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

Deterministic Construction of Binary, Bipolar and Ternary Compressed Sensing Matrices

In this paper we establish the connection between the Orthogonal Optical Codes (OOC) and binary compressed sensing matrices. We also introduce deterministic bipolar $m\times n$ RIP fulfilling $\pm 1$ matrices of order $k$ such that $m\leq\mathcal{O}\big(k (\log_2 n)^{\frac{\log_2 k}{\ln \log_2 k}}\big)$. The columns of these matrices are binary BCH code vectors where the zeros are replaced by -1. Since the RIP is established by means of coherence, the simple greedy algorithms such as Matching Pursuit are able to recover the sparse solution from the noiseless samples. Due to the cyclic property of the BCH codes, we show that the FFT algorithm can be employed in the reconstruction methods to considerably reduce the computational complexity. In addition, we combine the binary and bipolar matrices to form ternary sensing matrices ($\{0,1,-1\}$ elements) that satisfy the RIP condition.Comment: The paper is accepted for publication in IEEE Transaction on Information Theor

In situ method for power re-equalization of wavelength pulses inside of OCDMA codes

A simple in-situ method to equalize power among individual wavelengths pulses representing two-dimensional wavelength-hopping time-spreading OCDMA code originally generated by a fibre Bragg grating-based OCDMA encoder is presented. Experimental data obtained in a field-based multiuser OCDMA testbed shows that applying this method results in system performance enhancements which was demonstrated by observing improved bit error rate (BER) during the field trials

Spreads, arcs, and multiple wavelength codes

AbstractWe present several new families of multiple wavelength (2-dimensional) optical orthogonal codes (2D-OOCs) with ideal auto-correlation λa=0 (codes with at most one pulse per wavelength). We also provide a construction which yields multiple weight codes. All of our constructions produce codes that are either optimal with respect to the Johnson bound (J-optimal), or are asymptotically optimal and maximal. The constructions are based on certain pointsets in finite projective spaces of dimension k over GF(q) denoted PG(k,q)

Optical Time-Frequency Packing: Principles, Design, Implementation, and Experimental Demonstration

Time-frequency packing (TFP) transmission provides the highest achievable spectral efficiency with a constrained symbol alphabet and detector complexity. In this work, the application of the TFP technique to fiber-optic systems is investigated and experimentally demonstrated. The main theoretical aspects, design guidelines, and implementation issues are discussed, focusing on those aspects which are peculiar to TFP systems. In particular, adaptive compensation of propagation impairments, matched filtering, and maximum a posteriori probability detection are obtained by a combination of a butterfly equalizer and four 8-state parallel Bahl-Cocke-Jelinek-Raviv (BCJR) detectors. A novel algorithm that ensures adaptive equalization, channel estimation, and a proper distribution of tasks between the equalizer and BCJR detectors is proposed. A set of irregular low-density parity-check codes with different rates is designed to operate at low error rates and approach the spectral efficiency limit achievable by TFP at different signal-to-noise ratios. An experimental demonstration of the designed system is finally provided with five dual-polarization QPSK-modulated optical carriers, densely packed in a 100 GHz bandwidth, employing a recirculating loop to test the performance of the system at different transmission distances.Comment: This paper has been accepted for publication in the IEEE/OSA Journal of Lightwave Technolog

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