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

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

A General Upper Bound on the Size of Constant-Weight Conflict-Avoiding Codes

Conflict-avoiding codes are used in the multiple-access collision channel without feedback. The number of codewords in a conflict-avoiding code is the number of potential users that can be supported in the system. In this paper, a new upper bound on the size of conflict-avoiding codes is proved. This upper bound is general in the sense that it is applicable to all code lengths and all Hamming weights. Several existing constructions for conflict-avoiding codes, which are known to be optimal for Hamming weights equal to four and five, are shown to be optimal for all Hamming weights in general.Comment: 10 pages, 1 figur