Patterson function

Last updated

The Patterson function is used to solve the phase problem in X-ray crystallography. It was introduced in 1935 by Arthur Lindo Patterson while he was a visiting researcher in the laboratory of Bertram Eugene Warren at MIT. [1] [2]

Contents

The Patterson function is defined as

It is essentially the Fourier transform of the intensities rather than the structure factors. The Patterson function is also equivalent to the electron density convolved with its inverse:

Furthermore, a Patterson map of N points will have N(N − 1) peaks, excluding the central (origin) peak and any overlap.

The peaks' positions in the Patterson function are the interatomic distance vectors and the peak heights are proportional to the product of the number of electrons in the atoms concerned.

Because for each vector between atoms i and j there is an oppositely oriented vector of the same length (between atoms j and i), the Patterson function always has centrosymmetry.

One-dimensional example

Consider the series of delta functions given by

The Patterson function is given by the following series of delta functions and unit step functions

Related Research Articles

<span class="mw-page-title-main">Pauli matrices</span> Matrices important in quantum mechanics and the study of spin

In mathematical physics and mathematics, the Pauli matrices are a set of three 2 × 2 complex matrices which are Hermitian, involutory and unitary. Usually indicated by the Greek letter sigma, they are occasionally denoted by tau when used in connection with isospin symmetries.

<span class="mw-page-title-main">Schrödinger equation</span> Description of a quantum-mechanical system

The Schrödinger equation is a linear partial differential equation that governs the wave function of a quantum-mechanical system. Its discovery was a significant landmark in the development of quantum mechanics. The equation is named after Erwin Schrödinger, who postulated the equation in 1925 and published it in 1926, forming the basis for the work that resulted in his Nobel Prize in Physics in 1933.

<span class="mw-page-title-main">Green's function</span> Impulse response of an inhomogeneous linear differential operator

In mathematics, a Green's function is the impulse response of an inhomogeneous linear differential operator defined on a domain with specified initial conditions or boundary conditions.

In mathematics, a Casimir element is a distinguished element of the center of the universal enveloping algebra of a Lie algebra. A prototypical example is the squared angular momentum operator, which is a Casimir element of the three-dimensional rotation group.

<span class="mw-page-title-main">Reciprocal lattice</span> Fourier transform of a real-space lattice, important in solid-state physics

In physics, the reciprocal lattice represents the Fourier transform of another lattice. The direct lattice or real lattice is a periodic function in physical space, such as a crystal system. The reciprocal lattice exists in the mathematical space of spatial frequencies, known as reciprocal space or k space, where refers to the wavevector.

In theoretical physics, the Batalin–Vilkovisky (BV) formalism was developed as a method for determining the ghost structure for Lagrangian gauge theories, such as gravity and supergravity, whose corresponding Hamiltonian formulation has constraints not related to a Lie algebra. The BV formalism, based on an action that contains both fields and "antifields", can be thought of as a vast generalization of the original BRST formalism for pure Yang–Mills theory to an arbitrary Lagrangian gauge theory. Other names for the Batalin–Vilkovisky formalism are field-antifield formalism, Lagrangian BRST formalism, or BV–BRST formalism. It should not be confused with the Batalin–Fradkin–Vilkovisky (BFV) formalism, which is the Hamiltonian counterpart.

In solid-state physics, the tight-binding model is an approach to the calculation of electronic band structure using an approximate set of wave functions based upon superposition of wave functions for isolated atoms located at each atomic site. The method is closely related to the LCAO method used in chemistry. Tight-binding models are applied to a wide variety of solids. The model gives good qualitative results in many cases and can be combined with other models that give better results where the tight-binding model fails. Though the tight-binding model is a one-electron model, the model also provides a basis for more advanced calculations like the calculation of surface states and application to various kinds of many-body problem and quasiparticle calculations.

The Debye–Waller factor (DWF), named after Peter Debye and Ivar Waller, is used in condensed matter physics to describe the attenuation of x-ray scattering or coherent neutron scattering caused by thermal motion. It is also called the B factor, atomic B factor, or temperature factor. Often, "Debye–Waller factor" is used as a generic term that comprises the Lamb–Mössbauer factor of incoherent neutron scattering and Mössbauer spectroscopy.

In information theory, information dimension is an information measure for random vectors in Euclidean space, based on the normalized entropy of finely quantized versions of the random vectors. This concept was first introduced by Alfréd Rényi in 1959.

Ewald summation, named after Paul Peter Ewald, is a method for computing long-range interactions in periodic systems. It was first developed as the method for calculating the electrostatic energies of ionic crystals, and is now commonly used for calculating long-range interactions in computational chemistry. Ewald summation is a special case of the Poisson summation formula, replacing the summation of interaction energies in real space with an equivalent summation in Fourier space. In this method, the long-range interaction is divided into two parts: a short-range contribution, and a long-range contribution which does not have a singularity. The short-range contribution is calculated in real space, whereas the long-range contribution is calculated using a Fourier transform. The advantage of this method is the rapid convergence of the energy compared with that of a direct summation. This means that the method has high accuracy and reasonable speed when computing long-range interactions, and it is thus the de facto standard method for calculating long-range interactions in periodic systems. The method requires charge neutrality of the molecular system to accurately calculate the total Coulombic interaction. A study of the truncation errors introduced in the energy and force calculations of disordered point-charge systems is provided by Kolafa and Perram.

In condensed matter physics and crystallography, the static structure factor is a mathematical description of how a material scatters incident radiation. The structure factor is a critical tool in the interpretation of scattering patterns obtained in X-ray, electron and neutron diffraction experiments.

<span class="mw-page-title-main">Lattice Boltzmann methods</span> Class of computational fluid dynamics methods

The lattice Boltzmann methods (LBM), originated from the lattice gas automata (LGA) method (Hardy-Pomeau-Pazzis and Frisch-Hasslacher-Pomeau models), is a class of computational fluid dynamics (CFD) methods for fluid simulation. Instead of solving the Navier–Stokes equations directly, a fluid density on a lattice is simulated with streaming and collision (relaxation) processes. The method is versatile as the model fluid can straightforwardly be made to mimic common fluid behaviour like vapour/liquid coexistence, and so fluid systems such as liquid droplets can be simulated. Also, fluids in complex environments such as porous media can be straightforwardly simulated, whereas with complex boundaries other CFD methods can be hard to work with.

Molecular replacement is a method of solving the phase problem in X-ray crystallography. MR relies upon the existence of a previously solved protein structure which is similar to our unknown structure from which the diffraction data is derived. This could come from a homologous protein, or from the lower-resolution protein NMR structure of the same protein.

In mathematics, vector spherical harmonics (VSH) are an extension of the scalar spherical harmonics for use with vector fields. The components of the VSH are complex-valued functions expressed in the spherical coordinate basis vectors.

<span class="mw-page-title-main">Coulomb wave function</span>

In mathematics, a Coulomb wave function is a solution of the Coulomb wave equation, named after Charles-Augustin de Coulomb. They are used to describe the behavior of charged particles in a Coulomb potential and can be written in terms of confluent hypergeometric functions or Whittaker functions of imaginary argument.

In condensed matter physics, the dynamic structure factor is a mathematical function that contains information about inter-particle correlations and their time evolution. It is a generalization of the structure factor that considers correlations in both space and time. Experimentally, it can be accessed most directly by inelastic neutron scattering or X-ray Raman scattering.

In quantum mechanics, and especially quantum information theory, the purity of a normalized quantum state is a scalar defined as

An electric dipole transition is the dominant effect of an interaction of an electron in an atom with the electromagnetic field.

The Maxwell–Bloch equations, also called the optical Bloch equations describe the dynamics of a two-state quantum system interacting with the electromagnetic mode of an optical resonator. They are analogous to the Bloch equations which describe the motion of the nuclear magnetic moment in an electromagnetic field. The equations can be derived either semiclassically or with the field fully quantized when certain approximations are made.

Data-driven control systems are a broad family of control systems, in which the identification of the process model and/or the design of the controller are based entirely on experimental data collected from the plant.

References

  1. Patterson, A. L. (1934-09-01). "A Fourier Series Method for the Determination of the Components of Interatomic Distances in Crystals". Physical Review. 46 (5): 372–376. doi:10.1103/PhysRev.46.372. ISSN   0031-899X.
  2. Patterson, A. L. (1935). "A direct method for the determination of the components of interatomic distances in crystals". Zeitschrift für Kristallographie. 90 (1–6): 517. doi:10.1524/zkri.1935.90.1.517. S2CID   102041995.