Scalable, Time-Responsive, Digital, Energy-Efficient Molecular Circuits using DNA Strand Displacement

We propose a novel theoretical biomolecular design to implement any Boolean circuit using the mechanism of DNA strand displacement. The design is scalable: all species of DNA strands can in principle be mixed and prepared in a single test tube, rather than requiring separate purification of each species, which is a barrier to large-scale synthesis. The design is time-responsive: the concentration of output species changes in response to the concentration of input species, so that time-varying inputs may be continuously processed. The design is digital: Boolean values of wires in the circuit are represented as high or low concentrations of certain species, and we show how to construct a single-input, single-output signal restoration gate that amplifies the difference between high and low, which can be distributed to each wire in the circuit to overcome signal degradation. This means we can achieve a digital abstraction of the analog values of concentrations. Finally, the design is energy-efficient: if input species are specified ideally (meaning absolutely 0 concentration of unwanted species), then output species converge to their ideal concentrations at steady-state, and the system at steady-state is in (dynamic) equilibrium, meaning that no energy is consumed by irreversible reactions until the input again changes. Drawbacks of our design include the following. If input is provided non-ideally (small positive concentration of unwanted species), then energy must be continually expended to maintain correct output concentrations even at steady-state. In addition, our fuel species - those species that are permanently consumed in irreversible reactions - are not "generic"; each gate in the circuit is powered by its own specific type of fuel species. Hence different circuits must be powered by different types of fuel. Finally, we require input to be given according to the dual-rail convention, so that an input of 0 is specified not only by the absence of a certain species, but by the presence of another. That is, we do not construct a "true NOT gate" that sets its output to high concentration if and only if its input's concentration is low. It remains an open problem to design scalable, time-responsive, digital, energy-efficient molecular circuits that additionally solve one of these problems, or to prove that some subset of their resolutions are mutually incompatible.Comment: version 2: the paper itself is unchanged from version 1, but the arXiv software stripped some asterisk characters out of the abstract whose purpose was to highlight words. These characters have been replaced with underscores in version 2. The arXiv software also removed the second paragraph of the abstract, which has been (attempted to be) re-inserted. Also, although the secondary subject is "Soft Condensed Matter", this classification was chosen by the arXiv moderators after submission, not chosen by the authors. The authors consider this submission to be a theoretical computer science paper

Experiences of the Support Designs in the Two Large Underground Openings in India

Support requirements for two caverns arc worked out by empirical and the numerical approaches. The adequacy of the shotcrete-rock bolt support system is monitored by measuring the deformations of caverns walls and roof. The measurements are compared with the results obtained from the numerical approach. Brief geology, the supports, and the results of performance monitoring are presented in the paper

Why We Read Wikipedia

Wikipedia is one of the most popular sites on the Web, with millions of users relying on it to satisfy a broad range of information needs every day. Although it is crucial to understand what exactly these needs are in order to be able to meet them, little is currently known about why users visit Wikipedia. The goal of this paper is to fill this gap by combining a survey of Wikipedia readers with a log-based analysis of user activity. Based on an initial series of user surveys, we build a taxonomy of Wikipedia use cases along several dimensions, capturing users' motivations to visit Wikipedia, the depth of knowledge they are seeking, and their knowledge of the topic of interest prior to visiting Wikipedia. Then, we quantify the prevalence of these use cases via a large-scale user survey conducted on live Wikipedia with almost 30,000 responses. Our analyses highlight the variety of factors driving users to Wikipedia, such as current events, media coverage of a topic, personal curiosity, work or school assignments, or boredom. Finally, we match survey responses to the respondents' digital traces in Wikipedia's server logs, enabling the discovery of behavioral patterns associated with specific use cases. For instance, we observe long and fast-paced page sequences across topics for users who are bored or exploring randomly, whereas those using Wikipedia for work or school spend more time on individual articles focused on topics such as science. Our findings advance our understanding of reader motivations and behavior on Wikipedia and can have implications for developers aiming to improve Wikipedia's user experience, editors striving to cater to their readers' needs, third-party services (such as search engines) providing access to Wikipedia content, and researchers aiming to build tools such as recommendation engines.Comment: Published in WWW'17; v2 fixes caption of Table

Fully-dynamic Approximation of Betweenness Centrality

Betweenness is a well-known centrality measure that ranks the nodes of a network according to their participation in shortest paths. Since an exact computation is prohibitive in large networks, several approximation algorithms have been proposed. Besides that, recent years have seen the publication of dynamic algorithms for efficient recomputation of betweenness in evolving networks. In previous work we proposed the first semi-dynamic algorithms that recompute an approximation of betweenness in connected graphs after batches of edge insertions. In this paper we propose the first fully-dynamic approximation algorithms (for weighted and unweighted undirected graphs that need not to be connected) with a provable guarantee on the maximum approximation error. The transfer to fully-dynamic and disconnected graphs implies additional algorithmic problems that could be of independent interest. In particular, we propose a new upper bound on the vertex diameter for weighted undirected graphs. For both weighted and unweighted graphs, we also propose the first fully-dynamic algorithms that keep track of such upper bound. In addition, we extend our former algorithm for semi-dynamic BFS to batches of both edge insertions and deletions. Using approximation, our algorithms are the first to make in-memory computation of betweenness in fully-dynamic networks with millions of edges feasible. Our experiments show that they can achieve substantial speedups compared to recomputation, up to several orders of magnitude

Optimal discrete stopping times for reliability growth tests

Often, the duration of a reliability growth development test is specified in advance and the decision to terminate or continue testing is conducted at discrete time intervals. These features are normally not captured by reliability growth models. This paper adapts a standard reliability growth model to determine the optimal time for which to plan to terminate testing. The underlying stochastic process is developed from an Order Statistic argument with Bayesian inference used to estimate the number of faults within the design and classical inference procedures used to assess the rate of fault detection. Inference procedures within this framework are explored where it is shown the Maximum Likelihood Estimators possess a small bias and converges to the Minimum Variance Unbiased Estimator after few tests for designs with moderate number of faults. It is shown that the Likelihood function can be bimodal when there is conflict between the observed rate of fault detection and the prior distribution describing the number of faults in the design. An illustrative example is provided

Defending against Sybil Devices in Crowdsourced Mapping Services

Real-time crowdsourced maps such as Waze provide timely updates on traffic, congestion, accidents and points of interest. In this paper, we demonstrate how lack of strong location authentication allows creation of software-based {\em Sybil devices} that expose crowdsourced map systems to a variety of security and privacy attacks. Our experiments show that a single Sybil device with limited resources can cause havoc on Waze, reporting false congestion and accidents and automatically rerouting user traffic. More importantly, we describe techniques to generate Sybil devices at scale, creating armies of virtual vehicles capable of remotely tracking precise movements for large user populations while avoiding detection. We propose a new approach to defend against Sybil devices based on {\em co-location edges}, authenticated records that attest to the one-time physical co-location of a pair of devices. Over time, co-location edges combine to form large {\em proximity graphs} that attest to physical interactions between devices, allowing scalable detection of virtual vehicles. We demonstrate the efficacy of this approach using large-scale simulations, and discuss how they can be used to dramatically reduce the impact of attacks against crowdsourced mapping services.Comment: Measure and integratio

Fractional diffusion modeling of ion channel gating

An anomalous diffusion model for ion channel gating is put forward. This scheme is able to describe non-exponential, power-law like distributions of residence time intervals in several types of ion channels. Our method presents a generalization of the discrete diffusion model by Millhauser, Salpeter and Oswald [Proc. Natl. Acad. Sci. USA 85, 1503 (1988)] to the case of a continuous, anomalous slow conformational diffusion. The corresponding generalization is derived from a continuous time random walk composed of nearest neighbor jumps which in the scaling limit results in a fractional diffusion equation. The studied model contains three parameters only: the mean residence time, a characteristic time of conformational diffusion, and the index of subdiffusion. A tractable analytical expression for the characteristic function of the residence time distribution is obtained. In the limiting case of normal diffusion, our prior findings [Proc. Natl. Acad. Sci. USA 99, 3552 (2002)] are reproduced. Depending on the chosen parameters, the fractional diffusion model exhibits a very rich behavior of the residence time distribution with different characteristic time-regimes. Moreover, the corresponding autocorrelation function of conductance fluctuations displays nontrivial features. Our theoretical model is in good agreement with experimental data for large conductance potassium ion channels

Data Portraits and Intermediary Topics: Encouraging Exploration of Politically Diverse Profiles

In micro-blogging platforms, people connect and interact with others. However, due to cognitive biases, they tend to interact with like-minded people and read agreeable information only. Many efforts to make people connect with those who think differently have not worked well. In this paper, we hypothesize, first, that previous approaches have not worked because they have been direct -- they have tried to explicitly connect people with those having opposing views on sensitive issues. Second, that neither recommendation or presentation of information by themselves are enough to encourage behavioral change. We propose a platform that mixes a recommender algorithm and a visualization-based user interface to explore recommendations. It recommends politically diverse profiles in terms of distance of latent topics, and displays those recommendations in a visual representation of each user's personal content. We performed an "in the wild" evaluation of this platform, and found that people explored more recommendations when using a biased algorithm instead of ours. In line with our hypothesis, we also found that the mixture of our recommender algorithm and our user interface, allowed politically interested users to exhibit an unbiased exploration of the recommended profiles. Finally, our results contribute insights in two aspects: first, which individual differences are important when designing platforms aimed at behavioral change; and second, which algorithms and user interfaces should be mixed to help users avoid cognitive mechanisms that lead to biased behavior.Comment: 12 pages, 7 figures. To be presented at ACM Intelligent User Interfaces 201