Monte Carlo Study of the Phase Structure of Compact Polymer Chains

We study the phase behavior of single homopolymers in a simple hydrophobic/hydrophilic off-lattice model with sequence independent local interactions. The specific heat is, not unexpectedly, found to exhibit a pronounced peak well below the collapse temperature, signalling a possible low-temperature phase transition. The system size dependence at this maximum is investigated both with and without the local interactions, using chains with up to 50 monomers. The size dependence is found to be weak. The specific heat itself seems not to diverge. The homopolymer results are compared with those for two non-uniform sequences. Our calculations are performed using the methods of simulated and parallel tempering. The performances of these algorithms are discussed, based on careful tests for a small system.Comment: 13 pages LaTeX, 6 Postscript figures, References adde

Orthonormal Expansion l1-Minimization Algorithms for Compressed Sensing

Compressed sensing aims at reconstructing sparse signals from significantly reduced number of samples, and a popular reconstruction approach is $\ell_1$-norm minimization. In this correspondence, a method called orthonormal expansion is presented to reformulate the basis pursuit problem for noiseless compressed sensing. Two algorithms are proposed based on convex optimization: one exactly solves the problem and the other is a relaxed version of the first one. The latter can be considered as a modified iterative soft thresholding algorithm and is easy to implement. Numerical simulation shows that, in dealing with noise-free measurements of sparse signals, the relaxed version is accurate, fast and competitive to the recent state-of-the-art algorithms. Its practical application is demonstrated in a more general case where signals of interest are approximately sparse and measurements are contaminated with noise.Comment: 7 pages, 2 figures, 1 tabl

Organic Design of Massively Distributed Systems: A Complex Networks Perspective

The vision of Organic Computing addresses challenges that arise in the design of future information systems that are comprised of numerous, heterogeneous, resource-constrained and error-prone components or devices. Here, the notion organic particularly highlights the idea that, in order to be manageable, such systems should exhibit self-organization, self-adaptation and self-healing characteristics similar to those of biological systems. In recent years, the principles underlying many of the interesting characteristics of natural systems have been investigated from the perspective of complex systems science, particularly using the conceptual framework of statistical physics and statistical mechanics. In this article, we review some of the interesting relations between statistical physics and networked systems and discuss applications in the engineering of organic networked computing systems with predictable, quantifiable and controllable self-* properties.Comment: 17 pages, 14 figures, preprint of submission to Informatik-Spektrum published by Springe

Adaptive walks on time-dependent fitness landscapes

The idea of adaptive walks on fitness landscapes as a means of studying evolutionary processes on large time scales is extended to fitness landscapes that are slowly changing over time. The influence of ruggedness and of the amount of static fitness contributions are investigated for model landscapes derived from Kauffman's $NK$ landscapes. Depending on the amount of static fitness contributions in the landscape, the evolutionary dynamics can be divided into a percolating and a non-percolating phase. In the percolating phase, the walker performs a random walk over the regions of the landscape with high fitness.Comment: 7 pages, 6 eps-figures, RevTeX, submitted to Phys. Rev.

A Monte Carlo Approach for Studying Microphases Applied to the Axial Next-Nearest-Neighbor Ising and the Ising-Coulomb Models

The equilibrium phase behavior of microphase-forming systems is notoriously difficult to obtain because of the extended metastability of their modulated phases. In this paper we present a systematic simulation methodology for studying layered microphases and apply the approach to two prototypical lattice-based systems: the three-dimensional axial next-nearest-neighbor Ising (ANNNI) and Ising-Coulomb (IC) models. The method involves thermodynamically integrating along a reversible path established between a reference system of free spins under an ordering field and the system of interest. The resulting free energy calculations unambiguously locate the phase boundaries. The simple phases are not observed to play a particularly significant role in the devil's flowers. With the help of generalized order parameters, the paramagnetic-modulated critical transition of the ANNNI model is also studied. We confirm the XY universality of the paramagnetic-modulated transition and its isotropic nature. Interfacial roughening is found to play at most a small role in the ANNNI layered regime.Comment: 15 pages, 11 figures, 2 table

Activity-driven content adaptation for effective video summarisation

In this paper, we present a novel method for content adaptation and video summarization fully implemented in compressed-domain. Firstly, summarization of generic videos is modeled as the process of extracted human objects under various activities/events. Accordingly, frames are classified into five categories via fuzzy decision including shot changes (cut and gradual transitions), motion activities (camera motion and object motion) and others by using two inter-frame measurements. Secondly, human objects are detected using Haar-like features. With the detected human objects and attained frame categories, activity levels for each frame are determined to adapt with video contents. Continuous frames belonging to same category are grouped to form one activity entry as content of interest (COI) which will convert the original video into a series of activities. An overall adjustable quota is used to control the size of generated summarization for efficient streaming purpose. Upon this quota, the frames selected for summarization are determined by evenly sampling the accumulated activity levels for content adaptation. Quantitative evaluations have proved the effectiveness and efficiency of our proposed approach, which provides a more flexible and general solution for this topic as domain-specific tasks such as accurate recognition of objects can be avoided

Genomic plasticity and rapid host switching can promote the evolution of generalism : a case study in the zoonotic pathogen Campylobacter

This work was supported by the Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/I02464X/1, the Medical Research Council (MRC) grants MR/M501608/1 and MR/L015080/1, and the Wellcome Trust grant 088786/C/09/Z. GM was supported by a NISCHR Health Research Fellowship (HF-14–13).Peer reviewedPublisher PD