5 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…
Thermodynamic free energy map for the non-oxidative glycolysis pathways
Adittya Pal
Designing reaction pathways that maximize the production of a target compound in a given metabolic network is a fundamental problem in systems biology. In this study, we systematic…
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…
Estimating Reaction Barriers with Deep Reinforcement Learning
Adittya Pal
Stable states in complex systems correspond to local minima on the associated potential energy surface. Transitions between these local minima govern the dynamics of such systems.…