arXiv subjects

Boaz Moav

Publications and source records attributed to Boaz Moav.

3 recordsLinked to original sources

arXiv2026

Efficient Synthesis for Two-Dimensional Strand Arrays with Row Constraints

In large-scale array-based DNA synthesis, optical and chemical coupling between nearby sites can limit simultaneous activations. Motivated by this constraint, we study strands synthesized according to a fixed global synthesis sequence, with at most one strand per row advancing in each cycle. We focus on the fundamental case of two strands in a single row and analyze the expected completion time of row-constrained synthesis. We introduce the laggard-first (LF) policy, a simple rule that always advances the strand with fewer synthesized symbols when a conflict arises, and establish that it is asymptotically optimal among online policies without look-ahead. In the binary case, one-symbol look-ahead strictly improves on the no-look-ahead bound. We further show that even complete advance knowledge does not eliminate the scheduling loss, as even a globally optimal schedule incurs an unavoidable expected overhead that grows linearly with the strand length. Finally, we complement these scheduling results with a dynamic programming algorithm for computing an optimal offline synthesis order and a constant-redundancy binary coding scheme that yields a deterministic worst-case synthesis time guarantee.

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arXiv2025

Complex DNA Synthesis Sequences

DNA-based storage offers unprecedented density and durability, but its scalability is fundamentally limited by the efficiency of parallel strand synthesis. Existing methods either allow unconstrained nucleotide additions to individual strands, such as enzymatic synthesis, or enforce identical additions across many strands, such as photolithographic synthesis. We introduce and analyze a hybrid synthesis framework that generalizes both approaches: in each cycle, a nucleotide is selected from a restricted subset and incorporated in parallel. This model gives rise to a new notion of a complex synthesis sequence. Building on this framework, we extend the information rate definition of Lenz et al. and analyze an analog of the deletion ball, defined and studied in this setting, deriving tight expressions for the maximal information rate and its asymptotic behavior. These results bridge the theoretical gap between constrained models and the idealized setting in which every nucleotide is always available. For the case of known strands, we design a dynamic programming algorithm that computes an optimal complex synthesis sequence, highlighting structural similarities to the shortest common supersequence problem. We also define a distinct two-dimensional array model with synthesis constraints over the rows, which extends previous synthesis models in the literature and captures new structural limitations in large-scale strand arrays. Additionally, we develop a dynamic programming algorithm for this problem as well. Our results establish a new and comprehensive theoretical framework for constrained DNA, subsuming prior models and setting the stage for future advances in the field.

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arXiv2024

Tail-Erasure-Correcting Codes

The increasing demand for data storage has prompted the exploration of new techniques, with molecular data storage being a promising alternative. In this work, we develop coding schemes for a new storage paradigm that can be represented as a collection of two-dimensional arrays. Motivated by error patterns observed in recent prototype architectures, our study focuses on correcting erasures in the last few symbols of each row, and also correcting arbitrary deletions across rows. We present code constructions and explicit encoders and decoders that are shown to be nearly optimal in many scenarios. We show that the new coding schemes are capable of effectively mitigating these errors, making these emerging storage platforms potentially promising solutions.

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