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Reliably predicting the products of chemical reactions presents a fundamental challenge in synthetic chemistry. Existing machine learning approaches typically produce a reaction product by sequentially forming its subparts or intermediate…
Understanding the mechanisms underlying crystal formation is crucial. For most systems, crystallization typically goes through a nucleation process that involves dynamics that happen at short time and length scales. Due to this, molecular…
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…
Graph-based reaction systems were recently introduced as a generalization of the intensely studied set-based reaction systems. They deal with simple edge-labeled directed graphs, and dynamic semantics of graph-based reaction systems is…
Designing molecular structures with desired chemical properties is an essential task in drug discovery and material design. However, finding molecules with the optimized desired properties is still a challenging task due to combinatorial…
The analysis of the structure of chemical reaction networks is crucial for a better understanding of chemical processes. Such networks are well described as hypergraphs. However, due to the available methods, analyses regarding network…
We propose a new and general formalism for elementary chemical reactions where quantum electronic variables are used as reaction coordinates. This formalism is in principle applicable to all kinds of chemical reactions ionic or covalent.…
Chemical reactions involving diffusion of reactants and subsequent chemical fixation steps are generally termed "diffusion-influenced" (DI). Virtually all biochemical processes in living media can be counted among them, together with those…
We study chemical reaction between a single hydrogen atom and a graphene, which is the elemental reaction between hydrogen and graphitic carbon materials. In the present work, classical molecular dynamics simulation is used with modified…
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 reaction networks are mathematically well represented as…
In living cells, chemical reactions form a complex network. Complicated dynamics arising from such networks are the origins of biological functions. We propose a novel mathematical method to analyze bifurcation behaviors of a reaction…
Most elemental metals under ambient conditions adopt simple structures such as BCC, FCC and HCP in specific groupings across the Periodic Table, and on compression, many of these elements undergo transitions to surprisingly complex…
To clarify the yielding mechanism of small hydrocarbon molecules in chemical sputtering between hydrogen and graphene sheets, we made classical molecular dynamics simulation with modified Brenner's REBO potential which we proposed to deal…
We introduce the concept of hypergraphs to describe quantum optical experiments with probabilistic multi-photon sources. Every hyperedge represents a correlated photon source, and every vertex stands for an optical output path. Such general…
We study the energetics of chemical reactions between ultracold ground-state alkaline-earth-metal diatomic molecules. We show that the atom-exchange reactions forming homonuclear dimers are energetically allowed for all heteronuclear…
Aspects of cell metabolism are modeled by ordinary differential equations describing the change of intracellular chemical concentrations. There is a correspondence between this dynamical system and a complex network. As in the classic…
In this paper we discuss the question of how to decide when a general chemical reaction system is incapable of admitting multiple equilibria, regardless of parameter values such as reaction rate constants, and regardless of the type of…
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…
Motivated by a revision of the classical equations of electromagnetism that allow for the inclusion of solitary waves in the solution space, the material collected in these notes examines the consequences of adopting the modified model in…
Inspired by decomposition problems in rule-based formalisms in Computational Systems Biology and recent work on compositionality in graph transformation, this paper proposes to use arbitrary colimits to "deconstruct" models of reactions in…