Related papers: Optimal Information Encoding in Chemical Reaction …
A key concept of quantum information theory is that accessing information encoded in a quantum system requires us to discriminate between several possible states the system could be in. A natural generalization of this problem, namely,…
Chemical reaction network is an important method for modeling and exploring complex biological processes, bio-chemical interactions and the behavior of different dynamics in system biology. But, formulating such reaction kinetics takes…
For a broad class of input-output maps, arguments based on the coding theorem from algorithmic information theory (AIT) predict that simple (low Kolmogorov complexity) outputs are exponentially more likely to occur upon uniform random…
In this paper we give a definition for quantum Kolmogorov complexity. In the classical setting, the Kolmogorov complexity of a string is the length of the shortest program that can produce this string as its output. It is a measure of the…
We introduce a validity-filtered, certificate-based view of reactions grounded in Algorithmic Information Theory. A fixed, total, input-blind executor maps a self-delimiting advice string to a candidate response, accepted only if a…
We introduce a mixed-integer linear programming (MILP) framework capable of determining whether a chemical reaction network possesses the property of being endotactic or strongly endotactic. The network property of being strongly endotactic…
Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance.…
Recent work of M.D. Johnston et al. has produced sufficient conditions on the structure of a chemical reaction network which guarantee that the corresponding discrete state space system exhibits an extinction event. The conditions consist…
Chemical reactions occur in energy, environmental, biological, and many other natural systems, and the inference of the reaction networks is essential to understand and design the chemical processes in engineering and life sciences. Yet,…
This work considers the method of uniformisation for continuous-time Markov chains in the context of chemical reaction networks. Previous work in the literature has shown that uniformisation can be beneficial in the context of…
Efficient entanglement distribution is the foundational challenge in realizing large-scale Quantum Networks. However, state-of-the-art solutions are frequently limited by restrictive operational assumptions, prohibitive computational…
Molecular codes translate information written in one type of molecules into another molecular language. We introduce a simple model that treats molecular codes as noisy information channels. An optimal code is a channel that conveys…
Recent developments in computational chemistry facilitate the automated quantum chemical exploration of chemical reaction networks for the in-silico prediction of synthesis pathways, yield, and selectivity. However, the underlying quantum…
We construct a new reduced nuclear reaction network able to reproduce the energy production due to the photo-disintegration of heavy elements such as Ru, which are believed to occur during superbursts in mixed H/He accreting systems. We use…
Regenerating codes allow distributed storage systems to recover from the loss of a storage node while transmitting the minimum possible amount of data across the network. We present a systematic computer search for optimal systematic…
We develop numerical and analytical approaches to calculate mutual information between complete paths of two molecular components embedded into a larger reaction network. In particular, we focus on a continuous-time Markov chain formalism,…
Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
We study the amount of reliable information that can be stored in a DNA-based storage system with noisy sequencing, where each codeword is composed of short DNA molecules. We analyze a concatenated coding scheme, where the outer code is…
Chemical reaction network theory is a powerful framework to describe and analyze chemical systems. While much about the concentration profile in an equilibrium state can be determined in terms of the graph structure, the overall reaction's…