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Concept# Cylindrical coordinate system

Summary

A cylindrical coordinate system is a three-dimensional coordinate system that specifies point positions by the distance from a chosen reference axis (axis L in the image opposite), the direction from the axis relative to a chosen reference direction (axis A), and the distance from a chosen reference plane perpendicular to the axis (plane containing the purple section). The latter distance is given as a positive or negative number depending on which side of the reference plane faces the point.
The origin of the system is the point where all three coordinates can be given as zero. This is the intersection between the reference plane and the axis.
The axis is variously called the cylindrical or longitudinal axis, to differentiate it from the polar axis, which is the ray that lies in the reference plane, starting at the origin and pointing in the reference direction.
Other directions perpendicular to the longitudinal axis are called radial lines.
The distance from the axis may be called

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Le but du cours de physique générale est de donner à l'étudiant.e les notions de base nécessaires à la compréhension des phénomènes physiques. L'objectif est atteint lorsque l'étudiant.e est capable de prévoir quantitativement les conséquences de ces phénomènes avec des outils théoriques appropriés.

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We present a new method for analyzing ion, or molecule, distributions around helical nucleic acids and illustrate the approach by analyzing data derived from molecular dynamics simulations. The analysis is based on the use of curvilinear helicoidal coordinates and leads to highly localized ion densities compared to those obtained by simply superposing molecular dynamics snapshots in Cartesian space. The results identify highly populated and sequence-dependent regions where ions strongly interact with the nucleic and are coupled to its conformational fluctuations. The data from this approach is presented as ion populations or ion densities (in units of molarity) and can be analyzed in radial, angular and longitudinal coordinates using 1D or 2D graphics. It is also possible to regenerate 3D densities in Cartesian space. This approach makes it easy to understand and compare ion distributions and also allows the calculation of average ion populations in any desired zone surrounding a nucleic acid without requiring references to its constituent atoms. The method is illustrated using microsecond molecular dynamics simulations for two different DNA oligomers in the presence of 0.15 M potassium chloride. We discuss the results in terms of convergence, sequence-specific ion binding and coupling with DNA conformation.

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