Surface plasmon resonanceSurface plasmon resonance (SPR) is a phenomenon that occurs where electrons in a thin metal sheet become excited by light that is directed to the sheet with a particular angle of incidence, and then travel parallel to the sheet. Assuming a constant light source wavelength and that the metal sheet is thin, the angle of incidence that triggers SPR is related to the refractive index of the material and even a small change in the refractive index will cause SPR to not be observed.
Protein secondary structureProtein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone.
Nucleic acid secondary structureNucleic acid secondary structure is the basepairing interactions within a single nucleic acid polymer or between two polymers. It can be represented as a list of bases which are paired in a nucleic acid molecule. The secondary structures of biological DNAs and RNAs tend to be different: biological DNA mostly exists as fully base paired double helices, while biological RNA is single stranded and often forms complex and intricate base-pairing interactions due to its increased ability to form hydrogen bonds stemming from the extra hydroxyl group in the ribose sugar.
Biomolecular structureBiomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary.
Surface plasmonSurface plasmons (SPs) are coherent delocalized electron oscillations that exist at the interface between any two materials where the real part of the dielectric function changes sign across the interface (e.g. a metal-dielectric interface, such as a metal sheet in air). SPs have lower energy than bulk (or volume) plasmons which quantise the longitudinal electron oscillations about positive ion cores within the bulk of an electron gas (or plasma). The charge motion in a surface plasmon always creates electromagnetic fields outside (as well as inside) the metal.
Self-assemblySelf-assembly is a process in which a disordered system of pre-existing components forms an organized structure or pattern as a consequence of specific, local interactions among the components themselves, without external direction. When the constitutive components are molecules, the process is termed molecular self-assembly. Self-assembly can be classified as either static or dynamic. In static self-assembly, the ordered state forms as a system approaches equilibrium, reducing its free energy.
Localized surface plasmonA localized surface plasmon (LSP) is the result of the confinement of a surface plasmon in a nanoparticle of size comparable to or smaller than the wavelength of light used to excite the plasmon. When a small spherical metallic nanoparticle is irradiated by light, the oscillating electric field causes the conduction electrons to oscillate coherently. When the electron cloud is displaced relative to its original position, a restoring force arises from Coulombic attraction between electrons and nuclei.
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.
Multi-parametric surface plasmon resonanceMulti-parametric surface plasmon resonance (MP-SPR) is based on surface plasmon resonance (SPR), an established real-time label-free method for biomolecular interaction analysis, but it uses a different optical setup, a goniometric SPR configuration. While MP-SPR provides same kinetic information as SPR (equilibrium constant, dissociation constant, association constant), it provides also structural information (refractive index, layer thickness). Hence, MP-SPR measures both surface interactions and nanolayer properties.
Surface plasmon polaritonSurface plasmon polaritons (SPPs) are electromagnetic waves that travel along a metal–dielectric or metal–air interface, practically in the infrared or visible-frequency. The term "surface plasmon polariton" explains that the wave involves both charge motion in the metal ("surface plasmon") and electromagnetic waves in the air or dielectric ("polariton"). They are a type of surface wave, guided along the interface in much the same way that light can be guided by an optical fiber.
