arXiv subjects

Yannick Rondelez

Publications and source records attributed to Yannick Rondelez.

7 recordsLinked to original sources

arXiv2026

Synchronized DNA sources for unconditionally secure cryptography

Secure communication is the cornerstone of modern infrastructures, yet achieving unconditional security -resistant to any computational attack- remains a fundamental challenge. The One-Time Pad (OTP), proven by Shannon to offer perfect secrecy, requires a shared random key as long as the message, used only once. However, distributing large keys over long distances has been impractical due to the lack of secure and scalable sharing options. Here, we introduce a DNA-based cryptographic primitive that leverages random pools of synthetic DNA to install a synchronized entropy source between distant parties. Our approach uses duplicated DNA molecules -comprising random index-payload pairs- as a shared secret. These molecules are locally sequenced and digitized to generate a common binary mask for OTP encryption, achieving unconditional security without relying on computational assumptions. We experimentally demonstrate this protocol between Tokyo and Paris, using in-house sequencing, generating a shared secret mask of $\sim$ 400 Mb with a residual error rate to achieve the usual overall decryption failure rate of $2^{-128}$. The min-entropy of the binary mask meets the most recent National Institute of Standards and Technology requirements (SP 800-90B), and is comparable to that of approved cryptographic random number generators. Critically, our system can resist two types of adversarial interference through molecular copy-number statistics, providing an additional layer of security reminiscent of Quantum Key Distribution, but without distance limitations. This work establishes DNA as a scalable entropy source for long-distance OTP, enabling high-throughput and secure communications in sensitive contexts. By bridging molecular biology and cryptography, DNA-based key distribution opens a promising new route toward unconditional security in global communication networks.

cs.CR↗

arXiv2019

Natural selection in compartmentalized environment with reshuffling

The emerging field of high-throughput compartmentalized in vitro evolution is a promising new approach to protein engineering. In these experiments, libraries of mutant genotypes are randomly distributed and expressed in microscopic compartments - droplets of an emulsion. The selection of desirable variants is performed according to the phenotype of each compartment. The random partitioning leads to a fraction of compartments receiving more than one genotype making the whole process a lab implementation of the group selection. From a practical point of view (where efficient selection is typically sought), it is important to know the impact of the increase in the mean occupancy of compartments on the selection efficiency. We carried out a theoretical investigation of this problem in the context of selection dynamics for an infinite non-mutating subdivided population that randomly colonizes an infinite number of patches (compartments) at each reproduction cycle. We derive here an update equation for any distribution of phenotypes and any value of the mean occupancy. Using this result, we demonstrate that, for the linear additive fitness, the best genotype is still selected regardless of the mean occupancy. Furthermore, the selection process is remarkably resilient to the presence of multiple genotypes per compartments, and slows down approximately inversely proportional to the mean occupancy at high values. We extend out results to more general expressions that cover nonadditive and non-linear fitnesses, as well non-Poissonian distribution among compartments. Our conclusions may also apply to natural genetic compartmentalized replicators, such as viruses or early trans-acting RNA replicators.

q-bio.PE↗

arXiv2019

Synthesis and materialization of a reaction-diffusion French flag pattern

During embryo development, patterns of protein concentration appear in response to morphogen gradients. These patterns provide spatial and chemical information that directs the fate of the underlying cells. Here, we emulate this process within non-living matter and demonstrate the autonomous structuration of a synthetic material. Firstly, we use DNA-based reaction networks to synthesize a French flag, an archetypal pattern composed of three chemically-distinct zones with sharp borders whose synthetic analogue has remained elusive. A bistable network within a shallow concentration gradient creates an immobile, sharp and long-lasting concentration front through a reaction-diffusion mechanism. The combination of two bistable circuits generates a French flag pattern whose 'phenotype' can be reprogrammed by network mutation. Secondly, these concentration patterns control the macroscopic organization of DNA-decorated particles, inducing a French flag pattern of colloidal aggregation. This experimental framework could be used to test reaction-diffusion models and fabricate soft materials following an autonomous developmental program.

nlin.PS↗

arXiv2019

Selection strategies for randomly partitioned genetic replicators

The amplification cycle of many replicators (natural or artificial) involves the usage of a host compartment, inside of which the replicator express phenotypic compounds necessary to carry out its genetic replication. For example, viruses infect cells, where they express their own proteins and replicate. In this process, the host cell boundary limits the diffusion of the viral protein products, thereby ensuring that phenotypic compounds, such as proteins, promote the replication of the genes that encoded them. This role of maintaining spatial co-localization, also called genotype-phenotype linkage, is a critical function of compartments in natural selection. In most cases however, individual replicating elements do not distribute systematically among the hosts, but are randomly partitioned. Depending on the replicator-to-host ratio, more than one variant may thus occupy some compartments, blurring the genotype-phenotype linkage and affecting the effectiveness of natural selection. We derive selection equations for a variety of such random multiple occupancy situations, in particular considering the effect of replicator population polymorphism and internal replication dynamics. We conclude that the deleterious effect of random multiple occupancy on selection is relatively benign, and may even completely vanish is some specific cases. In addition, given that higher mean occupancy allows larger populations to be channeled through the selection process, and thus provide a better exploration of phenotypic diversity, we show that it may represent a valid strategy in both natural and technological cases.

q-bio.PE↗

arXiv2018

Quantifying the performance of high-throughput directed evolution protocols

Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at extracting the best variants. We introduce here a new metric named the Selection Quality Index (SQI), which can be computed from a simple mock experiment with a known initial fraction of active variants. As opposed to previous approaches, our index integrates the random co-encapsulation of entities in compartments and comes with a straightforward experimental interpretation. We further show how this new metric can be used to extract general trends of protocol efficiency, or reveal hidden mechanisms such as a counterintuitive form of beneficial poisoning in the Compartmentalized Self-Replication protocol.

q-bio.PE↗

arXiv2015

High-throughput and long-term observation of compartmentalized biochemical oscillators

We report the splitting of an oscillating DNA circuit into $\sim 700$ droplets with picoliter volumes. Upon incubation at constant temperature, the droplets display sustained oscillations that can be observed for more than a day. Superimposed to the bulk behaviour, we find two intriguing new phenomena - slow desynchronization between the compartments and kinematic spatial waves - and investigate their possible origin. This approach provides a route to study the influence of small volume effects in biology, and paves the way to technological applications of compartmentalized molecular programs controlling complex dynamics.

cond-mat.soft↗

arXiv2014

Programmable reaction-diffusion fronts

Morphogenesis is central to biology but remains largely unexplored in chemistry. Reaction-diffusion (RD) mechanisms are, however, essential to understand how shape emerges in the living world. While numerical methods confirm the incredible potential of RD mechanisms to generate patterns, their experimental implementation, despite great efforts, has yet to surpass the paradigm of stationary Turing patterns achieved 25 years ago. The principal reason for our difficulty to synthesize arbitrary concentration patterns from scratch is the lack of fully programmable reaction-diffusion systems. To solve this problem we introduce here a DNA-based system where kinetics and diffusion can be individually tuned. We demonstrate the capability to precisely control reaction-diffusion properties with an autocatalytic network that propagates in a one-dimensional reactor with uniform velocity, typically 100 μm min-1. The diffusion coefficient of the propagating species can be reduced up to a factor 2.7 using a species-specific strategy relying on self-assembled hydrodynamic drags. Our approach is modular as we illustrate by designing three alternative front generating systems, two of which can pass through each other with little interaction. Importantly, the strategies to control kinetics and diffusion are orthogonal to each other resulting in simple programming rules. Our results can be quantitatively predicted from first-principle RD equations and are in excellent agreement with a generalized Fisher- Kolmogorov-Petrovskii-Piscunov analytical model. Together, these advances open the way for the rational engineering of far-from-equilibrium arbitrary patterns and could lead to the synthesis of self-organizing materials.

nlin.PS↗