arXiv subjects

Frederik Walter

Publications and source records attributed to Frederik Walter.

4 recordsLinked to original sources

arXiv2026

A Security Framework for Chemical Functions

In this paper, we introduce chemical functions, a unified framework that models chemical systems as noisy challenge--response primitives, and formalize the associated chemical function infrastructure. Building on the theory of physical functions, we rigorously define robustness, unclonability, and unpredictability for chemical functions in both finite and asymptotic regimes, and specify security games that capture the adversary's power and the security goals. We instantiate the framework with two existing DNA-based constructions (operable random DNA and Genomic Sequence Encryption) and derive quantitative bounds for robustness, unclonability, and unpredictability. Our analysis develops maximum-likelihood verification rules under sequencing noise and partial-edit models, and provides high-precision estimates based on binomial distributions to guide parameter selection. The framework, definitions, and analyses yield a reproducible methodology for designing chemically unclonable authentication mechanisms. We demonstrate applications to in-product authentication and to shared key generation using standard extraction techniques.

cs.CR↗

arXiv2026

Coding Schemes for the Noisy Torn Paper Channel

To make DNA a suitable medium for archival data storage, it is essential to consider the decay process of the strands observed in DNA storage systems. This paper studies the decay process as a probabilistic noisy torn paper channel (TPC), which first corrupts the bits of the transmitted sequence in a probabilistic manner by substitutions, then breaks the sequence into a set of noisy unordered substrings. The present work devises coding schemes for the noisy TPC by embedding markers in the transmitted sequence. We investigate the use of static markers and markers connected to the data in the form of hash functions. These two tools have also been recently exploited to tackle the noiseless TPC. Simulations show that static markers excel at higher substitution probabilities, while data-dependent markers are superior at lower noise levels. Both approaches achieve reconstruction rates exceeding $99\%$ with no false decodings observed, primarily limited by computational resources.

cs.IT↗

arXiv2025

Coding for Strand Breaks in Composite DNA

Due to their sequential nature, traditional DNA synthesis methods are expensive in terms of time and resources. They also fabricate multiple copies of the same strand, introducing redundancy. This redundancy can be leveraged to enhance the information capacity of each synthesis cycle and DNA storage systems in general by employing composite DNA symbols. Unlike conventional DNA storage, composite DNA encodes information in the distribution of bases across a pool of strands rather than in the individual strands themselves. Consequently, error models for DNA storage must be adapted to account for this unique characteristic. One significant error model for long-term DNA storage is strand breaks, often caused by the decay of individual bases. This work extends the strand-break channel model to the composite DNA setting. To address this challenge, we propose a coding scheme that uses marker codes to correct single strand breaks. As part of this approach, we generalise run-length-limited (RLL) codes for the composite setting and derive bounds on their redundancy.

cs.IT↗

arXiv2024

Coding for Composite DNA to Correct Substitutions, Strand Losses, and Deletions

Composite DNA is a recent method to increase the base alphabet size in DNA-based data storage.This paper models synthesizing and sequencing of composite DNA and introduces coding techniques to correct substitutions, losses of entire strands, and symbol deletion errors. Non-asymptotic upper bounds on the size of codes with $t$ occurrences of these error types are derived. Explicit constructions are presented which can achieve the bounds.

cs.IT↗