The Lindemann index [1] is a simple measure of thermally driven disorder in atoms or molecules. The local Lindemann index is defined as: [2]
where angle brackets indicate a time average. The global Lindemann index is a system average of this quantity.
Care must be taken if the molecule possesses globally defined dynamics, such as about a hinge or pivot, because these motions will obscure the local motions which the Lindemann index is designed to quantify. An appropriate tactic in this circumstance is to sum the rij only over a small number of neighbouring atoms to arrive at each qi. A further variety of such modifications to the Lindemann index are available and have different merits, e.g. for the study of glassy vs crystalline materials. [4]
Melting, or fusion, is a physical process that results in the phase transition of a substance from a solid to a liquid. This occurs when the internal energy of the solid increases, typically by the application of heat or pressure, which increases the substance's temperature to the melting point. At the melting point, the ordering of ions or molecules in the solid breaks down to a less ordered state, and the solid melts to become a liquid.
Quantum entanglement is the phenomenon that occurs when a group of particles are generated, interact, or share spatial proximity in a way such that the quantum state of each particle of the group cannot be described independently of the state of the others, including when the particles are separated by a large distance. The topic of quantum entanglement is at the heart of the disparity between classical and quantum physics: entanglement is a primary feature of quantum mechanics not present in classical mechanics.
In condensed matter physics, a spin glass is a magnetic state characterized by randomness, besides cooperative behavior in freezing of spins at a temperature called 'freezing temperature' Tf. In ferromagnetic solids, component atoms' magnetic spins all align in the same direction. Spin glass when contrasted with a ferromagnet is defined as "disordered" magnetic state in which spins are aligned randomly or without a regular pattern and the couplings too are random.
Quantum decoherence is the loss of quantum coherence, the process in which a system's behaviour changes from that which can be explained by quantum mechanics to that which can be explained by classical mechanics. In quantum mechanics, particles such as electrons are described by a wave function, a mathematical representation of the quantum state of a system; a probabilistic interpretation of the wave function is used to explain various quantum effects. As long as there exists a definite phase relation between different states, the system is said to be coherent. A definite phase relationship is necessary to perform quantum computing on quantum information encoded in quantum states. Coherence is preserved under the laws of quantum physics.
The Ising model, named after the physicists Ernst Ising and Wilhelm Lenz, is a mathematical model of ferromagnetism in statistical mechanics. The model consists of discrete variables that represent magnetic dipole moments of atomic "spins" that can be in one of two states. The spins are arranged in a graph, usually a lattice, allowing each spin to interact with its neighbors. Neighboring spins that agree have a lower energy than those that disagree; the system tends to the lowest energy but heat disturbs this tendency, thus creating the possibility of different structural phases. The model allows the identification of phase transitions as a simplified model of reality. The two-dimensional square-lattice Ising model is one of the simplest statistical models to show a phase transition.
Cooperativity is a phenomenon displayed by systems involving identical or near-identical elements, which act dependently of each other, relative to a hypothetical standard non-interacting system in which the individual elements are acting independently. One manifestation of this is enzymes or receptors that have multiple binding sites where the affinity of the binding sites for a ligand is apparently increased, positive cooperativity, or decreased, negative cooperativity, upon the binding of a ligand to a binding site. For example, when an oxygen atom binds to one of hemoglobin's four binding sites, the affinity to oxygen of the three remaining available binding sites increases; i.e. oxygen is more likely to bind to a hemoglobin bound to one oxygen than to an unbound hemoglobin. This is referred to as cooperative binding.
In quantum physics, a measurement is the testing or manipulation of a physical system to yield a numerical result. A fundamental feature of quantum theory is that the predictions it makes are probabilistic. The procedure for finding a probability involves combining a quantum state, which mathematically describes a quantum system, with a mathematical representation of the measurement to be performed on that system. The formula for this calculation is known as the Born rule. For example, a quantum particle like an electron can be described by a quantum state that associates to each point in space a complex number called a probability amplitude. Applying the Born rule to these amplitudes gives the probabilities that the electron will be found in one region or another when an experiment is performed to locate it. This is the best the theory can do; it cannot say for certain where the electron will be found. The same quantum state can also be used to make a prediction of how the electron will be moving, if an experiment is performed to measure its momentum instead of its position. The uncertainty principle implies that, whatever the quantum state, the range of predictions for the electron's position and the range of predictions for its momentum cannot both be narrow. Some quantum states imply a near-certain prediction of the result of a position measurement, but the result of a momentum measurement will be highly unpredictable, and vice versa. Furthermore, the fact that nature violates the statistical conditions known as Bell inequalities indicates that the unpredictability of quantum measurement results cannot be explained away as due to ignorance about "hidden variables" within quantum systems.
A granular material is a conglomeration of discrete solid, macroscopic particles characterized by a loss of energy whenever the particles interact. The constituents that compose granular material are large enough such that they are not subject to thermal motion fluctuations. Thus, the lower size limit for grains in granular material is about 1 μm. On the upper size limit, the physics of granular materials may be applied to ice floes where the individual grains are icebergs and to asteroid belts of the Solar System with individual grains being asteroids.
The Schwinger–Dyson equations (SDEs) or Dyson–Schwinger equations, named after Julian Schwinger and Freeman Dyson, are general relations between correlation functions in quantum field theories (QFTs). They are also referred to as the Euler–Lagrange equations of quantum field theories, since they are the equations of motion corresponding to the Green's function. They form a set of infinitely many functional differential equations, all coupled to each other, sometimes referred to as the infinite tower of SDEs.
The Boltzmann equation or Boltzmann transport equation (BTE) describes the statistical behaviour of a thermodynamic system not in a state of equilibrium; it was devised by Ludwig Boltzmann in 1872. The classic example of such a system is a fluid with temperature gradients in space causing heat to flow from hotter regions to colder ones, by the random but biased transport of the particles making up that fluid. In the modern literature the term Boltzmann equation is often used in a more general sense, referring to any kinetic equation that describes the change of a macroscopic quantity in a thermodynamic system, such as energy, charge or particle number.
In statistical mechanics, the correlation function is a measure of the order in a system, as characterized by a mathematical correlation function. Correlation functions describe how microscopic variables, such as spin and density, at different positions are related. More specifically, correlation functions quantify how microscopic variables co-vary with one another on average across space and time. A classic example of such spatial correlations is in ferro- and antiferromagnetic materials, where the spins prefer to align parallel and antiparallel with their nearest neighbors, respectively. The spatial correlation between spins in such materials is shown in the figure to the right.
In quantum mechanics, the Hellmann–Feynman theorem relates the derivative of the total energy with respect to a parameter to the expectation value of the derivative of the Hamiltonian with respect to that same parameter. According to the theorem, once the spatial distribution of the electrons has been determined by solving the Schrödinger equation, all the forces in the system can be calculated using classical electrostatics.
Fluorescence correlation spectroscopy (FCS) is a statistical analysis, via time correlation, of stationary fluctuations of the fluorescence intensity. Its theoretical underpinning originated from L. Onsager's regression hypothesis. The analysis provides kinetic parameters of the physical processes underlying the fluctuations. One of the interesting applications of this is an analysis of the concentration fluctuations of fluorescent particles (molecules) in solution. In this application, the fluorescence emitted from a very tiny space in solution containing a small number of fluorescent particles (molecules) is observed. The fluorescence intensity is fluctuating due to Brownian motion of the particles. In other words, the number of the particles in the sub-space defined by the optical system is randomly changing around the average number. The analysis gives the average number of fluorescent particles and average diffusion time, when the particle is passing through the space. Eventually, both the concentration and size of the particle (molecule) are determined. Both parameters are important in biochemical research, biophysics, and chemistry.
In quantum field theory and statistical mechanics, the Mermin–Wagner theorem states that continuous symmetries cannot be spontaneously broken at finite temperature in systems with sufficiently short-range interactions in dimensions d ≤ 2. Intuitively, this means that long-range fluctuations can be created with little energy cost, and since they increase the entropy, they are favored.
The Jaynes–Cummings model is a theoretical model in quantum optics. It describes the system of a two-level atom interacting with a quantized mode of an optical cavity, with or without the presence of light. It was originally developed to study the interaction of atoms with the quantized electromagnetic field in order to investigate the phenomena of spontaneous emission and absorption of photons in a cavity.
The Gaussian network model (GNM) is a representation of a biological macromolecule as an elastic mass-and-spring network to study, understand, and characterize the mechanical aspects of its long-time large-scale dynamics. The model has a wide range of applications from small proteins such as enzymes composed of a single domain, to large macromolecular assemblies such as a ribosome or a viral capsid. Protein domain dynamics plays key roles in a multitude of molecular recognition and cell signalling processes. Protein domains, connected by intrinsically disordered flexible linker domains, induce long-range allostery via protein domain dynamics. The resultant dynamic modes cannot be generally predicted from static structures of either the entire protein or individual domains.
Resonance fluorescence is the process in which a two-level atom system interacts with the quantum electromagnetic field if the field is driven at a frequency near to the natural frequency of the atom.
The kicked rotator, also spelled as kicked rotor, is a paradigmatic model for both Hamiltonian chaos and quantum chaos. It describes a free rotating stick in an inhomogeneous "gravitation like" field that is periodically switched on in short pulses. The model is described by the Hamiltonian
Robustness, the ability to withstand failures and perturbations, is a critical attribute of many complex systems including complex networks.
In solid state physics, the Luttinger–Ward functional, proposed by Joaquin Mazdak Luttinger and John Clive Ward in 1960, is a scalar functional of the bare electron-electron interaction and the renormalized one-particle propagator. In terms of Feynman diagrams, the Luttinger–Ward functional is the sum of all closed, bold, two-particle irreducible diagrams, i.e., all diagrams without particles going in or out that do not fall apart if one removes two propagator lines. It is usually written as or , where is the one-particle Green's function and is the bare interaction.