The phrase "atoms represented by" is correct and usable in written English.
It can be used in scientific or technical contexts when discussing the representation or modeling of atoms in diagrams, equations, or simulations.
Example: "In the molecular structure diagram, the atoms represented by the blue spheres are oxygen atoms."
Alternatives: "atoms depicted by" or "atoms illustrated by".
Dewar's molecules were built from carbon atoms represented by black discs placed at the centre of pairs of copper bands.
This step consists in transforming the occupancy values of all atoms (represented by their labels) in every group into integer numbers of atoms distributed among all allowed positions in the group (Fig. 1e).
where v Iz is the z component of the velocity of particle I, and N is the number of atoms represented by particle I in the mesh-free particle model.
The activation energy as a function of composition can be linked to the bonding strength between the fastest diffusor, Cu, and its coordinating atoms, represented by the ratio of strong Cu Zr to weaker Cu Cu bonds.
In the case of dealkylation reactions, we considered the alkyl group as the fragment that is removed from the reacting atom represented by oxygen or by nitrogen.
2. Representation of interfacial atoms by un-directional graph; atoms are represented by labeled nodes, and distances connecting them are represented by labeled edges.
Ligand atoms were represented by the most similar Rosetta atom type, their coordinates were re-centered to the origin, and their partial charges were assigned by OpenEye's AM1-BCC implementation.
In these coarse-grained models, groups of approximately four atoms are represented by a single particle.
This model also known as CPK one, is a type of three-dimensional molecular model where the atoms are represented by spheres whose radii are proportional to the radii of the atoms and whose center-to-center distances are proportional to the ones between the atomic nuclei, all in the same scale.
The supercell program implementation assumes that atoms types (represented by different colors in Fig. 1) are separated into different atom labels obtained from the input cif file.
The other C and H atoms are represented by the smallest circles.
