3 papers
q-bio.QM2025
A Sensitivity Analysis Methodology for Rule-Based Stochastic Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +1
In this study, we introduce a sensitivity analysis methodology for stochastic systems in chemistry, where dynamics are often governed by random processes. Our approach is based on…
cs.CE2025
ChemReservoir -- An Open-Source Framework for Chemically-Inspired Reservoir Computing
Mehmet Aziz Yirik, Jakob Lykke Andersen, Rolf Fagerberg +1
Reservoir computing is a type of a recurrent neural network, mapping the inputs into higher dimensional space using fixed and nonlinear dynamical systems, called reservoirs. In the…
q-bio.MN2024
Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +3
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 rea…