Surface of revolutionA surface of revolution is a surface in Euclidean space created by rotating a curve (the generatrix) one full revolution around an axis of rotation (normally not intersecting the generatrix, except at its endpoints). The volume bounded by the surface created by this revolution is the solid of revolution. Examples of surfaces of revolution generated by a straight line are cylindrical and conical surfaces depending on whether or not the line is parallel to the axis.
PolyhedronIn geometry, a polyhedron (: polyhedra or polyhedrons; ) is a three-dimensional shape with flat polygonal faces, straight edges and sharp corners or vertices. A convex polyhedron is a polyhedron that bounds a convex set. Every convex polyhedron can be constructed as the convex hull of its vertices, and for every finite set of points, not all on the same plane, the convex hull is a convex polyhedron. Cubes and pyramids are examples of convex polyhedra. A polyhedron is a 3-dimensional example of a polytope, a more general concept in any number of dimensions.
Energy profile (chemistry)In theoretical chemistry, an energy profile is a theoretical representation of a chemical reaction or process as a single energetic pathway as the reactants are transformed into products. This pathway runs along the reaction coordinate, which is a parametric curve that follows the pathway of the reaction and indicates its progress; thus, energy profiles are also called reaction coordinate diagrams.
Toroidal polyhedronIn geometry, a toroidal polyhedron is a polyhedron which is also a toroid (a g-holed torus), having a topological genus (g) of 1 or greater. Notable examples include the Császár and Szilassi polyhedra. Toroidal polyhedra are defined as collections of polygons that meet at their edges and vertices, forming a manifold as they do. That is, each edge should be shared by exactly two polygons, and at each vertex the edges and faces that meet at the vertex should be linked together in a single cycle of alternating edges and faces, the link of the vertex.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Convex hullIn geometry, the convex hull or convex envelope or convex closure of a shape is the smallest convex set that contains it. The convex hull may be defined either as the intersection of all convex sets containing a given subset of a Euclidean space, or equivalently as the set of all convex combinations of points in the subset. For a bounded subset of the plane, the convex hull may be visualized as the shape enclosed by a rubber band stretched around the subset. Convex hulls of open sets are open, and convex hulls of compact sets are compact.
Reaction coordinateIn chemistry, a reaction coordinate is an abstract one-dimensional coordinate which represents progress along a reaction pathway. It is usually a geometric parameter that changes during the conversion of one or more molecular entities. In molecular dynamics simulations, a reaction coordinate is called collective variable. These coordinates can sometimes represent a real coordinate system (such as bond length, bond angle...), although, for more complex reactions especially, this can be difficult (and non geometric parameters are used, e.
Electronic correlationElectronic correlation is the interaction between electrons in the electronic structure of a quantum system. The correlation energy is a measure of how much the movement of one electron is influenced by the presence of all other electrons. Within the Hartree–Fock method of quantum chemistry, the antisymmetric wave function is approximated by a single Slater determinant. Exact wave functions, however, cannot generally be expressed as single determinants.
Nucleic acid structure predictionNucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).
