Anisotropy is the structural property of non-uniformity in different directions, as opposed to isotropy. An anisotropic object or pattern has properties that differ according to direction of measurement. For example, many materials exhibit very different physical or mechanical properties when measured along different axes, e.g. absorbance, refractive index, conductivity, and tensile strength.
Paramagnetism is a form of magnetism whereby some materials are weakly attracted by an externally applied magnetic field, and form internal, induced magnetic fields in the direction of the applied magnetic field. In contrast with this behavior, diamagnetic materials are repelled by magnetic fields and form induced magnetic fields in the direction opposite to that of the applied magnetic field. Paramagnetic materials include most chemical elements and some compounds; they have a relative magnetic permeability slightly greater than 1 and hence are attracted to magnetic fields. The magnetic moment induced by the applied field is linear in the field strength and rather weak. It typically requires a sensitive analytical balance to detect the effect and modern measurements on paramagnetic materials are often conducted with a SQUID magnetometer.
In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns. Sequence alignments are also used for non-biological sequences such as calculating the distance cost between strings in a natural language, or to display financial data.
A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes a corresponding protein with a 1:1 relationship. The term "protein family" should not be confused with family as it is used in taxonomy.
Structural 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. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which multiple unrelated amino acid sequences converge on a common tertiary structure.
Structural 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. The term structural has the same meaning as in structural biology, and structural bioinformatics can be seen as a part of computational structural biology. The main objective of structural bioinformatics is the creation of new methods of analysing and manipulating biological macromolecular data in order to solve problems in biology and generate new knowledge.
In mathematics, computer science and especially graph theory, a distance matrix is a square matrix containing the distances, taken pairwise, between the elements of a set. Depending upon the application involved, the distance being used to define this matrix may or may not be a metric. If there are N elements, this matrix will have size N×N. In graph-theoretic applications, the elements are more often referred to as points, nodes or vertices.
Data structure alignment is the way data is arranged and accessed in computer memory. It consists of three separate but related issues: data alignment, data structure padding, and packing.
Multiple sequence alignment (MSA) is the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. These alignments are used to infer evolutionary relationships via phylogenetic analysis and can highlight homologous features between sequences. Alignments highlight mutation events such as point mutations, insertion mutations and deletion mutations, and alignments are used to assess sequence conservation and infer the presence and activity of protein domains, tertiary structures, secondary structures, and individual amino acids or nucleotides.
In bioinformatics, the root mean square deviation of atomic positions, or simply root mean square deviation (RMSD), is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed molecules. In the study of globular protein conformations, one customarily measures the similarity in three-dimensional structure by the RMSD of the Cα atomic coordinates after optimal rigid body superposition.
UCSF Chimera is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use.
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "target" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein. Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of a sequence alignment that maps residues in the query sequence to residues in the template sequence. It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure.
The residual dipolar coupling between two spins in a molecule occurs if the molecules in solution exhibit a partial alignment leading to an incomplete averaging of spatially anisotropic dipolar couplings.
Band offset describes the relative alignment of the energy bands at a semiconductor heterojunction.
Large-screen television technology developed rapidly in the late 1990s and 2000s. Prior to the development of thin-screen technologies, rear-projection television was standard for larger displays, and jumbotron, a non-projection video display technology, was used at stadiums and concerts. Various thin-screen technologies are being developed, but only liquid crystal display (LCD), plasma display (PDP) and Digital Light Processing (DLP) have been publicly released. Recent technologies like organic light-emitting diode (OLED) as well as not-yet-released technologies like surface-conduction electron-emitter display (SED) or field-emission display (FED) are in development to supersede earlier flat-screen technologies in picture quality.
A blue phase mode LCD is a liquid crystal display (LCD) technology that uses highly twisted cholesteric phases in a blue phase. It was first proposed in 2007 to obtain a better display of moving images with, for example, frame rates of 100–120 Hz to improve the temporal response of LCDs. This operational mode for LCDs also does not require anisotropic alignment layers and thus theoretically simplifies the LCD manufacturing process.
Linear dichroism (LD) or diattenuation is the difference between absorption of light polarized parallel and polarized perpendicular to an orientation axis. It is the property of a material whose transmittance depends on the orientation of linearly polarized light incident upon it. As a technique, it is primarily used to study the functionality and structure of molecules. LD measurements are based on the interaction between matter and light and thus are a form of electromagnetic spectroscopy.
Biological data visualization is a branch of bioinformatics concerned with the application of computer graphics, scientific visualization, and information visualization to different areas of the life sciences. This includes visualization of sequences, genomes, alignments, phylogenies, macromolecular structures, systems biology, microscopy, and magnetic resonance imaging data. Software tools used for visualizing biological data range from simple, standalone programs to complex, integrated systems.
A protein superfamily is the largest grouping (clade) of proteins for which common ancestry can be inferred. Usually this common ancestry is inferred from structural alignment and mechanistic similarity, even if no sequence similarity is evident. Sequence homology can then be deduced even if not apparent. Superfamilies typically contain several protein families which show sequence similarity within each family. The term protein clan is commonly used for protease and glycosyl hydrolases superfamilies based on the MEROPS and CAZy classification systems.
Discontinuous aligned composites are a recent type of technical composite materials. This type of composite is neither random nor unidirectional, although it shares some characteristics with both. Discontinuous aligned composites are made of discontinuous fibers, just like random mat composites and a have preferential orientation closer to that of unidirectional composites.
