Contrast sensitivity for complex and random gratings

This thesis studied the effect of (i) the number of grating components and (ii) parameter randomisation on root-mean-square (r.m.s.) contrast sensitivity and spatial integration. The effectiveness of spatial integration without external spatial noise depended on the number of equally spaced orientation components in the sum of gratings. The critical area marking the saturation of spatial integration was found to decrease when the number of components increased from 1 to 5-6 but increased again at 8-16 components. The critical area behaved similarly as a function of the number of grating components when stimuli consisted of 3, 6 or 16 components with different orientations and/or phases embedded in spatial noise. Spatial integration seemed to depend on the global Fourier structure of the stimulus. Spatial integration was similar for sums of two vertical cosine or sine gratings with various Michelson contrasts in noise. The critical area for a grating sum was found to be a sum of logarithmic critical areas for the component gratings weighted by their relative Michelson contrasts. The human visual system was modelled as a simple image processor where the visual stimuli is first low-pass filtered by the optical modulation transfer function of the human eye and secondly high-pass filtered, up to the spatial cut-off frequency determined by the lowest neural sampling density, by the neural modulation transfer function of the visual pathways. The internal noise is then added before signal interpretation occurs in the brain. The detection is mediated by a local spatially windowed matched filter. The model was extended to include complex stimuli and its applicability to the data was found to be successful. The shape of spatial integration function was similar for non-randomised and randomised simple and complex gratings. However, orientation and/or phase randomised reduced r.m.s contrast sensitivity by a factor of 2. The effect of parameter randomisation on spatial integration was modelled under the assumption that human observers change the observer strategy from cross-correlation (i.e., a matched filter) to auto-correlation detection when uncertainty is introduced to the task. The model described the data accurately.

Incoherent fibre supercontinuum generation for all-optical random number generation

Random number generation is a central component of modern information technology, with crucial applications in ensuring communications and information security. The development of new physical mechanisms suitable to directly generate random bit sequences is thus a subject of intense current research, with particular interest in alloptical techniques suitable for the generation of data sequences with high bit rate. One such promising technique that has received much recent attention is the chaotic semiconductor laser systems producing high quality random output as a result of the intrinsic nonlinear dynamics of its architecture [1]. Here we propose a novel complementary concept of all-optical technique that might dramatically increase the generation rate of random bits by using simultaneously multiple spectral channels with uncorrelated signals - somewhat similar to use of wave-division-multiplexing in communications. We propose to exploit the intrinsic nonlinear dynamics of extreme spectral broadening and supercontinuum (SC) generation in optical fibre, a process known to be often associated with non-deterministic fluctuations [2]. In this paper, we report proof-of concept results indicating that the fluctuations in highly nonlinear fibre SC generation can potentially be used for random number generation.

Multi-wavelength erbium/Raman gain based random distributed feedback fiber laser

A multiwavelength generation in a random distributed feedback fiber laser based on hybrid Raman and erbium gain and a Lyot all-fiber spectral filter is demonstrated for the first time. The use of erbium-doped fiber allows a multi-wavelength generation to be achieved at lower pump powers in comparison with random fiber lasers based on Raman gain only. The operating bandwidth and flatness of power distribution between different lines in generation are also improved in the hybrid gain configuration.

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.

Design of a flat-top fiber Bragg filter via quasi-random modulation of the refractive index

The statistics of the reflection spectrum of a short-correlated disordered fiber Bragg grating are studied. The averaged spectrum appears to be flat inside the bandgap and has significantly suppressed sidelobes compared to the uniform grating of the same bandwidth. This is due to the Anderson localization of the modes of a disordered grating. This observation prompts a new algorithm for designing passband reflection gratings. Using the stochastic invariant imbedding approach it is possible to obtain the probability distribution function for the random reflection coefficient inside the bandgap and obtain both the variance of the averaged reflectivity as well as the distribution of the time delay of the grating.

Random input problem for the nonlinear Schrödinger equation

We consider the random input problem for a nonlinear system modeled by the integrable one-dimensional self-focusing nonlinear Schrödinger equation (NLSE). We concentrate on the properties obtained from the direct scattering problem associated with the NLSE. We discuss some general issues regarding soliton creation from random input. We also study the averaged spectral density of random quasilinear waves generated in the NLSE channel for two models of the disordered input field profile. The first model is symmetric complex Gaussian white noise and the second one is a real dichotomous (telegraph) process. For the former model, the closed-form expression for the averaged spectral density is obtained, while for the dichotomous real input we present the small noise perturbative expansion for the same quantity. In the case of the dichotomous input, we also obtain the distribution of minimal pulse width required for a soliton generation. The obtained results can be applied to a multitude of problems including random nonlinear Fraunhoffer diffraction, transmission properties of randomly apodized long period Fiber Bragg gratings, and the propagation of incoherent pulses in optical fibers.

Persistence in a random bond ising model of socio-econo dynamics

We study the persistence phenomenon in a socio-econo dynamics model using computer simulations at a nite temperature on hypercubic lattices in dimensions up to ve. The model includes a \social" local eld which contains the magnetization at time t. The nearest neighbour quenched interactions are drawn from a binary distribution which is a function of the bond concentration, p. The decay of the persistence probability in the model depends on both the spatial dimension and p. We nd no evidence of \blocking" in this model. We also discuss the implications of our results for possible applications in the social and economic elds. It is suggested that the absence, or otherwise, of blocking could be used as a criterion to decide on the validity of a given model in dierent scenarios.

The use of site-directed mutagenesis to study GPCRs

G protein coupled receptors (GPCRs) are highly flexible and dynamic proteins, which are able to interact with diverse ligands, effectors, and regulatory proteins. Site-directed mutagenesis (SDM) is a powerful tool for providing insight into how these proteins actually work, both in its own right and when used in conjunction with information provided by other techniques such as crystallography or molecular modelling. Mutagenesis has been used to identify and characterise a myriad of functionally important residues, motifs and domains within the GPCR architecture, and to identify aspects of similarity and differences between the major families of GPCRs. This chapter presents the necessary information for undertaking informative SDM of these proteins. Whilst this is relevant to protein structure/function studies in -general, specific pitfalls and protocols suited to investigating GPCRs in particular will be highlighted.

The throughput order of multicast traffics with physical-layer network coding in random wireless ad hoc networks

This paper attempts to address the effectiveness of physical-layer network coding (PNC) on the throughput improvement for multi-hop multicast in random wireless ad hoc networks (WAHNs). We prove that the per session throughput order with PNC is tightly bounded as T((nvmR (n))-1) if m = O(R-2 (n)), where n is the total number of nodes, R(n) is the communication range, and m is the number of destinations for each multicast session. We also show that per-session throughput order with PNC is tight bounded as T(n-1), when m = O(R-2(n)). The results of this paper imply that PNC cannot improve the throughput order of multicast in random WAHNs, which is different from the intuition that PNC may improve the throughput order as it allows simultaneous signal access and combination.

Similarity between class A and class B G-protein-coupled receptors exemplified through calcitonin gene-related peptide receptor modelling and mutagenesis studies

Modelling class B G-protein-coupled receptors (GPCRs) using class A GPCR structural templates is difficult due to lack of homology. The plant GPCR, GCR1, has homology to both class A and class B GPCRs. We have used this to generate a class A-class B alignment, and by incorporating maximum lagged correlation of entropy and hydrophobicity into a consensus score, we have been able to align receptor transmembrane regions. We have applied this analysis to generate active and inactive homology models of the class B calcitonin gene-related peptide (CGRP) receptor, and have supported it with site-directed mutagenesis data using 122 CGRP receptor residues and 144 published mutagenesis results on other class B GPCRs. The variation of sequence variability with structure, the analysis of polarity violations, the alignment of group-conserved residues and the mutagenesis results at 27 key positions were particularly informative in distinguishing between the proposed and plausible alternative alignments. Furthermore, we have been able to associate the key molecular features of the class B GPCR signalling machinery with their class A counterparts for the first time. These include the [K/R]KLH motif in intracellular loop 1, [I/L]xxxL and KxxK at the intracellular end of TM5 and TM6, the NPXXY/VAVLY motif on TM7 and small group-conserved residues in TM1, TM2, TM3 and TM7. The equivalent of the class A DRY motif is proposed to involve Arg(2.39), His(2.43) and Glu(3.46), which makes a polar lock with T(6.37). These alignments and models provide useful tools for understanding class B GPCR function.

From rogue waves to random walks:nonlinear instabilities in supercontinuum generation

The noise properties of supercontinuum generation continue to be a subject of wide interest within both pure and applied physics. Aside from immediate applications in supercontinuum source development, detailed studies of supercontinuum noise mechanisms have attracted interdisciplinary attention because of links with extreme instabilities in other physical systems, especially the infamous and destructive oceanic rogue waves. But the instabilities inherent in supercontinuum generation can also be interpreted in terms of natural links with the general field of random processes, and this raises new possibilities for applications in areas such as random number generation. In this contribution we will describe recent work where we interpret supercontinuum intensity and phase fluctuations in this way.

Tunable random fiber laser

An optical fiber is treated as a natural one-dimensional random system where lasing is possible due to a combination of Rayleigh scattering by refractive index inhomogeneities and distributed amplification through the Raman effect. We present such a random fiber laser that is tunable over a broad wavelength range with uniquely flat output power and high efficiency, which outperforms traditional lasers of the same category. Outstanding characteristics defined by deep underlying physics and the simplicity of the scheme make the demonstrated laser a very attractive light source both for fundamental science and practical applications.

Graphene based widely-tunable and singly-polarized pulse generation with random fiber lasers

Pulse generation often requires a stabilized cavity and its corresponding mode structure for initial phase-locking. Contrastingly, modeless cavity-free random lasers provide new possibilities for high quantum efficiency lasing that could potentially be widely tunable spectrally and temporally. Pulse generation in random lasers, however, has remained elusive since the discovery of modeless gain lasing. Here we report coherent pulse generation with modeless random lasers based on the unique polarization selectivity and broadband saturable absorption of monolayer graphene. Simultaneous temporal compression of cavity-free pulses are observed with such a polarization modulation, along with a broadly-tunable pulsewidth across two orders of magnitude down to 900 ps, a broadly-tunable repetition rate across three orders of magnitude up to 3 MHz, and a singly-polarized pulse train at 41 dB extinction ratio, about an order of magnitude larger than conventional pulsed fiber lasers. Moreover, our graphene-based pulse formation also demonstrates robust pulse-to-pulse stability and widewavelength operation due to the cavity-less feature. Such a graphene-based architecture not only provides a tunable pulsed random laser for fiber-optic sensing, speckle-free imaging, and laser-material processing, but also a new way for the non-random CW fiber lasers to generate widely tunable and singly-polarized pulses.

Random walks and random numbers from supercontinuum generation

We report a numerical study showing how the random intensity and phase fluctuations across the bandwidth of a broadband optical supercontinuum can be interpreted in terms of the random processes of random walks and Lévy flights. We also describe how the intensity fluctuations can be applied to physical random number generation. We conclude that the optical supercontinuum provides a highly versatile means of studying and generating a wide class of random processes at optical wavelengths. © 2012 Optical Society of America.

The dawn of the RNA World:toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation- based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered. Copyright © 2009 RNA Society.