Related papers: Computing with reaction networks at input-independ…
Classical computations can not capture the essence of infinite computations very well. This paper will focus on a class of infinite computations called convergent infinite computations}. A logic for convergent infinite computations is…
The hardware-friendly implementation of transcendental functions remains a longstanding challenge in design automation. These functions, which cannot be expressed as finite combinations of algebraic operations, pose significant complexity…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
Stochasticity is a key characteristic of intracellular processes such as gene regulation and chemical signalling. Therefore, characterising stochastic effects in biochemical systems is essential to understand the complex dynamics of living…
Chemical Reaction Networks (CRNs) provide a useful abstraction of molecular interaction networks in which molecular structures as well as mass conservation principles are abstracted away to focus on the main dynamical properties of the…
In this paper we study the exponential functionals of the processes $X$ with independent increments , namely $$I_t= \int _0^t\exp(-X_s)ds, _,\,\, t\geq 0,$$ and also $$I_{\infty}= \int _0^{\infty}\exp(-X_s)ds.$$ When $X$ is a…
For many stochastic models of interest in systems biology, such as those describing biochemical reaction networks, exact quantification of parameter uncertainty through statistical inference is intractable. Likelihood-free computational…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
Completing Loo-Keng Hua's approach to the real number system pioneered in 1962, this paper defines arithmetical operations directly on infinite decimals without appealing to any ordering structure. Therefore, the widespread belief that…
One of the crucial generic techniques for quantum computation is amplitude encoding. Although several approaches have been proposed, each of them often requires exponential classical-computational cost or an oracle whose explicit…
The Functional Machine Calculus (Heijltjes 2022) is a new approach to unifying the imperative and functional programming paradigms. It extends the lambda-calculus, preserving the key features of confluent reduction and typed termination, to…
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…
Analog quantum computation is an attractive paradigm for the simulation of time-dependent quantum systems. Programmable analog quantum computers have been realized in hardware using a variety of physical principles, including neutral-atom…
Transcriptional networks represent one of the most extensively studied types of systems in synthetic biology. Although the completeness of transcriptional networks for digital logic is well-established, *analog* computation plays a crucial…
We consider the important problem of estimating parameter sensitivities for stochastic models of reaction networks that describe the dynamics as a continuous-time Markov process over a discrete lattice. These sensitivity values are useful…
Continuous-time Markov chains are used to model stochastic systems where transitions can occur at irregular times, e.g., birth-death processes, chemical reaction networks, population dynamics, and gene regulatory networks. We develop a…
The aim of this work is to make available to the community a large collection of mass-action reaction networks of a given size for further research. The set is limited to what can be computed on a modern multi-core desktop in reasonable…
One-dimensional reaction-diffusion systems are mapped through a similarity transformation onto integrable (and a priori non-stochastic) quantum chains. Time-dependent properties of these chemical models can then be found exactly. The…
We first derive the Hamilton-Jacobi theory underlying continuous-time Markov processes, and then use the construction to develop a variational algorithm for estimating escape (least improbable or first passage) paths for a generic…
It is standard in chemistry to represent a sequence of reactions by a single overall reaction, often called a complex reaction in contrast to an elementary reaction. Photosynthesis $6 \text{CO}_2+6 \text{H}_2\text{O} \to \…