arXiv subjects

Chunhai Fan

Publications and source records attributed to Chunhai Fan.

6 recordsLinked to original sources

arXiv2026

Noise-immune and AI-enhanced DNA storage via adaptive partition mapping of digital data

Encoding digital information into DNA sequences offers an attractive potential solution for storing rapidly growing data under the information age and the rise of artificial intelligence. However, practical implementations of DNA storage are constrained by errors introduced during synthesis, preservation, and sequencing processes, and traditional error-correcting codes remain vulnerable to noise levels that exceed predefined thresholds. Here, we developed a Partitioning-mapping with Jump-rotating (PJ) encoding scheme, which exhibits exceptional noise resilience. PJ removes cross-strand information dependencies so that strand loss manifests as localized gaps rather than catastrophic file failure. It prioritizes file decodability under arbitrary noise conditions and leverages AI-based inference to enable controllable recovery of digital information. For the intra-strand encoding, we develop a jump-rotating strategy that relaxes sequence constraints relative to conventional rotating codes and provides tunable information density via an adjustable jump length. Based on this encoding architecture, the original file information can always be decoded and recovered under any strand loss ratio, with fidelity degrading smoothly as damage increases. We demonstrate that original files can be effectively recovered even with 10% strand loss, and machine learning datasets stored under these conditions retain their classification performance. Experiments further confirmed that PJ successfully decodes image files after extreme environmental disturbance using accelerated aging and high-intensity X-ray irradiation. By eliminating reliance on prior error probabilities, PJ establishes a general framework for robust, archival DNA storage capable of withstanding the rigorous conditions of real-world preservation.

cs.IT↗

arXiv2025

An AI-native experimental laboratory for autonomous biomolecular engineering

Autonomous scientific research, capable of independently conducting complex experiments and serving non-specialists, represents a long-held aspiration. Achieving it requires a fundamental paradigm shift driven by artificial intelligence (AI). While autonomous experimental systems are emerging, they remain confined to areas featuring singular objectives and well-defined, simple experimental workflows, such as chemical synthesis and catalysis. We present an AI-native autonomous laboratory, targeting highly complex scientific experiments for applications like autonomous biomolecular engineering. This system autonomously manages instrumentation, formulates experiment-specific procedures and optimization heuristics, and concurrently serves multiple user requests. Founded on a co-design philosophy of models, experiments, and instruments, the platform supports the co-evolution of AI models and the automation system. This establishes an end-to-end, multi-user autonomous laboratory that handles complex, multi-objective experiments across diverse instrumentation. Our autonomous laboratory supports fundamental nucleic acid functions-including synthesis, transcription, amplification, and sequencing. It also enables applications in fields such as disease diagnostics, drug development, and information storage. Without human intervention, it autonomously optimizes experimental performance to match state-of-the-art results achieved by human scientists. In multi-user scenarios, the platform significantly improves instrument utilization and experimental efficiency. This platform paves the way for advanced biomaterials research to overcome dependencies on experts and resource barriers, establishing a blueprint for science-as-a-service at scale.

cs.AI↗

arXiv2024

Multi-Convergence-Angle Ptychography with Simultaneous Strong Contrast and High Resolution

Advances in bioimaging methods and hardware facilities have revolutionised the determination of numerous biological structures at atomic or near-atomic resolution. Among these developments, electron ptychography has recently attracted considerable attention because of its superior resolution, remarkable sensitivity to light elements, and high electron dose efficiency. Here, we introduce an innovative approach called multi-convergence-angle (MCA) ptychography, which can simultaneously enhance both contrast and resolution with continuous information transfer across a wide spectrum of spatial frequency. Our work provides feasibility of future applications of MCA-ptychography in providing high-quality two-dimensional images as input to three-dimensional reconstruction methods, thereby facilitating more accurate determination of biological structures.

physics.optics↗

arXiv2023

Molecular tuning of DNA framework-programmed silicification by cationic silica cluster attachment

The organizational complexity of biominerals has long fascinated scientists seeking to understand biological programming and implement new developments in biomimetic materials chemistry. Nonclassical crystallization pathways have been observed and analyzed in typical crystalline biominerals, involving the controlled attachment and reconfiguration of nanoparticles and clusters on organic templates. However, the understanding of templated amorphous silica mineralization remains limited, hindering the rational design of complex silica-based materials. Here, we present a systematic study on the stabilization of self-capping cationic silica cluster (CSC) and their assembly dynamics using DNA nanostructures as programmable attachment templates. By tuning the composition and structure of CSC, we demonstrate high-fidelity silicification at single-cluster resolution, revealing a process of adaptive templating involving cooperative adjustments of both the DNA framework and cluster morphology. Our results provide a unified model of silicification by cluster attachment and pave the way towards the molecular tuning of pre- and post-nucleation stages of sol-gel reactions. Overall, our findings provide new insights for the design of silica-based materials with controlled organization and functionality, bridging the gap between biomineralization principles and the rational design of biomimetic material.

physics.chem-ph↗

arXiv2023

Twisted DNA origami-based chiral monolayers for spin filtering

DNA monolayers with inherent chirality play a pivotal role across various domains, including biosensors, DNA chips, and bioelectronics. Nonetheless, conventional DNA chiral monolayers, typically constructed from single-stranded DNA (ssDNA) or double-stranded DNA (dsDNA), often lack structural orderliness and design flexibility at the interface. Structural DNA nanotechnology emerges as a promising solution to tackle these challenges. In this study, we present a strategy for crafting highly adaptable twisted DNA origami-based chiral monolayers. These structures exhibit distinct interfacial assembly characteristics and effectively mitigate the structural disorder of dsDNA monolayers, which is constrained by a limited persistence length of ~50 nm of dsDNA. We highlight the spin-filtering capabilities of four representative DNA origami-based chiral monolayers, demonstrating a maximal one-order-of-magnitude increase in spin-filtering efficiency per unit area compared to conventional dsDNA chiral monolayers. Intriguingly, our findings reveal that the higher-order, tertiary, chiral structure of twisted DNA origami further enhances the spin-filtering efficiency. This work paves the way for the rational design of DNA chiral monolayers.

physics.chem-ph↗

arXiv2021

DNA origami

Biological materials are self-assembled with near-atomic precision in living cells, whereas synthetic 3D structures generally lack such precision and controllability. Recently, DNA nanotechnology, especially DNA origami technology, has been useful in the bottom-up fabrication of well-defined nanostructures ranging from tens of nanometres to sub-micrometres. In this Primer, we summarize the methodologies of DNA origami technology, including origami design, synthesis, functionalization and characterization. We highlight applications of origami structures in nanofabrication, nanophotonics and nanoelectronics, catalysis, computation, molecular machines, bioimaging, drug delivery and biophysics. We identify challenges for the field, including size limits, stability issues and the scale of production, and discuss their possible solutions. We further provide an outlook on next-generation DNA origami techniques that will allow in vivo synthesis and multiscale manufacturing.

physics.bio-ph↗