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The Energies of Atomic Orbitals

The Energies of Atomic Orbitals

In an atom, the negatively charged electrons are attracted to the positively charged nucleus. In a multielectron atom, electron-electron repulsions are also observed. The attractive and repulsive forces are dependent on the distance between the particles, as well as the sign and magnitude of the charges on the individual particles. When the charges on the particles are opposite, they attract each other. If both particles have the same charge, they repel each other.

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Atomic Mass

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Atoms — and the protons, neutrons, and electrons that compose them — are extremely small. For example, a carbon atom weighs less than 2 × 10−23 g. When describing the properties of tiny objects such as atoms, we use appropriately small units of measure, such as the atomic mass unit (amu). The amu was originally defined based on hydrogen, the lightest element, then later in terms of oxygen. Since 1961, it has been defined with regard to the most abundant isotope of carbon, atoms of which...

Atomic Orbitals

Atomic Orbitals

An atomic orbital represents the three-dimensional regions in an atom where an electron has the highest probability to reside. The radial distribution function indicates the total probability of finding an electron within the thin shell at a distance r from the nucleus. The atomic orbitals have distinct shapes which are determined by l, the angular momentum quantum number. The orbitals are often drawn with a boundary surface, enclosing densest regions of the cloud.

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The mathematical expression known as the wave function, ψ, contains information about each orbital and the wavelike properties of electrons in an isolated atom. When atoms are bound together in a molecule, the wave functions combine to produce new mathematical descriptions that have different shapes. This process of combining the wave functions for atomic orbitals is called hybridization and is mathematically accomplished by the linear combination of atomic orbitals. The new orbitals that...

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Cálculo de reglas de transformación de grafos de doble pushout y mapas átomo-a-átomo a partir de datos KEGG RCLASS

Nora Beier¹, Thomas Gatter¹, Jakob L Andersen²

¹Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, Universität Leipzig, Härtelstraße 16-18, D-04107, Leipzig, Germany.

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|January 30, 2026

Resumen

Este resumen es generado por máquina.

El nuevo software laveau genera reglas DPO explícitas y mapas átomo-a-átomo a partir de datos KEGG RCLASS, lo que permite modelos detallados a nivel atómico de redes metabólicas.

Palabras clave:

Mapeo átomo-a-átomo Reglas de doble pushout Reconstrucción de grafos Transformación de grafos KEGG Reacciones metabólicas RCLASS Reglas de reacción

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Área de la Ciencia:

Bioinformática
Química Computacional
Biología de Sistemas

Sus antecedentes:

Los mapas átomo-a-átomo son cruciales para muchas aplicaciones, pero difíciles de obtener.
La base de datos de reacciones KEGG utiliza RCLASSes, no mapas átomo-a-átomo directos, lo que dificulta la construcción de reglas.
Las reglas de transformación de grafos DPO ofrecen una representación eficiente para el mapeo a nivel atómico.

Objetivo del estudio:

Desarrollar un método para convertir datos KEGG RCLASS en reglas DPO.
Permitir la generación de mapas átomo-a-átomo explícitos a partir de datos de reacción KEGG existentes.

Principales métodos:

Se desarrolló 'laveau', una herramienta para calcular reglas DPO a partir de reacciones KEGG y datos RCLASS.
El algoritmo traduce códigos RDM a grafos de patrones RDM, los fusiona según incrustaciones y forma subgrafos de reactivos/productos.
Los mapas átomo-a-átomo se derivan de códigos RDM para definir reglas de transformación DPO.

Principales resultados:

laveau generó con éxito 1232 reglas DPO y 1594 mapas átomo-a-átomo a partir de 3195 RCLASSes.
Las reglas DPO generadas aplicadas a los reactivos producen mapas átomo-a-átomo completos.
La herramienta reconstruye eficazmente los detalles a nivel atómico a partir de datos RCLASS.

Conclusiones:

El software laveau extrae mapas átomo-a-átomo locales de KEGG RCLASSes para reacciones catalizadas por enzimas.
Proporciona reglas DPO para modelos de redes metabólicas a nivel atómico, abordando una brecha de datos.
Facilita el análisis detallado de transformaciones bioquímicas a nivel atómico.