Related papers: ChemSICal: Evaluating a Stochastic Chemical Reacti…
Optical chemical structure recognition (OCSR) systems aim to extract the molecular structure information, usually in the form of molecular graph or SMILES, from images of chemical molecules. While many tools have been developed for this…
This paper studies the problem of receiver modeling in molecular communication systems. We consider the diffusive molecular communication channel between a transmitter nano-machine and a receiver nano-machine in a fluid environment. The…
In this work we introduce some preliminary analyses on the role of a semi-permeable membrane in the dynamics of a stochastic model of catalytic reaction sets (CRSs) of molecules. The results of the simulations performed on ensembles of…
This paper presents new results about the optimization based generation of chemical reaction networks (CRNs) of higher deficiency. Firstly, it is shown that the graph structure of the realization containing the maximal number of reactions…
We investigate a class of stochastic chemical reaction networks with $n{\ge}1$ chemical species $S_1$, \ldots, $S_n$, and whose complexes are only of the form $k_iS_i$, $i{=}1$,\ldots, $n$, where $(k_i)$ are integers. The time evolution of…
Molecular computation in chemical reaction networks (CRNs) now constitutes a foundational framework for designing programmable biological systems. However, prevailing design methodologies primarily treat parallelism of chemical reactions as…
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations…
The study of the dynamics of chemical reactions, and in particular phenomena such as oscillating reactions, has led to the recognition that many dynamical properties of a chemical reaction can be predicted from graph theoretical properties…
Molecular Communication (MC) leverages the power of diffusion to transmit molecules from a transmitter to a receiver. A wide variety of modulation techniques based on molecule concentration, type, and release time have been extensively…
A family of results, referred to as inheritance results, tell us which enlargements of a chemical reaction network (CRN) preserve its capacity for nontrivial behaviours such as multistationarity and oscillation. In this paper, the following…
Chemical reaction networks, or CRNs, are known to stably compute semilinear Boolean-valued predicates and functions, provided that all reactions are irreversible. However, this property does not hold for wet-lab implementations, as all…
Inspired by Anderson et al. [J. R. Soc. Interface, 2014] we study the long-term behavior of discrete chemical reaction networks (CRNs). In particular, using techniques from both Petri net theory and CRN theory, we provide a powerful…
Background: Stochastic biochemical reaction networks are commonly modelled by the chemical master equation, and can be simulated as first order linear differential equations through a finite state projection. Due to the very high state…
Molecular communication (MC) is a concept in communication engineering, where diffusive molecules are used to transmit information between nano or micro-scale chemical reaction systems. Engineering MC to control the reaction systems in…
This paper considers a diffusion-based molecular communication system where the transmitter uses Reaction Shift Keying (RSK) as the modulation scheme. We focus on the demodulation of RSK signal at the receiver. The receiver consists of a…
Stochastic models for chemical reaction networks have become very popular in recent years. For such models, the estimation of parameter sensitivities is an important and challenging problem. Sensitivity values help in analyzing the network,…
We address a fundamental question: under which conditions do the dynamics and thermodynamics of open chemical reaction networks (CRNs), grounded on the notion of idealized chemostats that exchange selected species, emerge from underlying…
The thesis is dedicated to studying methods to improve the efficiency of random access schemes and to facilitate their deployment in machine-type communications (MTC). First, a joint user activity identification and channel estimation…
To support mechanism online learning and facilitate digital twin development for biomanufacturing processes, this paper develops an efficient Bayesian inference approach for partially observed enzymatic stochastic reaction network (SRN), a…
Molecular Communication via Diffusion (MCvD) is a prominent small-scale technology, which roots from the nature. With solid analytical foundations on channel response and advanced modulation techniques, molecular single-input-single-output…