Ergodic theoryErgodic theory is a branch of mathematics that studies statistical properties of deterministic dynamical systems; it is the study of ergodicity. In this context, "statistical properties" refers to properties which are expressed through the behavior of time averages of various functions along trajectories of dynamical systems. The notion of deterministic dynamical systems assumes that the equations determining the dynamics do not contain any random perturbations, noise, etc.
ErgodicityIn mathematics, ergodicity expresses the idea that a point of a moving system, either a dynamical system or a stochastic process, will eventually visit all parts of the space that the system moves in, in a uniform and random sense. This implies that the average behavior of the system can be deduced from the trajectory of a "typical" point. Equivalently, a sufficiently large collection of random samples from a process can represent the average statistical properties of the entire process.
Ensemble (mathematical physics)In physics, specifically statistical mechanics, an ensemble (also statistical ensemble) is an idealization consisting of a large number of virtual copies (sometimes infinitely many) of a system, considered all at once, each of which represents a possible state that the real system might be in. In other words, a statistical ensemble is a set of systems of particles used in statistical mechanics to describe a single system. The concept of an ensemble was introduced by J. Willard Gibbs in 1902.
Canonical ensembleIn statistical mechanics, a canonical ensemble is the statistical ensemble that represents the possible states of a mechanical system in thermal equilibrium with a heat bath at a fixed temperature. The system can exchange energy with the heat bath, so that the states of the system will differ in total energy. The principal thermodynamic variable of the canonical ensemble, determining the probability distribution of states, is the absolute temperature (symbol: T).
Ergodic hypothesisIn physics and thermodynamics, the ergodic hypothesis says that, over long periods of time, the time spent by a system in some region of the phase space of microstates with the same energy is proportional to the volume of this region, i.e., that all accessible microstates are equiprobable over a long period of time. Liouville's theorem states that, for a Hamiltonian system, the local density of microstates following a particle path through phase space is constant as viewed by an observer moving with the ensemble (i.
Microcanonical ensembleIn statistical mechanics, the microcanonical ensemble is a statistical ensemble that represents the possible states of a mechanical system whose total energy is exactly specified. The system is assumed to be isolated in the sense that it cannot exchange energy or particles with its environment, so that (by conservation of energy) the energy of the system does not change with time. The primary macroscopic variables of the microcanonical ensemble are the total number of particles in the system (symbol: N), the system's volume (symbol: V), as well as the total energy in the system (symbol: E).
Grand canonical ensembleIn statistical mechanics, the grand canonical ensemble (also known as the macrocanonical ensemble) is the statistical ensemble that is used to represent the possible states of a mechanical system of particles that are in thermodynamic equilibrium (thermal and chemical) with a reservoir. The system is said to be open in the sense that the system can exchange energy and particles with a reservoir, so that various possible states of the system can differ in both their total energy and total number of particles.
Partition function (mathematics)The partition function or configuration integral, as used in probability theory, information theory and dynamical systems, is a generalization of the definition of a partition function in statistical mechanics. It is a special case of a normalizing constant in probability theory, for the Boltzmann distribution. The partition function occurs in many problems of probability theory because, in situations where there is a natural symmetry, its associated probability measure, the Gibbs measure, has the Markov property.
Ergodic processIn physics, statistics, econometrics and signal processing, a stochastic process is said to be in an ergodic regime if an observable's ensemble average equals the time average. In this regime, any collection of random samples from a process must represent the average statistical properties of the entire regime. Conversely, a process that is not in ergodic regime is said to be in non-ergodic regime. One can discuss the ergodicity of various statistics of a stochastic process.
Conservative systemIn mathematics, a conservative system is a dynamical system which stands in contrast to a dissipative system. Roughly speaking, such systems have no friction or other mechanism to dissipate the dynamics, and thus, their phase space does not shrink over time. Precisely speaking, they are those dynamical systems that have a null wandering set: under time evolution, no portion of the phase space ever "wanders away", never to be returned to or revisited. Alternately, conservative systems are those to which the Poincaré recurrence theorem applies.
Partition function (statistical mechanics)In physics, a partition function describes the statistical properties of a system in thermodynamic equilibrium. Partition functions are functions of the thermodynamic state variables, such as the temperature and volume. Most of the aggregate thermodynamic variables of the system, such as the total energy, free energy, entropy, and pressure, can be expressed in terms of the partition function or its derivatives. The partition function is dimensionless.
Nucleic acid structure predictionNucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).
Partition function (number theory)In number theory, the partition function p(n) represents the number of possible partitions of a non-negative integer n. For instance, p(4) = 5 because the integer 4 has the five partitions 1 + 1 + 1 + 1, 1 + 1 + 2, 1 + 3, 2 + 2, and 4. No closed-form expression for the partition function is known, but it has both asymptotic expansions that accurately approximate it and recurrence relations by which it can be calculated exactly. It grows as an exponential function of the square root of its argument.
Protein structure predictionProtein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes).
Partition function (quantum field theory)In quantum field theory, partition functions are generating functionals for correlation functions, making them key objects of study in the path integral formalism. They are the imaginary time versions of statistical mechanics partition functions, giving rise to a close connection between these two areas of physics. Partition functions can rarely be solved for exactly, although free theories do admit such solutions. Instead, a perturbative approach is usually implemented, this being equivalent to summing over Feynman diagrams.
Phase transitionIn chemistry, thermodynamics, and other related fields, a phase transition (or phase change) is the physical process of transition between one state of a medium and another. Commonly the term is used to refer to changes among the basic states of matter: solid, liquid, and gas, and in rare cases, plasma. A phase of a thermodynamic system and the states of matter have uniform physical properties. During a phase transition of a given medium, certain properties of the medium change as a result of the change of external conditions, such as temperature or pressure.
Partition (number theory)In number theory and combinatorics, a partition of a non-negative integer n, also called an integer partition, is a way of writing n as a sum of positive integers. Two sums that differ only in the order of their summands are considered the same partition. (If order matters, the sum becomes a composition.) For example, 4 can be partitioned in five distinct ways: 4 3 + 1 2 + 2 2 + 1 + 1 1 + 1 + 1 + 1 The only partition of zero is the empty sum, having no parts.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
Rank of a partitionIn mathematics, particularly in the fields of number theory and combinatorics, the rank of a partition of a positive integer is a certain integer associated with the partition. In fact at least two different definitions of rank appear in the literature. The first definition, with which most of this article is concerned, is that the rank of a partition is the number obtained by subtracting the number of parts in the partition from the largest part in the partition.
