8 papers
A Collision-based strategy for Network-free Exploration of Complex Molecular Networks
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
This work presents a stochastic exploration framework for large, implicitly defined chemical reaction spaces that are too large to be generated and stored as explicit molecular net…
Finding Pathways in Reaction Networks guided by Energy Barriers using Integer Linear Programming
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen +2
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This…
ChemRecon: a Consolidated Meta-Database Platform for Biochemical Data Integration
Casper Asbjørn Eriksen, Jakob Lykke Andersen, Rolf Fagerberg +1
In this paper, we present ChemRecon, a meta-database and Python interface for integrating and exploring biochemical data across multiple heterogeneous resources by consolidating co…
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…
Rule-Based Gillespie Simulation of Chemical Systems
Erika M. Herrera Machado, Jakob L. Andersen, Rolf Fagerberg +3
The MÃD computational framework implements rule-based generative chemistries as explicit transformations of graphs representing chemical structural formulae. Here, we expand MÃD…
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…