Related papers: Automated Discovery of Elementary Chemical Reactio…

We have developed an end-to-end, retrosynthesis system, named ChemiRise, that can propose complete retrosynthesis routes for organic compounds rapidly and reliably. The system was trained on a processed patent database of over 3 million…

We present a novel multiscale simulation approach for modeling stochasticity in chemical reaction networks. The approach seamlessly integrates exact-stochastic and "leaping" methodologies into a single "partitioned leaping" algorithmic…

Understanding the set of elementary steps and kinetics in each reaction is extremely valuable to make informed decisions about creating the next generation of catalytic materials. With physical and mechanistic complexity of industrial…

We employ an evolutionary algorithm to automatically optimize different stages of a cold atom experiment without human intervention. This approach closes the loop between computer based experimental control systems and automatic real time…

Popular methods for identifying transition paths between energy minima, such as the nudged elastic band and string methods, typically do not incorporate potential energy curvature information, leading to slow relaxation to the minimum…

Process discovery aims to learn a process model from observed process behavior. From a user's perspective, most discovery algorithms work like a black box. Besides parameter tuning, there is no interaction between the user and the…

Low-temperature plasmas are partially ionized gases, where ions and neutrals coexist in a highly reactive environment. This creates a rich chemistry, which is often difficult to understand in its full complexity. In this work, we develop a…

The efficiency of atomic simulations of materials and molecules can rapidly deteriorate when large free energy barriers exist between local minima. We propose smooth basin classification, a universal method to define reaction coordinates…

We investigate catalysis in the framework of elementary thermal operations, leveraging the distinct features of such operations to illuminate catalytic dynamics. As groundwork, we establish new technical tools that enhance the computability…

Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction. Changing the energy barrier along the reaction pathway allows one to modulate the performance of a…

Reaction systems are a formal model that has been introduced to investigate the interactive behaviors of biochemical reactions. Based on the formal framework of reaction systems, we propose new computing models called reaction automata that…

Analyzing the physical and chemical properties of single DNA based molecular machines such as polymerases and helicases often necessitates to track stepping motion on the length scale of base pairs. Although high resolution instruments have…

We introduce, analyze, and implement a new method for parameter identification for system of ordinary differential equations that are used to model sets of biochemical reactions. Our method relies on the integral formulation of the ODE…

An algorithm is given in this paper for the computation of dynamically equivalent weakly reversible realizations with the maximal number of reactions, for chemical reaction networks (CRNs) with mass action kinetics. The original problem…

The aim of this article is to determine the dynamic response of the railway system composed of train, track and bridge, suggesting a method for assembling the elementary matrices to obtain differential equations of the overall system. The…

The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…

We propose a low-computational strategy for the efficient implementation of the "atom selection step" in sparse representation algorithms. The proposed procedure is based on simple tests enabling to identify subsets of atoms which cannot be…

Interpretable reaction coordinates are essential for understanding rare conformational transitions in molecular dynamics. The Atomistic Mechanism Of Rare Events in Molecular Dynamics (AMORE-MD) framework enhances interpretability of…

Process mining discovers and analyzes a process model from historical event logs. The prior art methods use the key attributes of case-id, activity, and timestamp hidden in an event log as clues to discover a process model. However, a user…

The prediction of organic reaction outcomes is a fundamental problem in computational chemistry. Since a reaction may involve hundreds of atoms, fully exploring the space of possible transformations is intractable. The current solution…