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

Parsing a sequence of qubits

We develop a theoretical framework for frame synchronization, also known as block synchronization, in the quantum domain which makes it possible to attach classical and quantum metadata to quantum information over a noisy channel even when the information source and sink are frame-wise asynchronous. This eliminates the need of frame synchronization at the hardware level and allows for parsing qubit sequences during quantum information processing. Our framework exploits binary constant-weight codes that are self-synchronizing. Possible applications may include asynchronous quantum communication such as a self-synchronizing quantum network where one can hop into the channel at any time, catch the next coming quantum information with a label indicating the sender, and reply by routing her quantum information with control qubits for quantum switches all without assuming prior frame synchronization between users.Comment: 11 pages, 2 figures, 1 table. Final accepted version for publication in the IEEE Transactions on Information Theor