EntropyEntropy is a scientific concept, as well as a measurable physical property, that is most commonly associated with a state of disorder, randomness, or uncertainty. The term and the concept are used in diverse fields, from classical thermodynamics, where it was first recognized, to the microscopic description of nature in statistical physics, and to the principles of information theory.
Master equationIn physics, chemistry, and related fields, master equations are used to describe the time evolution of a system that can be modeled as being in a probabilistic combination of states at any given time, and the switching between states is determined by a transition rate matrix. The equations are a set of differential equations – over time – of the probabilities that the system occupies each of the different states. The name was proposed in 1940.
Entropy (classical thermodynamics)In classical thermodynamics, entropy () is a property of a thermodynamic system that expresses the direction or outcome of spontaneous changes in the system. The term was introduced by Rudolf Clausius in the mid-19th century to explain the relationship of the internal energy that is available or unavailable for transformations in form of heat and work. Entropy predicts that certain processes are irreversible or impossible, despite not violating the conservation of energy.
Entropy productionEntropy production (or generation) is the amount of entropy which is produced during heat process to evaluate the efficiency of the process. Entropy is produced in irreversible processes. The importance of avoiding irreversible processes (hence reducing the entropy production) was recognized as early as 1824 by Carnot. In 1865 Rudolf Clausius expanded his previous work from 1854 on the concept of "unkompensierte Verwandlungen" (uncompensated transformations), which, in our modern nomenclature, would be called the entropy production.
Stochastic differential equationA stochastic differential equation (SDE) is a differential equation in which one or more of the terms is a stochastic process, resulting in a solution which is also a stochastic process. SDEs have many applications throughout pure mathematics and are used to model various behaviours of stochastic models such as stock prices, random growth models or physical systems that are subjected to thermal fluctuations. SDEs have a random differential that is in the most basic case random white noise calculated as the derivative of a Brownian motion or more generally a semimartingale.
Langevin equationIn physics, a Langevin equation (named after Paul Langevin) is a stochastic differential equation describing how a system evolves when subjected to a combination of deterministic and fluctuating ("random") forces. The dependent variables in a Langevin equation typically are collective (macroscopic) variables changing only slowly in comparison to the other (microscopic) variables of the system. The fast (microscopic) variables are responsible for the stochastic nature of the Langevin equation.
Coarse-grained modelingCoarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water.
Maximum entropy thermodynamicsIn physics, maximum entropy thermodynamics (colloquially, MaxEnt thermodynamics) views equilibrium thermodynamics and statistical mechanics as inference processes. More specifically, MaxEnt applies inference techniques rooted in Shannon information theory, Bayesian probability, and the principle of maximum entropy. These techniques are relevant to any situation requiring prediction from incomplete or insufficient data (e.g., , signal processing, spectral analysis, and inverse problems).
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.
H-theoremIn classical statistical mechanics, the H-theorem, introduced by Ludwig Boltzmann in 1872, describes the tendency to decrease in the quantity H (defined below) in a nearly-ideal gas of molecules. As this quantity H was meant to represent the entropy of thermodynamics, the H-theorem was an early demonstration of the power of statistical mechanics as it claimed to derive the second law of thermodynamics—a statement about fundamentally irreversible processes—from reversible microscopic mechanics.
