Molecule editorA molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages.
Binary collision approximationIn condensed-matter physics, the binary collision approximation (BCA) is a heuristic used to more efficiently simulate the penetration depth and defect production by energetic ions (with kinetic energies in the kilo-electronvolt (keV) range or higher) in solids. In the method, the ion is approximated to travel through a material by experiencing a sequence of independent binary collisions with sample atoms (nuclei). Between the collisions, the ion is assumed to travel in a straight path, experiencing electronic stopping power, but losing no energy in collisions with nuclei.
Random coilIn polymer chemistry, a random coil is a conformation of polymers where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules. The conformation's name is derived from the idea that, in the absence of specific, stabilizing interactions, a polymer backbone will "sample" all possible conformations randomly.
Dihedral angleA dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes.
Radiation material scienceRadiation materials science is a subfield of materials science which studies the interaction of radiation with matter: a broad subject covering many forms of irradiation and of matter. Some of the most profound effects of irradiation on materials occur in the core of nuclear power reactors where atoms comprising the structural components are displaced numerous times over the course of their engineering lifetimes.
Semi-empirical quantum chemistry methodSemi-empirical quantum chemistry methods are based on the Hartree–Fock formalism, but make many approximations and obtain some parameters from empirical data. They are very important in computational chemistry for treating large molecules where the full Hartree–Fock method without the approximations is too expensive. The use of empirical parameters appears to allow some inclusion of electron correlation effects into the methods. Within the framework of Hartree–Fock calculations, some pieces of information (such as two-electron integrals) are sometimes approximated or completely omitted.
Q (software)Q is a computer software package for molecular dynamics (MD) simulation (current release: Q6). Unlike other MD codes, it has specialized since its conception (Marelius et al. 1998) on three specific types of free energy calculations. These calculations are based on the methods: empirical valence bond (EVB), free energy perturbation (FEP), and linear interaction energy (LIE), as well as, more recently, also path integral calculations using the bisection quantum classical path (BQCP) approach.
Rosetta (bioinformatics)Rosetta is a software package for protein structure prediction. Originally introduced by the Baker laboratory at the University of Washington in 1998 as an ab initio approach to structure prediction, Rosetta has since branched into several development streams and distinct services, providing features such as macromolecular docking and protein design. Many of the graduate students and other researchers involved in Rosetta's initial development have since moved to other universities and research institutions, and subsequently enhanced different parts of the Rosetta project.
Stopping power (particle radiation)In nuclear and materials physics, stopping power is the retarding force acting on charged particles, typically alpha and beta particles, due to interaction with matter, resulting in loss of particle kinetic energy. Its application is important in areas such as radiation protection, ion implantation and nuclear medicine. Both charged and uncharged particles lose energy while passing through matter. Positive ions are considered in most cases below. The stopping power depends on the type and energy of the radiation and on the properties of the material it passes.
