Thermodynamic systemA thermodynamic system is a body of matter and/or radiation, considered as separate from its surroundings, and studied using the laws of thermodynamics. Thermodynamic systems may be isolated, closed, or open. An isolated system exchanges no matter or energy with its surroundings, whereas a closed system does not exchange matter but may exchange heat and experience and exert forces. An open system can interact with its surroundings by exchanging both matter and energy.
Stochastic processIn probability theory and related fields, a stochastic (stəˈkæstɪk) or random process is a mathematical object usually defined as a sequence of random variables, where the index of the sequence has the interpretation of time. Stochastic processes are widely used as mathematical models of systems and phenomena that appear to vary in a random manner. Examples include the growth of a bacterial population, an electrical current fluctuating due to thermal noise, or the movement of a gas molecule.
LindbladianIn quantum mechanics, the Gorini–Kossakowski–Sudarshan–Lindblad equation (GKSL equation, named after Vittorio Gorini, Andrzej Kossakowski, George Sudarshan and Göran Lindblad), master equation in Lindblad form, quantum Liouvillian, or Lindbladian is one of the general forms of Markovian master equations describing open quantum systems. It generalizes the Schrödinger equation to open quantum systems; that is, systems in contacts with their surroundings.
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Principle of maximum entropyThe principle of maximum entropy states that the probability distribution which best represents the current state of knowledge about a system is the one with largest entropy, in the context of precisely stated prior data (such as a proposition that expresses testable information). Another way of stating this: Take precisely stated prior data or testable information about a probability distribution function. Consider the set of all trial probability distributions that would encode the prior data.
Conformational entropyIn chemical thermodynamics, conformational entropy is the entropy associated with the number of conformations of a molecule. The concept is most commonly applied to biological macromolecules such as proteins and RNA, but also be used for polysaccharides and other molecules. To calculate the conformational entropy, the possible conformations of the molecule may first be discretized into a finite number of states, usually characterized by unique combinations of certain structural parameters, each of which has been assigned an energy.
Supersymmetric theory of stochastic dynamicsSupersymmetric theory of stochastic dynamics or stochastics (STS) is an exact theory of stochastic (partial) differential equations (SDEs), the class of mathematical models with the widest applicability covering, in particular, all continuous time dynamical systems, with and without noise. The main utility of the theory from the physical point of view is a rigorous theoretical explanation of the ubiquitous spontaneous long-range dynamical behavior that manifests itself across disciplines via such phenomena as 1/f, flicker, and crackling noises and the power-law statistics, or Zipf's law, of instantonic processes like earthquakes and neuroavalanches.
Water modelIn computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
DiffusionDiffusion is the net movement of anything (for example, atoms, ions, molecules, energy) generally from a region of higher concentration to a region of lower concentration. Diffusion is driven by a gradient in Gibbs free energy or chemical potential. It is possible to diffuse "uphill" from a region of lower concentration to a region of higher concentration, like in spinodal decomposition. Diffusion is a stochastic process due to the inherent randomness of the diffusing entity and can be used to model many real-life stochastic scenarios.
Entropy and lifeResearch concerning the relationship between the thermodynamic quantity entropy and both the origin and evolution of life began around the turn of the 20th century. In 1910, American historian Henry Adams printed and distributed to university libraries and history professors the small volume A Letter to American Teachers of History proposing a theory of history based on the second law of thermodynamics and on the principle of entropy. The 1944 book What is Life? by Nobel-laureate physicist Erwin Schrödinger stimulated further research in the field.
