Design of Geometric Molecular Bonds

An example of a nonspecific molecular bond is the affinity of any positive charge for any negative charge (like-unlike), or of nonpolar material for itself when in aqueous solution (like-like). This contrasts specific bonds such as the affinity of the DNA base A for T, but not for C, G, or another A. Recent experimental breakthroughs in DNA nanotechnology demonstrate that a particular nonspecific like-like bond ("blunt-end DNA stacking" that occurs between the ends of any pair of DNA double-helices) can be used to create specific "macrobonds" by careful geometric arrangement of many nonspecific blunt ends, motivating the need for sets of macrobonds that are orthogonal: two macrobonds not intended to bind should have relatively low binding strength, even when misaligned. To address this need, we introduce geometric orthogonal codes that abstractly model the engineered DNA macrobonds as two-dimensional binary codewords. While motivated by completely different applications, geometric orthogonal codes share similar features to the optical orthogonal codes studied by Chung, Salehi, and Wei. The main technical difference is the importance of 2D geometry in defining codeword orthogonality.Comment: Accepted to appear in IEEE Transactions on Molecular, Biological, and Multi-Scale Communication

Fast Decoder for Overloaded Uniquely Decodable Synchronous Optical CDMA

In this paper, we propose a fast decoder algorithm for uniquely decodable (errorless) code sets for overloaded synchronous optical code-division multiple-access (O-CDMA) systems. The proposed decoder is designed in a such a way that the users can uniquely recover the information bits with a very simple decoder, which uses only a few comparisons. Compared to maximum-likelihood (ML) decoder, which has a high computational complexity for even moderate code lengths, the proposed decoder has much lower computational complexity. Simulation results in terms of bit error rate (BER) demonstrate that the performance of the proposed decoder for a given BER requires only 1-2 dB higher signal-to-noise ratio (SNR) than the ML decoder.Comment: arXiv admin note: substantial text overlap with arXiv:1806.0395

Proceedings of the second "international Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST'14)

The implicit objective of the biennial "international - Traveling Workshop on Interactions between Sparse models and Technology" (iTWIST) is to foster collaboration between international scientific teams by disseminating ideas through both specific oral/poster presentations and free discussions. For its second edition, the iTWIST workshop took place in the medieval and picturesque town of Namur in Belgium, from Wednesday August 27th till Friday August 29th, 2014. The workshop was conveniently located in "The Arsenal" building within walking distance of both hotels and town center. iTWIST'14 has gathered about 70 international participants and has featured 9 invited talks, 10 oral presentations, and 14 posters on the following themes, all related to the theory, application and generalization of the "sparsity paradigm": Sparsity-driven data sensing and processing; Union of low dimensional subspaces; Beyond linear and convex inverse problem; Matrix/manifold/graph sensing/processing; Blind inverse problems and dictionary learning; Sparsity and computational neuroscience; Information theory, geometry and randomness; Complexity/accuracy tradeoffs in numerical methods; Sparsity? What's next?; Sparse machine learning and inference.Comment: 69 pages, 24 extended abstracts, iTWIST'14 website: http://sites.google.com/site/itwist1

Spirality: A Novel Way to Measure Spiral Arm Pitch Angle

We present the MATLAB code Spirality, a novel method for measuring spiral arm pitch angles by fitting galaxy images to spiral templates of known pitch. Computation time is typically on the order of 2 minutes per galaxy, assuming at least 8 GB of working memory. We tested the code using 117 synthetic spiral images with known pitches, varying both the spiral properties and the input parameters. The code yielded correct results for all synthetic spirals with galaxy-like properties. We also compared the code's results to two-dimensional Fast Fourier Transform (2DFFT) measurements for the sample of nearby galaxies defined by DMS PPak. Spirality's error bars overlapped 2DFFT's error bars for 26 of the 30 galaxies. The two methods' agreement correlates strongly with galaxy radius in pixels and also with i-band magnitude, but not with redshift, a result that is consistent with at least some galaxies' spiral structure being fully formed by z=1.2, beyond which there are few galaxies in our sample. The Spirality code package also includes GenSpiral, which produces FITS images of synthetic spirals, and SpiralArmCount, which uses a one-dimensional Fast Fourier Transform to count the spiral arms of a galaxy after its pitch is determined. The code package is freely available online; see Comments for URL.Comment: 19 pages, 9 figures, 3 tables. The code package is available at http://dafix.uark.edu/~doug/SpiralityCode

Fornax: a Flexible Code for Multiphysics Astrophysical Simulations

This paper describes the design and implementation of our new multi-group, multi-dimensional radiation hydrodynamics (RHD) code Fornax and provides a suite of code tests to validate its application in a wide range of physical regimes. Instead of focusing exclusively on tests of neutrino radiation hydrodynamics relevant to the core-collapse supernova problem for which Fornax is primarily intended, we present here classical and rigorous demonstrations of code performance relevant to a broad range of multi-dimensional hydrodynamic and multi-group radiation hydrodynamic problems. Our code solves the comoving-frame radiation moment equations using the M1 closure, utilizes conservative high-order reconstruction, employs semi-explicit matter and radiation transport via a high-order time stepping scheme, and is suitable for application to a wide range of astrophysical problems. To this end, we first describe the philosophy, algorithms, and methodologies of Fornax and then perform numerous stringent code tests, that collectively and vigorously exercise the code, demonstrate the excellent numerical fidelity with which it captures the many physical effects of radiation hydrodynamics, and show excellent strong scaling well above 100k MPI tasks.Comment: Accepted to the Astrophysical Journal Supplement Series; A few more textual and reference updates; As before, one additional code test include

The Optical Frequency Comb as a One-Way Quantum Computer

In the one-way model of quantum computing, quantum algorithms are implemented using only measurements on an entangled initial state. Much of the hard work is done up-front when creating this universal resource, known as a cluster state, on which the measurements are made. Here we detail a new proposal for a scalable method of creating cluster states using only a single multimode optical parametric oscillator (OPO). The method generates a continuous-variable cluster state that is universal for quantum computation and encoded in the quadratures of the optical frequency comb of the OPO. This work expands on the presentation in Phys. Rev. Lett. 101, 130501 (2008).Comment: 20 pages, 8 figures. v2 corrects minor error in published versio