Related papers: Optimal Information Encoding in Chemical Reaction …
Finding optimal pathways in chemical reaction networks is essential for elucidating and designing chemical processes, with significant applications such as synthesis planning and metabolic pathway analysis. Such a chemical pathway-finding…
We investigate the dynamics of chemical reaction networks (CRNs) with the goal of deriving an upper bound on their reaction rates. This task is challenging due to the nonlinear nature and discrete structure inherent in CRNs. To address…
The search for pathways that optimize the formation of a particular target molecule in a reaction network is a key problem in many settings, including reactor systems. Chemical reaction networks are mathematically well represented as…
Recent progress in machine learning has sparked increased interest in utilizing this technology to predict the outcomes of chemical reactions. The ultimate aim of such endeavors is to develop a universal model that can predict products for…
Motivation: Stochastic reaction networks are a widespread model to describe biological systems where the presence of noise is relevant, such as in cell regulatory processes. Unfortu-nately, in all but simplest models the resulting discrete…
In this paper, it is presented a methodology for implementing arbitrarily constructed time-homogenous Markov chains with biochemical systems. Not only discrete but also continuous-time Markov chains are allowed to be computed. By employing…
We study coding schemes for error correction in interactive communications. Such interactive coding schemes simulate any $n$-round interactive protocol using $N$ rounds over an adversarial channel that corrupts up to $\rho N$ transmissions.…
We explore the range of probabilistic behaviours that can be engineered with Chemical Reaction Networks (CRNs). We show that at steady state CRNs are able to "program" any distribution with finite support in $\mathbb{N}^m$, with $m \geq 1$.…
We study the problem of decoding classical information encoded on quantum states at the output of a quantum channel, with particular focus on increasing the communication rates towards the maximum allowed by Quantum Mechanics. After a brief…
We consider experimentally feasible chains of trapped ions with pseudo-spin 1/2, and find models that can potentially be used to implement error-resistant quantum computation. Similar in spirit to classical neural networks, the…
In molecular communications, the direct detection of signaling molecules may be challenging due to a lack of suitable sensors and interference in the environment. Motivated by research in molecular biology, we investigate an indirect…
We consider how to generate chemical reaction networks (CRNs) from functional specifications. We propose a two-stage approach that combines synthesis by satisfiability modulo theories and Markov chain Monte Carlo based optimisation. First,…
Consider a joint quantum state of a system and its environment. A measurement on the environment induces a decomposition of the system state. Using algorithmic information theory, we define the preparation information of a pure or mixed…
We consider coding schemes for computationally bounded channels, which can introduce an arbitrary set of errors as long as (a) the fraction of errors is bounded with high probability by a parameter $p$ and (b) the process which adds the…
In a molecular communication network, transmitters may encode information in concentration or frequency of signalling molecules. When the signalling molecules reach the receivers, they react, via a set of chemical reactions or a molecular…
We propose a measure based upon the fundamental theoretical concept in algorithmic information theory that provides a natural approach to the problem of evaluating $n$-dimensional complexity by using an $n$-dimensional deterministic Turing…
Chemical reaction networks (CRNs) are a standard formalism used in chemistry and biology to reason about the dynamics of molecular interaction networks. In their interpretation by ordinary differential equations, CRNs provide a…
Reversibility, weak reversibility and deficiency, detailed and complex balancing are generally not "encoded" in the kinetic differential equations but they are realization properties that may imply local or even global asymptotic stability…
The Kolmogorov complexity of x, denoted C(x), is the length of the shortest program that generates x. For such a simple definition, Kolmogorov complexity has a rich and deep theory, as well as applications to a wide variety of topics…
The construction of a reaction network containing all relevant intermediates and elementary reactions is necessary for the accurate description of chemical processes. In the case of a complex chemical reaction (involving, for instance, many…