arXiv subjects

Yannick De Decker

Publications and source records attributed to Yannick De Decker.

3 recordsLinked to original sources

arXiv2026

Topological bounds on the dynamical growth rate of chemical reaction networks

Growth and decay are system-level properties of chemical reaction networks (CRNs) relevant from prebiotic chemistry to cellular metabolism. Their properties are typically analyzed through the kinetics of particular models, which requires specification of the full set of kinetic laws and parameters. In this work, assuming a steady balanced-growth regime, we derive stoichiometry-based constraints on the growth (or shrinkage) rate. The resulting bounds are controlled by a topological quantity, the maximum amplification factor, defined via a von Neumann max-min problem over feasible fluxes as illustrated by numerical tests on random-network ensembles of CRNs. We argue for the relevance of our results in the context of origins of life studies and the design of synthetic chemical reaction networks.

q-bio.MN↗

arXiv2019

Stochastic efficiency of thermodiffusion: an extended local equilibrium approach

The recently established connection between stochastic thermodynamics and fluctuating hydrodynamics is applied to a study of efficiencies in the coupled transport of heat and matter on a small scale. A stochastic model for a mesoscopic cell connected to two macroscopic reservoirs of heat and particles is developed, based on fluctuating hydrodynamics. Within this approach, the fluctuating separation and thermodynamic efficiencies are defined. The conditions required to observe bimodal distributions of these efficiencies are determined, and the evolution of these distributions is investigated in the large-size and in the long-time limits. The results obtained are not restricted to thermodiffusion and can be generalized to systems where efficiency is defined as a ratio of stochastic state variables or dissipation rates.

cond-mat.stat-mech↗

arXiv2012

Towards an efficient multiscale modeling of low-dimensional reactive systems: study of numerical closure procedures

In this paper, we present a study on how to develop an efficient multiscale simulation strategy for the dynamics of chemically active systems on low-dimensional supports. Such reactions are encountered in a wide variety of situations, ranging from heterogeneous catalysis to electrochemical or (membrane) biological processes, to cite a few. We analyzed in this context different techniques within the framework of an important multiscale approach known as the equation free method (EFM), which "bridges the multiscale gap" by building microscopic configurations using macroscopic-level information only. We hereby considered two simple reactive processes on a one-dimensional lattice, the simplicity of which allowed for an in-depth understanding of the parameters controlling the efficiency of this approach. We demonstrate in particular that it is not enough to base the EFM on the time evolution of the average concentrations of particles on the lattice, but that the time evolution of clusters of particles has to be included as well. We also show how important it is for the accuracy of this method to carefully choose the procedure with which microscopic states are constructed, starting from the measured macroscopic quantities. As we also demonstrate that some errors cannot be corrected by increasing the number of observed macroscopic variables, this work points towards which procedures should be used in order to generate efficient and reliable multiscale simulations of these systems.

physics.comp-ph↗