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.
Fluctuation theoremThe fluctuation theorem (FT), which originated from statistical mechanics, deals with the relative probability that the entropy of a system which is currently away from thermodynamic equilibrium (i.e., maximum entropy) will increase or decrease over a given amount of time. While the second law of thermodynamics predicts that the entropy of an isolated system should tend to increase until it reaches equilibrium, it became apparent after the discovery of statistical mechanics that the second law is only a statistical one, suggesting that there should always be some nonzero probability that the entropy of an isolated system might spontaneously decrease; the fluctuation theorem precisely quantifies this probability.
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.
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.
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
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.
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.
Fluctuation-dissipation theoremThe fluctuation–dissipation theorem (FDT) or fluctuation–dissipation relation (FDR) is a powerful tool in statistical physics for predicting the behavior of systems that obey detailed balance. Given that a system obeys detailed balance, the theorem is a proof that thermodynamic fluctuations in a physical variable predict the response quantified by the admittance or impedance (to be intended in their general sense, not only in electromagnetic terms) of the same physical variable (like voltage, temperature difference, etc.
Thermodynamic temperatureThermodynamic temperature is a quantity defined in thermodynamics as distinct from kinetic theory or statistical mechanics. Historically, thermodynamic temperature was defined by Lord Kelvin in terms of a macroscopic relation between thermodynamic work and heat transfer as defined in thermodynamics, but the kelvin was redefined by international agreement in 2019 in terms of phenomena that are now understood as manifestations of the kinetic energy of free motion of microscopic particles such as atoms, molecules, and electrons.
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.
Lagrangian (field theory)Lagrangian field theory is a formalism in classical field theory. It is the field-theoretic analogue of Lagrangian mechanics. Lagrangian mechanics is used to analyze the motion of a system of discrete particles each with a finite number of degrees of freedom. Lagrangian field theory applies to continua and fields, which have an infinite number of degrees of freedom.
Boltzmann constantThe Boltzmann constant (kB or k) is the proportionality factor that relates the average relative thermal energy of particles in a gas with the thermodynamic temperature of the gas. It occurs in the definitions of the kelvin and the gas constant, and in Planck's law of black-body radiation and Boltzmann's entropy formula, and is used in calculating thermal noise in resistors. The Boltzmann constant has dimensions of energy divided by temperature, the same as entropy. It is named after the Austrian scientist Ludwig Boltzmann.
