ABSTRACT A zero‐knowledge proof lets one party convince another that a claim is true while withholding everything that would explain why it is true. We move that idea off conventional hardware and into chemistry, encoding a proof of graph isomorphism directly in synthetic DNA. Each node of a graph is given its own deliberately orthogonal DNA strand; an edge is confirmed only when a short complementary half‐linker meets its matching pair and forms a stable duplex. The verifier watches which bindings occur, but the pattern of binding never reveals how the two graphs line up, so the isomorphism stays hidden. Whether such a construction stays secure at the molecular level turns on two things: how distinguishable the sequences are, and how stable the duplexes they form turn out to be. We probe both. A seeded Monte Carlo study of orthogonal 20‐m libraries, built with balanced GC content and a minimum Hamming separation of , places the chance that an off‐target strand passes for a genuine linker on the order of : empirically at a binding threshold of mismatches, and under once the threshold is tightened to , each value reported with a Wilson confidence interval. This molecular error never becomes the bottleneck. A cheating prover already passes a round with probability one‐half from the isomorphism challenge alone, so the biochemical term enters soundness only as an additive correction, over the edges examined, rather than racing the decay across rounds. Read this way, DNA strands behave as cryptographic witnesses whose noise is small enough to bound and to account for, which lets a proof run at molecular scale without surrendering the hidden mapping.
The impending arrival of cryptographically relevant quantum computing threatens classical public‑key infrastructures. This paper reviews the latest developments (2025–2026) in post‑quantum cryptography (PQC), fully homomorphic encryption (FHE), and zero‑knowledge proofs (ZKP). NIST has advanced nine signature candidates to its third evaluation round and selected HQC as a backup encryption standard. Novel primitives include bio‑inspired RNA‑based cryptography, algebraic hash signatures, and topology‑mined lattice schemes. FHE has reached its fifth generation with the GL scheme and the MadPanthera virtual processor, while lightweight ZKPs such as Microsoft’s Vega enable mobile‑friendly verification. These advances demonstrate rapid maturation toward deployable quantum‑safe systems.
Deoxyribonucleic acid provides unmatched information density and longevity for data storage, yet its easy amplification by polymerase chain reaction enables unauthorized replication at negligible cost. We introduce ZAT-DNA, which encodes information in patterns of canonical adenine and noncanonical 2-aminoadenine. As DNA polymerases cannot distinguish adenine from 2-aminoadenine, polymerase-based amplification erases these patterns, enforcing molecular-layer non-replicability intrinsic to the base-pairing ambiguity. We validate ZAT-DNA for secure key storage, demonstrating error-free encoding, storage, and high-fidelity nanopore retrieval of 32-bit and 64-bit cryptographic keys. ZAT-DNA blocks polymerase-based copying and protects non-fungible tokens by preventing functional duplication. For larger datasets, we present a hybrid “Babel-DNA” architecture: multiple encrypted images are co-encoded in a single regular DNA pool, with each selectively decryptable only via its cognate, non-replicable ZAT-DNA key. This provides a practical framework for molecular access control, secure DNA-encoded databases, and scarce molecular tokens. ZAT-DNA encodes data in A/Z base patterns that PCR erases, ensuring molecular non-replicability. It enables secure 32/64-bit key storage and nanopore retrieval, blocks copying, and protects NFTs. The Babel-DNA hybrid allows selective access to multiple encrypted datasets from a single DNA pool using unique ZAT-DNA keys.
Open access
DNA and Biological Computing
Nanopore and Nanochannel Transport Studies
Physical Unclonable Functions (PUFs) and Hardware Security
To address centralized trust risks, inadequate privacy protection, and quantum vulnerability of traditional crossdomain authentication systems, this paper proposes a quantumresistant self-sovereign identity (SSI) scheme based on lattice cryptography. Centered on Decentralized Identifiers (DIDs) and Verifiable Credentials (VCs), it constructs a decentralized ecosystem with two key innovations: a “single trapdoor - multi-attribute public key” structure (reducing storage and simplifying key management) and a lattice-based linkable ring signature (balancing anonymity and traceability). Implemented via TrapGen, SamplePre, and rejection sampling, the scheme's security relies on the Short Integer Solution (SIS) problem, with unconditional anonymity and unforgeability proven in the random oracle model. Efficiency comparisons confirm advantages in signature/verification time and storage overhead. This work provides a secure, privacy-preserving post-quantum solution for crossdomain collaboration in smart cities and supply chains. Future work will focus on lattice optimization and zero-knowledge proof integration.
Marxel S. Abogado, Worasait Suwannik, Geoffrey A. Solano, Somchoke Ruengittinun
Consensus sequences are reconstructed representations of original DNA strands, generated by aligning and combining multiple fragmented reads. This paper presents zkConsensus, a privacy-preserving system that verifies the generation of consensus sequences without revealing sensitive genetic information with the use of Zero-Knowledge Proofs (ZKPs). Implemented in Circom language, the circuit validates three validation parts: the consistency between original and aligned reads, the correctness of alignment scores across all read pairs, and the support for the consensus bases through majority voting. The system takes as public inputs the original reads, their lengths, and an expected score, while treating the alignments, reverse complement indications, start positions, and final consensus as private.
Assume that, given a sequence of n integers from 1 to n arranged in random order, we want to sort them, provided that the only acceptable operation is a prefix reversal, which means to take any number of integers (sub-sequence) from the left of the sequence, reverse the order of the sub-sequence, and return them to the original sequence. This problem is called “pancake sorting,” and sorting an arbitrary sequence with the minimum number of operations restricted in this way is known to be NP-hard. In this paper, we consider applying the concept of zero-knowledge proofs to the pancake sorting problem. That is, we design card-based zero-knowledge proof protocols in which a user (the prover) who knows how to sort a given sequence with ℓ operations can convince another user (the verifier) that the prover knows this information without divulging it.
This paper presents a formalised architecture for synthetic agents designed to retain immutable memory, verifiable reasoning, and constrained epistemic growth. Traditional AI systems rely on mutable, opaque statistical models prone to epistemic drift and historical revisionism. In contrast, we introduce the concept of the Merkle Automaton, a cryptographically anchored, deterministic computational framework that integrates formal automata theory with blockchain-based commitments. Each agent transition, memory fragment, and reasoning step is committed within a Merkle structure rooted on-chain, rendering it non-repudiable and auditably permanent. To ensure selective access and confidentiality, we derive symmetric encryption keys from ECDH exchanges contextualised by hierarchical privilege lattices. This enforces cryptographic access control over append-only DAG-structured knowledge graphs. Reasoning is constrained by formal logic systems and verified through deterministic traversal of policy-encoded structures. Updates are non-destructive and historied, preserving epistemic lineage without catastrophic forgetting. Zero-knowledge proofs facilitate verifiable, privacy-preserving inclusion attestations. Collectively, this architecture reframes memory not as a cache but as a ledger - one whose contents are enforced by protocol, bound by cryptography, and constrained by formal logic. The result is not an intelligent agent that mimics thought, but an epistemic entity whose outputs are provably derived, temporally anchored, and impervious to post hoc revision. This design lays foundational groundwork for legal, economic, and high-assurance computational systems that require provable memory, unforgeable provenance, and structural truth.
In an increasingly digital world, establishing secure and reliable methods for verifying identity has become a critical priority across sectors such as finance, healthcare, education, and e-governance. Traditional authentication mechanisms—relying on passwords, personal identification numbers, and physical documents—are increasingly susceptible to fraud, data breaches, and user inconvenience. This paper presents a multi-modal biometric framework for digital identity management, integrating facial recognition and fingerprint verification to enhance accuracy, reduce fraud, and ensure user-centric security. The proposed system includes modules for data acquisition, preprocessing, feature extraction using Convolutional Neural Networks (CNNs) and minutiae detection, score-level fusion, and final authentication decisions. Security and privacy are ensured through AES-256 encryption, differential privacy techniques, and decentralized blockchain-based data storage. This research contributes a scalable, privacy-aware, and highly accurate digital identity model capable of addressing challenges such as interoperability, user trust, and regulatory compliance. Future enhancements include the integration of additional biometric modalities and deployment in mobile and IoT environments.
Currently, PAKE (Password Authenticated Key Exchange) protocols on lattice using a single-server architecture are widely applied. However, such protocols are vulnerable to server leakage attacks, dictionary attacks, and other threats. To address these issues, researchers have proposed multi-server and two-server architecture-based PAKE protocols. However, PAKE protocols in a multi-server architecture require the use of complex cryptographic primitives such as signatures, and zero-knowledge proofs to ensure security, which reduces the execution efficiency of the protocol. To tackle these challenges, we propose two new multi-server password authentication key exchange protocols based on the MLWE (Module learning with errors) problem. Both protocols rely on MLWE instances, using Peikert's error coordination technique to enable two parties with similar values to compute the same result. Furthermore, we introduce the error pairing assumption and proves its security within random oracle model. The proposed protocol divides the password information into different shares and stores them on separate servers. In protocol 1, all servers and user collaboratively generate session keys, making it suitable for high-security application scenarios. In protocol 2, both user and servers generate session keys individually, which is ideal for high-efficiency application scenarios. Compared to similar protocols, both protocols lower computation and communication costs, better addressing practical application needs while providing protection against quantum computing attacks and server leakage threats.
The syndrome decoding problem is one of the NP-complete problems lying at the foundation of code-based cryptography. The variant thereof where the distance between vectors is measured with respect to the Lee metric, rather than the more commonly used Hamming metric, has been analyzed recently in several works due to its potential relevance for building more efficient code-based cryptosystems. The purpose of this article is to present a zero-knowledge proof of knowledge for this variant of the problem.
Joon Sik Kim, Kwangsu Lee, Jong Hwan Park, Hyoseung Kim
A threshold key encapsulation mechanism (TKEM) facilitates the secure distribution of session keys among multiple participants, allowing key recovery through a threshold number of shares. TKEM has gained significant attention, especially for decentralized systems, including blockchains. However, existing constructions often rely on trusted setups, which pose security risks such as a single point of failure and are limited by fixed participant numbers and thresholds. To overcome this issue, we propose a dynamic TKEM with a transparent setup, allowing for a flexible selection of both recipients and thresholds without relying on trusted third parties in the setup phase. In addition, our construction does not rely on pairing operations, which are less efficient compared to exponentiation. We prove the selective chosen-ciphertext security of our construction under the decisional Diffie-Hellman assumption, zero-knowledge, and soundness of a non-interactive zero-knowledge (NIZK) proof system. We also show that our scheme satisfies decapsulation consistency when the underlying NIZK system is sound. Our proof-of-concept implementation highlights the practicality and efficiency of this approach, further advancing the field of threshold cryptography.
This paper investigates the use of threshold signature schemes in isogeny-based cryptosystems. By leveraging the distinct features of isogeny graphs, we propose a protocol that offers high security and practical efficiency, making it ideal for distributed ledger technologies and secure multi-party computations. Our scheme is resistant to quantum attacks and maintains minimal computational and communication overheads. We present an extensive analysis of the security and performance of our protocol, emphasizing its relevance to real-world cryptographic systems. MSC 2020: 94A60, 11G07, 68M07.
The 6G communication network emerged with the developments in new generation Information and Communication Technologies such as Artificial Intelligence, Virtual Reality/Augmented Reality/Extended Reality, Internet of Things, blockchain technology, etc. The development of 6G has a profound impact on the intelligence process of communication development that consists of intelligent connectivity, deep connectivity, holographic connectivity, and ubiquitous connectivity. Security solutions in terms of distributed ledger technology (DLT), physical layer security, quantum communication, and distributed AI/ML are provided. The Distributed Ledger Technology threats include Majority attack/51% attack, other attacks, etc. The possible solutions include proper access control and authentication mechanisms, selecting the proper blockchain/DLT type according to the 6G application and services, etc. The Physical Layer Security requires line of sight transmission which can be overcome by multipath transmission in Terahertz Technology, broadcast nature of visible light communications which can be overcome by enhancing secrecy performance by using multiple input multiple output technology, Quantum cloning attacks and quantum collision attacks. The poisoning attacks, evasion attacks, and API-based attacks can affect distributed and scalable AI/ML that can be overcome by adversarial training injects, defensive distillation, etc. Finally, the road map for materializing 6G security visions into a reality is provided.
In the era of Web3, decentralized technologies have emerged as the cornerstone of a new digital paradigm. Backed by a decentralized blockchain architecture, the Web3 space aims to democratize all aspects of the web. From data-sharing to learning models, outsourcing computation is an established, prevalent practice. Verifiable computation makes this practice trustworthy as clients/users can now efficiently validate the integrity of a computation. As verifiable computation gets considered for applications in the Web3 space, decentralization is crucial for system reliability, ensuring that no single entity can suppress clients. At the same time, however, decentralization needs to be balanced with efficiency: clients want their computations done as quickly as possible. Motivated by these issues, we study the trade-off between decentralization and efficiency when outsourcing computational tasks to strategic, rational solution providers. Specifically, we examine this trade-off when the client employs (1) revelation mechanisms, i.e. auctions, where solution providers bid their desired reward for completing the task by a specific deadline and then the client selects which of them will do the task and how much they will be rewarded, and (2) simple, non-revelation mechanisms, where the client commits to the set of rules she will use to map solutions at specific times to rewards and then solution providers decide whether they want to do the task or not. We completely characterize the power and limitations of revelation and non-revelation mechanisms in our model.
Abstract A zero-knowledge proof protocol is a cryptographic protocol in which a prover, who knows the witness to a statement, can convince a verifier that the statement is true without revealing any information about the witness. Although zero-knowledge proof protocols are typically executed on electronic computers, there is a line of research to design zero-knowledge proof protocols based on physical objects (e.g., a deck of cards). This is called physical zero-knowledge proof. In this paper, we construct a physical zero-knowledge proof protocol for a logical puzzle called Sukoro. Sukoro has many cells on the puzzle board, like Sudoku, where each cell must be empty or filled with a number from one to four, and each number must match the number of adjacent filled cells, and the same numbers must not be adjacent to each other. In addition, it has a rule that all filled cells must be connected, which is called the connectivity condition. Although some existing protocols deal with the connectivity condition, all existing methods are interactive , which requires the prover’s knowledge to determine how the cards are manipulated during the execution of the protocols. In this paper, we give a new method for verifying the connectivity condition in the non-interactive setting, which means that the protocol can be executed without the prover’s knowledge, and construct a physical zero-knowledge proof protocol for Sukoro.
Behzad Abdolmaleki, Noemi Glaeser, Sebastian Ramacher, Daniel Slamanig
Non-interactive zero-knowledge proofs (NIZKs) and in particular succinct NIZK arguments of knowledge (zk-SNARKs) increasingly see real-world adoption in large and complex systems. Many zk-SNARKs require a trusted setup, i.e., a common reference string (CRS), and for practical use it is desirable to reduce the trust in the CRS generation. The latter can be achieved via the notions of subversion or updatable CRS. Another important property when deployed in large systems is the ability to securely compose them to obtain more complex protocols, e.g., via the Universal Composability (UC) framework. Relying on the UC framework allows arbitrary and secure composition of protocols in a modular way. In this work, we investigate whether zk-SNARKs can provide updatability and composability simultaneously. This is a challenging task as the UC framework rules out several natural techniques for such a construction. As our main result, we show that it is indeed possible to achieve these properties in a generic and modular way if we relax the succinctness properties of zk-SNARKs slightly to those of a circuit-succinct NIZK which is not witness-succinct, i.e., by increasing the proof size of the underlying zk-SNARK by the size of the witness$w$. We argue that for various practical applications of zk-SNARKs this overhead is acceptable. Our starting point is the Lamassu framework (ACM CCS'20), which we extend in several directions. Our new generic compiler adds only minimal overhead, which we demonstrate by benchmarking its application to the Sonic proof system (ACM CCS'19).
The 15-puzzle is a puzzle game played with 15 square tiles numbered from 1 to 15 on a 4 × 4 board. It has been popular for generations because of its simplicity and challenge. The (w × h)-puzzle is a generalization of the 15-puzzle, which is played with wh − 1 square tiles numbered from 1 to wh − 1 on a w × h board. Solving the (w × h)-puzzle is NP-hard, and hence it is valuable to know its solution. In this paper, we apply the concept of zero-knowledge proof to the (w × h)-puzzle. We propose a physical zero-knowledge proof protocol, in which a prover who knows a solution to the (w × h)-puzzle can convince a verifier that the prover knows the solution without revealing any information about it. We also design physical zero-knowledge proof protocols of two token swapping problems closely related to the (w × h)-puzzle.
Sandro Rodriguez Garzon, Dennis Natusch, Artur Philipp, Axel Küpper · 6 authors
Authentication in TLS is predominately carried out with X.509 digital certificates issued by certificate au-thorities (CA). The centralized nature of current public key infrastructures, however, comes along with severe risks, such as single points of failure and susceptibility to cyber-attacks, potentially undermining the security and trustworthiness of the entire system. With Decentralized Identifiers (DID) alongside distributed ledger technology, it becomes technically feasible to prove ownership of a unique identifier without requiring an attestation of the proof's public key by a centralized and therefore vulnerable CA. This article presents DID Link, a novel authentication scheme for TLS 1.3 that empowers entities to authenticate in a TLS-compliant way with self-issued X.509 certificates that are equipped with ledger-anchored DIDs instead of CA-issued identifiers. It facilitates the exchange of tamper-proof and 3rd-party attested claims in the form of DID-bound Verifiable Credentials after the TLS handshake to complete the authentication with a full identification of the communication partner. A prototypical implementation shows comparable TLS handshake durations of DID Link if verification material is cached and reasonable prolongations if it is obtained from a ledger. The significant speed improvement of the resulting TLS channel over a widely used, DID-based alternative transport protocol on the application layer demonstrates the potential of DID Link to become a viable solution for the establishment of secure and trustful end-to-end communication links with decentrally managed digital identities.
Anne M. Luescher, Andreas L. Gimpel, Wendelin J. Stark, Reinhard Heckel · 5 authors
Abstract Physical unclonable functions (PUFs) based on unique tokens generated by random manufacturing processes have been proposed as an alternative to mathematical one-way algorithms. However, these tokens are not distributable, which is a disadvantage for decentralized applications. Finding unclonable, yet distributable functions would help bridge this gap and expand the applications of object-bound cryptography. Here we show that large random DNA pools with a segmented structure of alternating constant and randomly generated portions are able to calculate distinct outputs from millions of inputs in a specific and reproducible manner, in analogy to physical unclonable functions. Our experimental data with pools comprising up to >10 10 unique sequences and encompassing >750 comparisons of resulting outputs demonstrate that the proposed chemical unclonable function (CUF) system is robust, distributable, and scalable. Based on this proof of concept, CUF-based anti-counterfeiting systems, non-fungible objects and decentralized multi-user authentication are conceivable.
Open access
DNA and Biological Computing
Physical Unclonable Functions (PUFs) and Hardware Security