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Vladimir Y. Lunin

Publications and source records attributed to Vladimir Y. Lunin.

2 recordsLinked to original sources

Gaussian-convolution-invariant shell approximation to spherically-symmetric functions

We develop a class of functions Omega_N(x; mu, nu) in N-dimensional space concentrated around a spherical shell of the radius mu and such that, being convoluted with an isotropic Gaussian function, these functions do not change their expression but only a value of its 'width' parameter, nu. Isotropic Gaussian functions are a particular case of Omega_N(x; mu, nu) corresponding to mu = 0. Due to their features, these functions are an efficient tool to build approximations to smooth and continuous spherically-symmetric functions including oscillating ones. Atomic images in limited-resolution maps of the electron density, electrostatic scattering potential and other scalar fields studied in physics, chemistry, biology, and other natural sciences are examples of such functions. We give simple analytic expressions of Omega_N(x; mu, nu) for N = 1, 2, 3 and analyze properties of these functions. Representation of oscillating functions by a sum of Omega_N(x; mu, nu) allows calculating distorted maps for the same cost as the respective theoretical fields. We give practical examples of such representation for the interference functions of the uniform unit spheres for N = 1, 2, 3 that define the resolution of the respective images. Using the chain rule and analytic expressions of the Omega_N(x; mu, nu) derivatives makes simple refinement of parameters of the models which describe these fields.

math.NA↗

Programs and algorithms for the shell decomposition of oscillating functions in space

Real-space refinement of atomic models in macromolecular crystallography or in cryo electron microscopy fits a model to a map obtained experimentally. This requires generating model maps of a limited resolution which moreover may vary from one molecular region to another. Calculating such map as a sum of atomic contributions requires that these contributions reflect the local resolution of the experimental map. A possibility to refine the parameters of these contribution means to express it as a function of atomic coordinates, displacement factor and eventually of resolution. Recently, Urzhumtsev & Lunin (BioRxiv, 10.1101/2022.03.28.486044) suggested to decompose finite-resolution atomic images, and more generally spherically symmetric oscillating functions in space, into a sum of specially designed terms analytically dependent on all atomic parameters. Each term is a spherically symmetric function concentrated in a spherical shell. Here we describe the software and respective algorithms to carry out such shell decomposition of oscillating functions.

cs.CE↗