-diffusion systems, time-delay feedback can lead to the instability of uniform oscillations with respect to formation of standing waves. Here, we investigate how the presence of additive, Gaussian white noise can induce the appearance of standing waves. Combining analytical solutions of the model with spatio-temporal simulations, we find that noise can promote standing waves in regimes where the deterministic uniform oscillatory modes are stabilized. As the deterministic phase boundary is approached, the spatio-temporal correlations become stronger, such that even small noise can induce standing waves in this parameter regime. With larger noise strengths, standing waves could be induced at finite distances from the (deterministic) phase boundary. The overall dynamics is defined through the interplay of noisy forcing with the inherent reaction-diffusion dynamics.

Dynamic variability in adaptive systems

One of the reasons for using variability in the software product line (SPL) approach (see Apel et al., 2006; Figueiredo et al., 2008; Kastner et al., 2007; Mezini & Ostermann, 2004) is to delay a design decision (Svahnberg et al., 2005). Instead of deciding on what system to develop in advance, with the SPL approach a set of components and a reference architecture are specified and implemented (during domain engineering, see Czarnecki & Eisenecker, 2000) out of which individual systems are composed at a later stage (during application engineering, see Czarnecki & Eisenecker, 2000). By postponing the design decisions in such a manner, it is possible to better fit the resultant system in its intended environment, for instance, to allow selection of the system interaction mode to be made after the customers have purchased particular hardware, such as a PDA vs. a laptop. Such variability is expressed through variation points which are locations in a software-based system where choices are available for defining a specific instance of a system (Svahnberg et al., 2005). Until recently it had sufficed to postpone committing to a specific system instance till before the system runtime. However, in the recent years the use and expectations of software systems in human society has undergone significant changes.Today's software systems need to be always available, highly interactive, and able to continuously adapt according to the varying environment conditions, user characteristics and characteristics of other systems that interact with them. Such systems, called adaptive systems, are expected to be long-lived and able to undertake adaptations with little or no human intervention (Cheng et al., 2009). Therefore, the variability now needs to be present also at system runtime, which leads to the emergence of a new type of system: adaptive systems with dynamic variability.

Quantization of the Inhomogeneous Bianchi I model:quasi-Heisenberg picture

The quantization scheme is suggested for a spatially inhomogeneous 1+1 Bianchi I model. The scheme consists in quantization of the equations of motion and gives the operator (so called quasi-Heisenberg) equations describing explicit evolution of a system. Some particular gauge suitable for quantization is proposed. The Wheeler-DeWitt equation is considered in the vicinity of zero scale factor and it is used to construct a space where the quasi-Heisenberg operators act. Spatial discretization as a UV regularization procedure is suggested for the equations of motion.

Pole tip recession in linear tape systems

The tribology of linear tape storage system including Linear Tape Open (LTO) and Travan5 was investigated by combining X-ray Photoelectron Spectroscopy (XPS), Auger Electron Spectroscopy (AES), Optical Microscopy and Atomic Force Microscopy (AFM) technologies. The purpose of this study was to understand the tribology mechanism of linear tape systems then projected recording densities may be achieved in future systems. Water vapour pressure or Normalized Water Content (NWC) rather than the Relative Humidity (RH) values (as are used almost universally in this field) determined the extent of PTR and stain (if produced) in linear heads. Approximately linear dependencies were found for saturated PTR increasing with normalized water content increasing over the range studied using the same tape. Fe Stain (if produced) preferentially formed on the head surfaces at the lower water contents. The stain formation mechanism had been identified. Adhesive bond formation is a chemical process that is governed by temperature. Thus the higher the contact pressure, the higher the contact temperature in the interface of head and tape, was produced higher the probability of adhesive bond formation and the greater the amount of transferred material (stain). Water molecules at the interface saturate the surface bonds and makes adhesive junctions less likely. Tape polymeric binder formulation also has a significant role in stain formation, with the latest generation binders producing less transfer of material. This is almost certainly due to higher cohesive bonds within the body of the magnetic layer. TiC in the two-phase ceramic tape-bearing surface (AlTiC) was found to oxidise to form TiO2.The oxidation rate of TiC increased with water content increasing. The oxide was less dense than the underlying carbide; hence the interface between TiO2 oxide and TiC was stressed. Removals of the oxide phase results in the formation of three-body abrasive particles that were swept across the tape head, and gave rise to three-body abrasive wear, particularly in the pole regions. Hence, PTR and subsequent which signal loss and error growth. The lower contact pressure of the LTO system comparing with the Travan5 system ensures that fewer and smaller three-body abrasive particles were swept across the poles and insulator regions. Hence, lower contact pressure, as well as reducing stain in the same time significantly reduces PTR in the LTO system.

Typical case behaviour of spin systems in random graph and composite ensembles

This thesis includes analysis of disordered spin ensembles corresponding to Exact Cover, a multi-access channel problem, and composite models combining sparse and dense interactions. The satisfiability problem in Exact Cover is addressed using a statistical analysis of a simple branch and bound algorithm. The algorithm can be formulated in the large system limit as a branching process, for which critical properties can be analysed. Far from the critical point a set of differential equations may be used to model the process, and these are solved by numerical integration and exact bounding methods. The multi-access channel problem is formulated as an equilibrium statistical physics problem for the case of bit transmission on a channel with power control and synchronisation. A sparse code division multiple access method is considered and the optimal detection properties are examined in typical case by use of the replica method, and compared to detection performance achieved by interactive decoding methods. These codes are found to have phenomena closely resembling the well-understood dense codes. The composite model is introduced as an abstraction of canonical sparse and dense disordered spin models. The model includes couplings due to both dense and sparse topologies simultaneously. The new type of codes are shown to outperform sparse and dense codes in some regimes both in optimal performance, and in performance achieved by iterative detection methods in finite systems.

Analysis of clogging in constructed wetlands using magnetic resonance

In this work we demonstrate the potential of permanent magnet based magnetic resonance sensors to monitor and assess the extent of pore clogging in water filtration systems. The performance of the sensor was tested on artificially clogged gravel substrates and on gravel bed samples from constructed wetlands used to treat wastewater. Data indicate that the spin lattice relaxation time is linearly related to the hydraulic conductivity in such systems. In addition, within biologically active filters we demonstrate the ability to determine the relative ratio of biomass to abiotic solids, a measurement which is not possible using alternative techniques. © 2011 The Royal Society of Chemistry.