Graph theoryIn mathematics, graph theory is the study of graphs, which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of vertices (also called nodes or points) which are connected by edges (also called links or lines). A distinction is made between undirected graphs, where edges link two vertices symmetrically, and directed graphs, where edges link two vertices asymmetrically. Graphs are one of the principal objects of study in discrete mathematics.
Laplacian matrixIn the mathematical field of graph theory, the Laplacian matrix, also called the graph Laplacian, admittance matrix, Kirchhoff matrix or discrete Laplacian, is a matrix representation of a graph. Named after Pierre-Simon Laplace, the graph Laplacian matrix can be viewed as a matrix form of the negative discrete Laplace operator on a graph approximating the negative continuous Laplacian obtained by the finite difference method. The Laplacian matrix relates to many useful properties of a graph.
Line graphIn the mathematical discipline of graph theory, the line graph of an undirected graph G is another graph L(G) that represents the adjacencies between edges of G. L(G) is constructed in the following way: for each edge in G, make a vertex in L(G); for every two edges in G that have a vertex in common, make an edge between their corresponding vertices in L(G). The name line graph comes from a paper by although both and used the construction before this.
Graph databaseA graph database (GDB) is a database that uses graph structures for semantic queries with nodes, edges, and properties to represent and store data. A key concept of the system is the graph (or edge or relationship). The graph relates the data items in the store to a collection of nodes and edges, the edges representing the relationships between the nodes. The relationships allow data in the store to be linked together directly and, in many cases, retrieved with one operation.
Final topologyIn general topology and related areas of mathematics, the final topology (or coinduced, strong, colimit, or inductive topology) on a set with respect to a family of functions from topological spaces into is the finest topology on that makes all those functions continuous. The quotient topology on a quotient space is a final topology, with respect to a single surjective function, namely the quotient map. The disjoint union topology is the final topology with respect to the inclusion maps.
Order topologyIn mathematics, an order topology is a certain topology that can be defined on any totally ordered set. It is a natural generalization of the topology of the real numbers to arbitrary totally ordered sets. If X is a totally ordered set, the order topology on X is generated by the subbase of "open rays" for all a, b in X. Provided X has at least two elements, this is equivalent to saying that the open intervals together with the above rays form a base for the order topology.
Graph automorphismIn the mathematical field of graph theory, an automorphism of a graph is a form of symmetry in which the graph is mapped onto itself while preserving the edge–vertex connectivity. Formally, an automorphism of a graph G = (V, E) is a permutation σ of the vertex set V, such that the pair of vertices (u, v) form an edge if and only if the pair (σ(u), σ(v)) also form an edge. That is, it is a graph isomorphism from G to itself. Automorphisms may be defined in this way both for directed graphs and for undirected graphs.
Structural alignmentStructural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.
Initial topologyIn general topology and related areas of mathematics, the initial topology (or induced topology or weak topology or limit topology or projective topology) on a set with respect to a family of functions on is the coarsest topology on that makes those functions continuous. The subspace topology and product topology constructions are both special cases of initial topologies. Indeed, the initial topology construction can be viewed as a generalization of these.
General topologyIn mathematics, general topology (or point set topology) is the branch of topology that deals with the basic set-theoretic definitions and constructions used in topology. It is the foundation of most other branches of topology, including differential topology, geometric topology, and algebraic topology. The fundamental concepts in point-set topology are continuity, compactness, and connectedness: Continuous functions, intuitively, take nearby points to nearby points.
Structural bioinformaticsStructural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular folding, evolution, binding interactions, and structure/function relationships, working both from experimentally solved structures and from computational models.
Unit distance graphIn mathematics, particularly geometric graph theory, a unit distance graph is a graph formed from a collection of points in the Euclidean plane by connecting two points whenever the distance between them is exactly one. To distinguish these graphs from a broader definition that allows some non-adjacent pairs of vertices to be at distance one, they may also be called strict unit distance graphs or faithful unit distance graphs. As a hereditary family of graphs, they can be characterized by forbidden induced subgraphs.
TopologyIn mathematics, topology (from the Greek words τόπος, and λόγος) is concerned with the properties of a geometric object that are preserved under continuous deformations, such as stretching, twisting, crumpling, and bending; that is, without closing holes, opening holes, tearing, gluing, or passing through itself. A topological space is a set endowed with a structure, called a topology, which allows defining continuous deformation of subspaces, and, more generally, all kinds of continuity.
Structural genomicsStructural genomics seeks to describe the 3-dimensional structure of every protein encoded by a given genome. This genome-based approach allows for a high-throughput method of structure determination by a combination of experimental and modeling approaches. The principal difference between structural genomics and traditional structural prediction is that structural genomics attempts to determine the structure of every protein encoded by the genome, rather than focusing on one particular protein.
Subspace topologyIn topology and related areas of mathematics, a subspace of a topological space X is a subset S of X which is equipped with a topology induced from that of X called the subspace topology (or the relative topology, or the induced topology, or the trace topology). Given a topological space and a subset of , the subspace topology on is defined by That is, a subset of is open in the subspace topology if and only if it is the intersection of with an open set in .
Perfect graphIn graph theory, a perfect graph is a graph in which the chromatic number equals the size of the maximum clique, both in the graph itself and in every induced subgraph. In all graphs, the chromatic number is greater than or equal to the size of the maximum clique, but they can be far apart. A graph is perfect when these numbers are equal, and remain equal after the deletion of arbitrary subsets of vertices. The perfect graphs include many important families of graphs and serve to unify results relating colorings and cliques in those families.
Graph rewritingIn computer science, graph transformation, or graph rewriting, concerns the technique of creating a new graph out of an original graph algorithmically. It has numerous applications, ranging from software engineering (software construction and also software verification) to layout algorithms and picture generation. Graph transformations can be used as a computation abstraction. The basic idea is that if the state of a computation can be represented as a graph, further steps in that computation can then be represented as transformation rules on that graph.
Graph coloringIn graph theory, graph coloring is a special case of graph labeling; it is an assignment of labels traditionally called "colors" to elements of a graph subject to certain constraints. In its simplest form, it is a way of coloring the vertices of a graph such that no two adjacent vertices are of the same color; this is called a vertex coloring. Similarly, an edge coloring assigns a color to each edge so that no two adjacent edges are of the same color, and a face coloring of a planar graph assigns a color to each face or region so that no two faces that share a boundary have the same color.
Cayley graphIn mathematics, a Cayley graph, also known as a Cayley color graph, Cayley diagram, group diagram, or color group, is a graph that encodes the abstract structure of a group. Its definition is suggested by Cayley's theorem (named after Arthur Cayley), and uses a specified set of generators for the group. It is a central tool in combinatorial and geometric group theory. The structure and symmetry of Cayley graphs makes them particularly good candidates for constructing families of expander graphs.
Comparison of topologiesIn topology and related areas of mathematics, the set of all possible topologies on a given set forms a partially ordered set. This order relation can be used for comparison of the topologies. A topology on a set may be defined as the collection of subsets which are considered to be "open". An alternative definition is that it is the collection of subsets which are considered "closed". These two ways of defining the topology are essentially equivalent because the complement of an open set is closed and vice versa.
