Related papers: Blind search for complex chemical pathways using H…
Fueled by advances in hardware and algorithm design, large-scale automated explorations of chemical reaction space have become possible. Here, we present our approach to an open-source, extensible framework for explorations of chemical…
Parsing chemical reaction diagrams from scientific literature is challenging due to heterogeneous layouts, intertwined visual elements, and the difficulty of integrating recognition and reasoning. Existing vision-language models advance…
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. Precisely determining the transition pathways in complex and…
Determining the complete set of ligands' binding/unbinding pathways is important for drug discovery and to rationally interpret mutation data. Here we have developed a metadynamics-based technique that addressed this issue and allows…
We report a method to convert discrete representations of molecules to and from a multidimensional continuous representation. This model allows us to generate new molecules for efficient exploration and optimization through open-ended…
Metabolic pathways describe chains of enzymatic reactions. Their modelling is a key point to understand living systems. An enzymatic reaction is an interaction between one or several metabolites (substrates) and an enzyme (simple protein or…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
Reaction prediction, a critical task in synthetic chemistry, is to predict the outcome of a reaction based on given reactants. Generative models like Transformer have typically been employed to predict the reaction product. However, these…
Metadynamics, a member of the `flat histogram' class of advanced sampling algorithms, has been widely used in molecular simulations to drive the exploration of states separated by high free energy barriers and promote comprehensive sampling…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Comprehension of metabolic pathways is considerably enhanced by metabolic flux analysis (MFA-ILE) in isotope labeling experiments. The balance equations are given by hundreds of algebraic (stationary MFA) or ordinary differential equations…
Hamiltonian mechanics is an effective tool to represent many physical processes with concise yet well-generalized mathematical expressions. A well-modeled Hamiltonian makes it easy for researchers to analyze and forecast many related…
Many chemical engineering systems are governed by mechanisms that switch across operating regimes, making the data-driven discovery of regime-dependent governing equations essential for predictive modeling, optimization, and control. We…
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…
Two roads are presently being followed in order to establish the existence of a liquid-gas phase transition in finite nuclear systems from nuclear reactions at high energy. The clean experiment of observing the thermodynamic properties of a…
Reaction networks in the bulk and on surfaces are widespread in physical, chemical and biological systems. In macroscopic systems, which include large populations of reactive species, stochastic fluctuations are negligible and the reaction…
The presence of intermediate confounders, also called recanting witnesses, is a fundamental challenge to the investigation of causal mechanisms in mediation analysis, preventing the identification of natural path-specific effects. Proposed…
All living systems can function only far away from equilibrium, and for this reason chemical kinetic methods are critically important for uncovering the mechanisms of biological processes. Here we present a new theoretical method of…
Biochemical reactions involving three or more reactants, called higher-molecular reactions, play an important role in theoretical systems and synthetic biology. In particular, such reactions underpin a variety of important bio-dynamical…
Studies of chemical reactions by a single pair of atoms in a well defined quantum state constitute a corner stone in quantum chemistry. Yet, the number of demonstrated techniques which enable observation and control of a single chemical…