Two computational primitives for algorithmic self-assembly: Copying and counting

Copying and counting are useful primitive operations for computation and construction. We have made DNA crystals that copy and crystals that count as they grow. For counting, 16 oligonucleotides assemble into four DNA Wang tiles that subsequently crystallize on a polymeric nucleating scaffold strand, arranging themselves in a binary counting pattern that could serve as a template for a molecular electronic demultiplexing circuit. Although the yield of counting crystals is low, and per-tile error rates in such crystals is roughly 10%, this work demonstrates the potential of algorithmic self-assembly to create complex nanoscale patterns of technological interest. A subset of the tiles for counting form information-bearing DNA tubes that copy bit strings from layer to layer along their length

An information-bearing seed for nucleating algorithmic self-assembly

Self-assembly creates natural mineral, chemical, and biological structures of great complexity. Often, the same starting materials have the potential to form an infinite variety of distinct structures; information in a seed molecule can determine which form is grown as well as where and when. These phenomena can be exploited to program the growth of complex supramolecular structures, as demonstrated by the algorithmic self-assembly of DNA tiles. However, the lack of effective seeds has limited the reliability and yield of algorithmic crystals. Here, we present a programmable DNA origami seed that can display up to 32 distinct binding sites and demonstrate the use of seeds to nucleate three types of algorithmic crystals. In the simplest case, the starting materials are a set of tiles that can form crystalline ribbons of any width; the seed directs assembly of a chosen width with >90% yield. Increased structural diversity is obtained by using tiles that copy a binary string from layer to layer; the seed specifies the initial string and triggers growth under near-optimal conditions where the bit copying error rate is 17 kb of sequence information. In sum, this work demonstrates how DNA origami seeds enable the easy, high-yield, low-error-rate growth of algorithmic crystals as a route toward programmable bottom-up fabrication

Negatively Charged Strangelet Search using the E864 Spectrometer at the AGS

We provide a status report on the progress of searching for negatively charged strangelets using the E864 spectrometer at the AGS. About 200 million recorded events representing approximately 14 billion 10% central interactions of Au + Pt at 11.5 GeV/c taken during the 1996-1997 run of the experiment are used in the analysis. No strangelet candidates are seen for charges Z=-1 and Z=-2, corresponding to a 90% confidence level for upper limits of strangelet production of ~1 x 10^{-8} and ~4 x 10^{-9} per central collision respectively. The limits are nearly uniform over a wide range of masses and are valid only for strangelets which are stable or have lifetimes greater than ~50 ns.Comment: 6 pages, 4 figures; Talk at SQM'98, Padova, Italy (July 20-24, 1998

Detecting a stochastic background of gravitational waves in the presence of non-Gaussian noise: A performance of generalized cross-correlation statistic

We discuss a robust data analysis method to detect a stochastic background of gravitational waves in the presence of non-Gaussian noise. In contrast to the standard cross-correlation (SCC) statistic frequently used in the stochastic background searches, we consider a {\it generalized cross-correlation} (GCC) statistic, which is nearly optimal even in the presence of non-Gaussian noise. The detection efficiency of the GCC statistic is investigated analytically, particularly focusing on the statistical relation between the false-alarm and the false-dismissal probabilities, and the minimum detectable amplitude of gravitational-wave signals. We derive simple analytic formulae for these statistical quantities. The robustness of the GCC statistic is clarified based on these formulae, and one finds that the detection efficiency of the GCC statistic roughly corresponds to the one of the SCC statistic neglecting the contribution of non-Gaussian tails. This remarkable property is checked by performing the Monte Carlo simulations and successful agreement between analytic and simulation results was found.Comment: 15 pages, 8 figures, presentation and some figures modified, final version to be published in PR

Gravitational radiation from collapsing magnetized dust

In this article we study the influence of magnetic fields on the axial gravitational waves emitted during the collapse of a homogeneous dust sphere. We found that while the energy emitted depends weakly on the initial matter perturbations it has strong dependence on the strength and the distribution of the magnetic field perturbations. The gravitational wave output of such a collapse can be up to an order of magnitude larger or smaller calling for detailed numerical 3D studies of collapsing magnetized configurations

b-quark decay in the collinear approximation

The semileptonic decay of a b-quark, b--> c l nu, is considered in the relativistic limit where the decay products are approximately collinear. Analytic results for the double differential lepton energy distributions are given for finite charm-quark mass. Their use for the fast simulation of isolated lepton backgrounds from heavy quark decays is discussed.Comment: 7 pages, 1 figure, submitted to Phys.Rev.

Coherent Bayesian inference on compact binary inspirals using a network of interferometric gravitational wave detectors

Presented in this paper is a Markov chain Monte Carlo (MCMC) routine for conducting coherent parameter estimation for interferometric gravitational wave observations of an inspiral of binary compact objects using data from multiple detectors. The MCMC technique uses data from several interferometers and infers all nine of the parameters (ignoring spin) associated with the binary system, including the distance to the source, the masses, and the location on the sky. The Metropolis-algorithm utilises advanced MCMC techniques, such as importance resampling and parallel tempering. The data is compared with time-domain inspiral templates that are 2.5 post-Newtonian (PN) in phase and 2.0 PN in amplitude. Our routine could be implemented as part of an inspiral detection pipeline for a world wide network of detectors. Examples are given for simulated signals and data as seen by the LIGO and Virgo detectors operating at their design sensitivity.Comment: 10 pages, 4 figure

Optimal self-assembly of finite shapes at temperature 1 in 3D

Working in a three-dimensional variant of Winfree's abstract Tile Assembly Model, we show that, for an arbitrary finite, connected shape $X \subset \mathbb{Z}^2$, there is a tile set that uniquely self-assembles into a 3D representation of a scaled-up version of $X$ at temperature 1 in 3D with optimal program-size complexity (the "program-size complexity", also known as "tile complexity", of a shape is the minimum number of tile types required to uniquely self-assemble it). Moreover, our construction is "just barely" 3D in the sense that it only places tiles in the $z = 0$ and $z = 1$ planes. Our result is essentially a just-barely 3D temperature 1 simulation of a similar 2D temperature 2 result by Soloveichik and Winfree (SICOMP 2007)

Optimal combination of signals from co-located gravitational wave interferometers for use in searches for a stochastic background

This article derives an optimal (i.e., unbiased, minimum variance) estimator for the pseudo-detector strain for a pair of co-located gravitational wave interferometers (such as the pair of LIGO interferometers at its Hanford Observatory), allowing for possible instrumental correlations between the two detectors. The technique is robust and does not involve any assumptions or approximations regarding the relative strength of gravitational wave signals in the detector pair with respect to other sources of correlated instrumental or environmental noise. An expression is given for the effective power spectral density of the combined noise in the pseudo-detector. This can then be introduced into the standard optimal Wiener filter used to cross-correlate detector data streams in order to obtain an optimal estimate of the stochastic gravitational wave background. In addition, a dual to the optimal estimate of strain is derived. This dual is constructed to contain no gravitational wave signature and can thus be used as on "off-source" measurement to test algorithms used in the "on-source" observation.Comment: 14 pages, 4 figures, submitted to Physical Review D Resubmitted after editing paper in response to referee comments. Removed appendices A, B and edited text accordingly. Improved legibility of figures. Corrected several references. Corrected reference to science run number (S1 vs. S2) in text and figure caption