Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Fourier transformIn physics and mathematics, the Fourier transform (FT) is a transform that converts a function into a form that describes the frequencies present in the original function. The output of the transform is a complex-valued function of frequency. The term Fourier transform refers to both this complex-valued function and the mathematical operation. When a distinction needs to be made the Fourier transform is sometimes called the frequency domain representation of the original function.
Fourier analysisIn mathematics, Fourier analysis (ˈfʊrieɪ,_-iər) is the study of the way general functions may be represented or approximated by sums of simpler trigonometric functions. Fourier analysis grew from the study of Fourier series, and is named after Joseph Fourier, who showed that representing a function as a sum of trigonometric functions greatly simplifies the study of heat transfer. The subject of Fourier analysis encompasses a vast spectrum of mathematics.
Fourier seriesA Fourier series (ˈfʊrieɪ,_-iər) is an expansion of a periodic function into a sum of trigonometric functions. The Fourier series is an example of a trigonometric series, but not all trigonometric series are Fourier series. By expressing a function as a sum of sines and cosines, many problems involving the function become easier to analyze because trigonometric functions are well understood. For example, Fourier series were first used by Joseph Fourier to find solutions to the heat equation.
Density matrixIn quantum mechanics, a density matrix (or density operator) is a matrix that describes the quantum state of a physical system. It allows for the calculation of the probabilities of the outcomes of any measurement performed upon this system, using the Born rule. It is a generalization of the more usual state vectors or wavefunctions: while those can only represent pure states, density matrices can also represent mixed states.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Harmonic analysisHarmonic analysis is a branch of mathematics concerned with investigating the connections between a function and its representation in frequency. The frequency representation is found by using the Fourier transform for functions on the real line, or by Fourier series for periodic functions. Generalizing these transforms to other domains is generally called Fourier analysis, although the term is sometimes used interchangeably with harmonic analysis.
Least-squares spectral analysisLeast-squares spectral analysis (LSSA) is a method of estimating a frequency spectrum based on a least-squares fit of sinusoids to data samples, similar to Fourier analysis. Fourier analysis, the most used spectral method in science, generally boosts long-periodic noise in the long and gapped records; LSSA mitigates such problems. Unlike in Fourier analysis, data need not be equally spaced to use LSSA.
Projection-valued measureIn mathematics, particularly in functional analysis, a projection-valued measure (PVM) is a function defined on certain subsets of a fixed set and whose values are self-adjoint projections on a fixed Hilbert space. Projection-valued measures are formally similar to real-valued measures, except that their values are self-adjoint projections rather than real numbers. As in the case of ordinary measures, it is possible to integrate complex-valued functions with respect to a PVM; the result of such an integration is a linear operator on the given Hilbert space.
Joseph FourierJean-Baptiste Joseph Fourier (ˈfʊrieɪ,_-iər; fuʁje; 21 March 1768 – 16 May 1830) was a French mathematician and physicist born in Auxerre and best known for initiating the investigation of Fourier series, which eventually developed into Fourier analysis and harmonic analysis, and their applications to problems of heat transfer and vibrations. The Fourier transform and Fourier's law of conduction are also named in his honour. Fourier is also generally credited with the discovery of the greenhouse effect.
Position operatorIn quantum mechanics, the position operator is the operator that corresponds to the position observable of a particle. When the position operator is considered with a wide enough domain (e.g. the space of tempered distributions), its eigenvalues are the possible position vectors of the particle. In one dimension, if by the symbol we denote the unitary eigenvector of the position operator corresponding to the eigenvalue , then, represents the state of the particle in which we know with certainty to find the particle itself at position .
Discrete-time Fourier transformIn mathematics, the discrete-time Fourier transform (DTFT), also called the finite Fourier transform, is a form of Fourier analysis that is applicable to a sequence of values. The DTFT is often used to analyze samples of a continuous function. The term discrete-time refers to the fact that the transform operates on discrete data, often samples whose interval has units of time. From uniformly spaced samples it produces a function of frequency that is a periodic summation of the continuous Fourier transform of the original continuous function.
Laplace operatorIn mathematics, the Laplace operator or Laplacian is a differential operator given by the divergence of the gradient of a scalar function on Euclidean space. It is usually denoted by the symbols , (where is the nabla operator), or . In a Cartesian coordinate system, the Laplacian is given by the sum of second partial derivatives of the function with respect to each independent variable. In other coordinate systems, such as cylindrical and spherical coordinates, the Laplacian also has a useful form.
Spectrum (physical sciences)In the physical sciences, the term spectrum was introduced first into optics by Isaac Newton in the 17th century, referring to the range of colors observed when white light was dispersed through a prism. Soon the term referred to a plot of light intensity or power as a function of frequency or wavelength, also known as a spectral density plot. Later it expanded to apply to other waves, such as sound waves and sea waves that could also be measured as a function of frequency (e.g., noise spectrum, sea wave spectrum).
Multiplier (Fourier analysis)In Fourier analysis, a multiplier operator is a type of linear operator, or transformation of functions. These operators act on a function by altering its Fourier transform. Specifically they multiply the Fourier transform of a function by a specified function known as the multiplier or symbol. Occasionally, the term multiplier operator itself is shortened simply to multiplier. In simple terms, the multiplier reshapes the frequencies involved in any function.
Fractional Fourier transformIn mathematics, in the area of harmonic analysis, the fractional Fourier transform (FRFT) is a family of linear transformations generalizing the Fourier transform. It can be thought of as the Fourier transform to the n-th power, where n need not be an integer — thus, it can transform a function to any intermediate domain between time and frequency. Its applications range from filter design and signal analysis to phase retrieval and pattern recognition.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Trace classIn mathematics, specifically functional analysis, a trace-class operator is a linear operator for which a trace may be defined, such that the trace is a finite number independent of the choice of basis used to compute the trace. This trace of trace-class operators generalizes the trace of matrices studied in linear algebra. All trace-class operators are compact operators. In quantum mechanics, mixed states are described by density matrices, which are certain trace class operators.
FrequencyFrequency (symbol f) is the number of occurrences of a repeating event per unit of time. It is also occasionally referred to as temporal frequency for clarity and to distinguish it from spatial frequency. Frequency is measured in hertz (symbol Hz) which is equal to one event per second. Ordinary frequency is related to angular frequency (symbol ω, in radians per second) by a scaling factor of 2π. The period (symbol T) is the interval of time between events, so the period is the reciprocal of the frequency, f=1/T.
Quantum operationIn quantum mechanics, a quantum operation (also known as quantum dynamical map or quantum process) is a mathematical formalism used to describe a broad class of transformations that a quantum mechanical system can undergo. This was first discussed as a general stochastic transformation for a density matrix by George Sudarshan. The quantum operation formalism describes not only unitary time evolution or symmetry transformations of isolated systems, but also the effects of measurement and transient interactions with an environment.
