Scaling and Universality in the Counterion-Condensation Transition at Charged Cylinders

We address the critical and universal aspects of counterion-condensation transition at a single charged cylinder in both two and three spatial dimensions using numerical and analytical methods. By introducing a novel Monte-Carlo sampling method in logarithmic radial scale, we are able to numerically simulate the critical limit of infinite system size (corresponding to infinite-dilution limit) within tractable equilibration times. The critical exponents are determined for the inverse moments of the counterionic density profile (which play the role of the order parameters and represent the inverse localization length of counterions) both within mean-field theory and within Monte-Carlo simulations. In three dimensions (3D), correlation effects (neglected within mean-field theory) lead to an excessive accumulation of counterions near the charged cylinder below the critical temperature (condensation phase), while surprisingly, the critical region exhibits universal critical exponents in accord with the mean-field theory. In two dimensions (2D), we demonstrate, using both numerical and analytical approaches, that the mean-field theory becomes exact at all temperatures (Manning parameters), when number of counterions tends to infinity. For finite particle number, however, the 2D problem displays a series of peculiar singular points (with diverging heat capacity), which reflect successive de-localization events of individual counterions from the central cylinder. In both 2D and 3D, the heat capacity shows a universal jump at the critical point, and the energy develops a pronounced peak. The asymptotic behavior of the energy peak location is used to locate the critical temperature, which is also found to be universal and in accordance with the mean-field prediction.Comment: 31 pages, 16 figure

Polyelectrolyte Persistence Length: Attractive Effect of Counterion Correlations and Fluctuations

The persistence length of a single, strongly charged, stiff polyelectrolyte chain is investigated theoretically. Path integral formulation is used to obtain the effective electrostatic interaction between the monomers. We find significant deviations from the classical Odijk, Skolnick and Fixman (OSF) result. An induced attraction between monomers is due to thermal fluctuations and correlations between bound counterions. The electrostatic persistence length is found to be smaller than the OSF value and indicates a possible mechanical instability (collapse) for highly charged polyelectrolytes with multivalent counterions. In addition, we calculate the amount of condensed counterions on a slightly bent polyelectrolyte. More counterions are found to be adsorbed as compared to the Manning condensation on a cylinder.Comment: 5 pages, 1 ps figur

Mechanical response of plectonemic DNA: an analytical solution

We consider an elastic rod model for twisted DNA in the plectonemic regime. The molecule is treated as an impenetrable tube with an effective, adjustable radius. The model is solved analytically and we derive formulas for the contact pressure, twisting moment and geometrical parameters of the supercoiled region. We apply our model to magnetic tweezer experiments of a DNA molecule subjected to a tensile force and a torque, and extract mechanical and geometrical quantities from the linear part of the experimental response curve. These reconstructed values are derived in a self-contained manner, and are found to be consistent with those available in the literature.Comment: 14 pages, 4 figure

Not all surveillance data are created equal—A multi‐method dynamic occupancy approach to determine rabies elimination from wildlife

1. A necessary component of elimination programmes for wildlife disease is effective surveillance. The ability to distinguish between disease freedom and non‐detection can mean the difference between a successful elimination campaign and new epizootics. Understanding the contribution of different surveillance methods helps to optimize and better allocate effort and develop more effective surveillance programmes. 2. We evaluated the probability of rabies virus elimination (disease freedom) in an enzootic area with active management using dynamic occupancy modelling of 10 years of raccoon rabies virus (RABV) surveillance data (2006–2015) collected from three states in the eastern United States. We estimated detection probability of RABV cases for each surveillance method (e.g. strange acting reports, roadkill, surveillance‐trapped animals, nuisance animals and public health samples) used by the USDA National Rabies Management Program. 3. Strange acting, found dead and public health animals were the most likely to detect RABV when it was present, and generally detectability was higher in fall– winter compared to spring–summer. Found dead animals in fall–winter had the highest detection at 0.33 (95% CI: 0.20, 0.48). Nuisance animals had the lowest detection probabilities (~0.02). 4. Areas with oral rabies vaccination (ORV) management had reduced occurrence probability compared to enzootic areas without ORV management. RABV occurrence was positively associated with deciduous and mixed forests and medium to high developed areas, which are also areas with higher raccoon (Procyon lotor) densities. By combining occupancy and detection estimates we can create a probability of elimination surface that can be updated seasonally to provide guidance on areas managed for wildlife disease. 5. Synthesis and applications. Wildlife disease surveillance is often comprised of a combination of targeted and convenience‐based methods. Using a multi‐method analytical approach allows us to compare the relative strengths of these methods, providing guidance on resource allocation for surveillance actions. Applying this multi‐method approach in conjunction with dynamic occupancy analyses better informs management decisions by understanding ecological drivers of disease occurrence

Locating bugs without looking back

Bug localisation is a core program comprehension task in software maintenance: given the observation of a bug, e.g. via a bug report, where is it located in the source code? Information retrieval (IR) approaches see the bug report as the query, and the source code files as the documents to be retrieved, ranked by relevance. Such approaches have the advantage of not requiring expensive static or dynamic analysis of the code. However, current state-of-the-art IR approaches rely on project history, in particular previously fixed bugs or previous versions of the source code. We present a novel approach that directly scores each current file against the given report, thus not requiring past code and reports. The scoring method is based on heuristics identified through manual inspection of a small sample of bug reports. We compare our approach to eight others, using their own five metrics on their own six open source projects. Out of 30 performance indicators, we improve 27 and equal 2. Over the projects analysed, on average we find one or more affected files in the top 10 ranked files for 76% of the bug reports. These results show the applicability of our approach to software projects without history

A personalized and context-aware news offer for mobile devices

For classical domains, such as movies, recommender systems have proven their usefulness. But recommending news is more challenging due to the short life span of news content and the demand for up-to-date recommendations. This paper presents a news recommendation service with a content-based algorithm that uses features of a search engine for content processing and indexing, and a collaborative filtering algorithm for serendipity. The extension towards a context-aware algorithm is made to assess the information value of context in a mobile environment through a user study. Analyzing interaction behavior and feedback of users on three recommendation approaches shows that interaction with the content is crucial input for user modeling. Context-aware recommendations using time and device type as context data outperform traditional recommendations with an accuracy gain dependent on the contextual situation. These findings demonstrate that the user experience of news services can be improved by a personalized context-aware news offer

Why is the condensed phase of DNA preferred at higher temperature? DNA compaction in the presence of a multivalent cation

Upon the addition of multivalent cations, a giant DNA chain exhibits a large discrete transition from an elongated coil into a folded compact state. We performed single-chain observation of long DNAs in the presence of a tetravalent cation (spermine), at various temperatures and monovalent salt concentrations. We confirmed that the compact state is preferred at higher temperatures and at lower monovalent salt concentrations. This result is interpreted in terms of an increase in the net translational entropy of small ions due to ionic exchange between higher and lower valence ions.Comment: 4pages,3figure

Effective and Efficient Similarity Index for Link Prediction of Complex Networks

Predictions of missing links of incomplete networks like protein-protein interaction networks or very likely but not yet existent links in evolutionary networks like friendship networks in web society can be considered as a guideline for further experiments or valuable information for web users. In this paper, we introduce a local path index to estimate the likelihood of the existence of a link between two nodes. We propose a network model with controllable density and noise strength in generating links, as well as collect data of six real networks. Extensive numerical simulations on both modeled networks and real networks demonstrated the high effectiveness and efficiency of the local path index compared with two well-known and widely used indices, the common neighbors and the Katz index. Indeed, the local path index provides competitively accurate predictions as the Katz index while requires much less CPU time and memory space, which is therefore a strong candidate for potential practical applications in data mining of huge-size networks.Comment: 8 pages, 5 figures, 3 table