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Inferring free-energy barriers and kinetic rates from molecular dynamics via underdamped Langevin models

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Numerical stability

In the mathematical subfield of numerical analysis, numerical stability is a generally desirable property of numerical algorithms. The precise definition of stability depends on the context. One is numerical linear algebra and the other is algorithms for solving ordinary and partial differential equations by discrete approximation. In numerical linear algebra, the principal concern is instabilities caused by proximity to singularities of various kinds, such as very small or nearly colliding eigenvalues.

Ergodicity

In 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.

Numerical analysis

Numerical analysis is the study of algorithms that use numerical approximation (as opposed to symbolic manipulations) for the problems of mathematical analysis (as distinguished from discrete mathematics). It is the study of numerical methods that attempt at finding approximate solutions of problems rather than the exact ones. Numerical analysis finds application in all fields of engineering and the physical sciences, and in the 21st century also the life and social sciences, medicine, business and even the arts.

Kinetic isotope effect

In physical organic chemistry, a kinetic isotope effect (KIE) is the change in the reaction rate of a chemical reaction when one of the atoms in the reactants is replaced by one of its isotopes. Formally, it is the ratio of rate constants for the reactions involving the light (kL) and the heavy (kH) isotopically substituted reactants (isotopologues): This change in reaction rate is a quantum mechanical effect that primarily results from heavier isotopologues having lower vibrational frequencies compared to their lighter counterparts.

Linux kernel

The Linux kernel is a free and open-source, monolithic, modular, multitasking, Unix-like operating system kernel. It was originally written in 1991 by Linus Torvalds for his i386-based PC, and it was soon adopted as the kernel for the GNU operating system, which was written to be a free (libre) replacement for Unix. Linux is provided under the GNU General Public License version 2 only, but it contains files under other compatible licenses.

Numerical integration

In analysis, numerical integration comprises a broad family of algorithms for calculating the numerical value of a definite integral, and by extension, the term is also sometimes used to describe the numerical solution of differential equations. This article focuses on calculation of definite integrals. The term numerical quadrature (often abbreviated to quadrature) is more or less a synonym for numerical integration, especially as applied to one-dimensional integrals.

Reaction mechanism

In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical reaction occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction.

Reaction rate

The reaction rate or rate of reaction is the speed at which a chemical reaction takes place, defined as proportional to the increase in the concentration of a product per unit time and to the decrease in the concentration of a reactant per unit time. Reaction rates can vary dramatically. For example, the oxidative rusting of iron under Earth's atmosphere is a slow reaction that can take many years, but the combustion of cellulose in a fire is a reaction that takes place in fractions of a second.

Loadable kernel module

In computing, a loadable kernel module (LKM) is an that contains code to extend the running kernel, or so-called base kernel, of an operating system. LKMs are typically used to add support for new hardware (as device drivers) and/or s, or for adding system calls. When the functionality provided by an LKM is no longer required, it can be unloaded in order to free memory and other resources.

Statistical dispersion

In statistics, dispersion (also called variability, scatter, or spread) is the extent to which a distribution is stretched or squeezed. Common examples of measures of statistical dispersion are the variance, standard deviation, and interquartile range. For instance, when the variance of data in a set is large, the data is widely scattered. On the other hand, when the variance is small, the data in the set is clustered. Dispersion is contrasted with location or central tendency, and together they are the most used properties of distributions.