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.
PermittivityIn electromagnetism, the absolute permittivity, often simply called permittivity and denoted by the Greek letter ε (epsilon), is a measure of the electric polarizability of a dielectric. A material with high permittivity polarizes more in response to an applied electric field than a material with low permittivity, thereby storing more energy in the material. In electrostatics, the permittivity plays an important role in determining the capacitance of a capacitor.
Relative permittivityThe relative permittivity (in older texts, dielectric constant) is the permittivity of a material expressed as a ratio with the electric permittivity of a vacuum. A dielectric is an insulating material, and the dielectric constant of an insulator measures the ability of the insulator to store electric energy in an electrical field. Permittivity is a material's property that affects the Coulomb force between two point charges in the material. Relative permittivity is the factor by which the electric field between the charges is decreased relative to vacuum.
Empty setIn mathematics, the empty set is the unique set having no elements; its size or cardinality (count of elements in a set) is zero. Some axiomatic set theories ensure that the empty set exists by including an axiom of empty set, while in other theories, its existence can be deduced. Many possible properties of sets are vacuously true for the empty set. Any set other than the empty set is called non-empty. In some textbooks and popularizations, the empty set is referred to as the "null set".
Set (mathematics)A set is the mathematical model for a collection of different things; a set contains elements or members, which can be mathematical objects of any kind: numbers, symbols, points in space, lines, other geometrical shapes, variables, or even other sets. The set with no element is the empty set; a set with a single element is a singleton. A set may have a finite number of elements or be an infinite set. Two sets are equal if they have precisely the same elements. Sets are ubiquitous in modern mathematics.
Set theorySet theory is the branch of mathematical logic that studies sets, which can be informally described as collections of objects. Although objects of any kind can be collected into a set, set theory, as a branch of mathematics, is mostly concerned with those that are relevant to mathematics as a whole. The modern study of set theory was initiated by the German mathematicians Richard Dedekind and Georg Cantor in the 1870s. In particular, Georg Cantor is commonly considered the founder of set theory.
DielectricIn electromagnetism, a dielectric (or dielectric medium) is an electrical insulator that can be polarised by an applied electric field. When a dielectric material is placed in an electric field, electric charges do not flow through the material as they do in an electrical conductor, because they have no loosely bound, or free, electrons that may drift through the material, but instead they shift, only slightly, from their average equilibrium positions, causing dielectric polarisation.
Hardware description languageIn computer engineering, a hardware description language (HDL) is a specialized computer language used to describe the structure and behavior of electronic circuits, and most commonly, digital logic circuits. A hardware description language enables a precise, formal description of an electronic circuit that allows for the automated analysis and simulation of an electronic circuit.
Dielectric lossIn electrical engineering, dielectric loss quantifies a dielectric material's inherent dissipation of electromagnetic energy (e.g. heat). It can be parameterized in terms of either the loss angle δ or the corresponding loss tangent tan(δ). Both refer to the phasor in the complex plane whose real and imaginary parts are the resistive (lossy) component of an electromagnetic field and its reactive (lossless) counterpart.
Rough setIn computer science, a rough set, first described by Polish computer scientist Zdzisław I. Pawlak, is a formal approximation of a crisp set (i.e., conventional set) in terms of a pair of sets which give the lower and the upper approximation of the original set. In the standard version of rough set theory (Pawlak 1991), the lower- and upper-approximation sets are crisp sets, but in other variations, the approximating sets may be fuzzy sets. The following section contains an overview of the basic framework of rough set theory, as originally proposed by Zdzisław I.
Set-builder notationIn set theory and its applications to logic, mathematics, and computer science, set-builder notation is a mathematical notation for describing a set by enumerating its elements, or stating the properties that its members must satisfy. Defining sets by properties is also known as set comprehension, set abstraction or as defining a set's intension. Set (mathematics)#Roster notation A set can be described directly by enumerating all of its elements between curly brackets, as in the following two examples: is the set containing the four numbers 3, 7, 15, and 31, and nothing else.
Vacuum permittivityVacuum permittivity, commonly denoted ε0 (pronounced "epsilon nought" or "epsilon zero"), is the value of the absolute dielectric permittivity of classical vacuum. It may also be referred to as the permittivity of free space, the electric constant, or the distributed capacitance of the vacuum. It is an ideal (baseline) physical constant. Its CODATA value is: (farads per meter), with a relative uncertainty of It is a measure of how dense of an electric field is "permitted" to form in response to electric charges and relates the units for electric charge to mechanical quantities such as length and force.
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.
Folding@homeFolding@home (FAH or F@h) is a distributed computing project aimed to help scientists develop new therapeutics for a variety of diseases by the means of simulating protein dynamics. This includes the process of protein folding and the movements of proteins, and is reliant on simulations run on volunteers' personal computers. Folding@home is currently based at the University of Pennsylvania and led by Greg Bowman, a former student of Vijay Pande.
Low-κ dielectricIn semiconductor manufacturing, a low-κ is a material with a small relative dielectric constant (κ, kappa) relative to silicon dioxide. Low-κ dielectric material implementation is one of several strategies used to allow continued scaling of microelectronic devices, colloquially referred to as extending Moore's law. In digital circuits, insulating dielectrics separate the conducting parts (wire interconnects and transistors) from one another.
Protein foldingProtein folding is the physical process where a protein chain is translated into its native three-dimensional structure, typically a "folded" conformation, by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA into a linear chain of amino acids.
PeptidePeptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides which have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. Peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others.
GROMACSGROMACS is a molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. It was originally developed in the Biophysical Chemistry department of University of Groningen, and is now maintained by contributors in universities and research centers worldwide. GROMACS is one of the fastest and most popular software packages available, and can run on central processing units (CPUs) and graphics processing units (GPUs). It is free, open-source software released under the GNU General Public License (GPL), and starting with version 4.
High-κ dielectricIn the semiconductor industry, the term high-κ dielectric refers to a material with a high dielectric constant (κ, kappa), as compared to silicon dioxide. High-κ dielectrics are used in semiconductor manufacturing processes where they are usually used to replace a silicon dioxide gate dielectric or another dielectric layer of a device. The implementation of high-κ gate dielectrics is one of several strategies developed to allow further miniaturization of microelectronic components, colloquially referred to as extending Moore's Law.
AmideIn organic chemistry, an amide, also known as an organic amide or a carboxamide, is a compound with the general formula , where R, R', and R′′ represent any group, typically organyl groups or hydrogen atoms. The amide group is called a peptide bond when it is part of the main chain of a protein, and an isopeptide bond when it occurs in a side chain, such as in the amino acids asparagine and glutamine. It can be viewed as a derivative of a carboxylic acid () with the hydroxyl group () replaced by an amine group (); or, equivalently, an acyl (alkanoyl) group () joined to an amine group.
