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

n-Dimensional Optical Orthogonal Codes, Bounds and Optimal Constructions

We generalized to higher dimensions the notions of optical orthogonal codes. We establish uper bounds on the capacity of general $n$-dimensional OOCs, and on specific types of ideal codes (codes with zero off-peak autocorrelation). The bounds are based on the Johnson bound, and subsume many of the bounds that are typically applied to codes of dimension three or less. We also present two new constructions of ideal codes; one furnishes an infinite family of optimal codes for each dimension $n\ge 2$, and another which provides an asymptotically optimal family for each dimension $n\ge 2$. The constructions presented are based on certain point-sets in finite projective spaces of dimension $k$ over $GF(q)$ denoted $PG(k,q)$.Comment: 13 pages. arXiv admin note: text overlap with arXiv:1702.0645