Transmission electron microscopyTransmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a grid. An image is formed from the interaction of the electrons with the sample as the beam is transmitted through the specimen. The image is then magnified and focused onto an imaging device, such as a fluorescent screen, a layer of photographic film, or a sensor such as a scintillator attached to a charge-coupled device.
Electron microscopeAn electron microscope is a microscope that uses a beam of electrons as a source of illumination. They use electron optics that are analogous to the glass lenses of an optical light microscope. As the wavelength of an electron can be up to 100,000 times shorter than that of visible light, electron microscopes have a higher resolution of about 0.1 nm, which compares to about 200 nm for light microscopes.
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.
Electron diffractionElectron diffraction refers to changes in the direction of electron beams due to interactions with atoms. Close to the atoms the changes are described as Fresnel diffraction; far away they are called Fraunhofer diffraction. The resulting map of the directions of the electrons far from the sample (Fraunhofer diffraction) is called a diffraction pattern, see for instance Figure 1. These patterns are similar to x-ray and neutron diffraction patterns, and are used to study the atomic structure of gases, liquids, surfaces and bulk solids.
Structural biologyStructural biology is a field that is many centuries old which, as defined by the Journal of Structural Biology, deals with structural analysis of living material (formed, composed of, and/or maintained and refined by living cells) at every level of organization. Early structural biologists throughout the 19th and early 20th centuries were primarily only able to study structures to the limit of the naked eye's visual acuity and through magnifying glasses and light microscopes.
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.
ElectronThe electron (_Electron or _beta-) is a subatomic particle with a negative one elementary electric charge. Electrons belong to the first generation of the lepton particle family, and are generally thought to be elementary particles because they have no known components or substructure. The electron's mass is approximately 1/1836 that of the proton. Quantum mechanical properties of the electron include an intrinsic angular momentum (spin) of a half-integer value, expressed in units of the reduced Planck constant, ħ.
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.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Scanning electron microscopeA scanning electron microscope (SEM) is a type of electron microscope that produces images of a sample by scanning the surface with a focused beam of electrons. The electrons interact with atoms in the sample, producing various signals that contain information about the surface topography and composition of the sample. The electron beam is scanned in a raster scan pattern, and the position of the beam is combined with the intensity of the detected signal to produce an image.
Ultrafast laser spectroscopyUltrafast laser spectroscopy is a spectroscopic technique that uses ultrashort pulse lasers for the study of dynamics on extremely short time scales (attoseconds to nanoseconds). Different methods are used to examine the dynamics of charge carriers, atoms, and molecules. Many different procedures have been developed spanning different time scales and photon energy ranges; some common methods are listed below. Dynamics on the as to fs time scale are in general too fast to be measured electronically.
Ultrashort pulseIn optics, an ultrashort pulse, also known as an ultrafast event, is an electromagnetic pulse whose time duration is of the order of a picosecond (10−12 second) or less. Such pulses have a broadband optical spectrum, and can be created by mode-locked oscillators. Amplification of ultrashort pulses almost always requires the technique of chirped pulse amplification, in order to avoid damage to the gain medium of the amplifier. They are characterized by a high peak intensity (or more correctly, irradiance) that usually leads to nonlinear interactions in various materials, including air.
Valence electronIn chemistry and physics, a valence electron is an electron in the outer shell associated with an atom, and that can participate in the formation of a chemical bond if the outer shell is not closed. In a single covalent bond, a shared pair forms with both atoms in the bond each contributing one valence electron. The presence of valence electrons can determine the element's chemical properties, such as its valence—whether it may bond with other elements and, if so, how readily and with how many.
Coherence (physics)In physics, coherence expresses the potential for two waves to interfere. Two monochromatic beams from a single source always interfere. Physical sources are not strictly monochromatic: they may be partly coherent. Beams from different sources are mutually incoherent. When interfering, two waves add together to create a wave of greater amplitude than either one (constructive interference) or subtract from each other to create a wave of minima which may be zero (destructive interference), depending on their relative phase.
DiffractionDiffraction is the interference or bending of waves around the corners of an obstacle or through an aperture into the region of geometrical shadow of the obstacle/aperture. The diffracting object or aperture effectively becomes a secondary source of the propagating wave. Italian scientist Francesco Maria Grimaldi coined the word diffraction and was the first to record accurate observations of the phenomenon in 1660.
Electron countingIn chemistry, electron counting is a formalism for assigning a number of valence electrons to individual atoms in a molecule. It is used for classifying compounds and for explaining or predicting their electronic structure and bonding. Many rules in chemistry rely on electron-counting: Octet rule is used with Lewis structures for main group elements, especially the lighter ones such as carbon, nitrogen, and oxygen, 18-electron rule in inorganic chemistry and organometallic chemistry of transition metals, Hückel's rule for the π-electrons of aromatic compounds, Polyhedral skeletal electron pair theory for polyhedral cluster compounds, including transition metals and main group elements and mixtures thereof, such as boranes.
Delocalized electronIn chemistry, delocalized electrons are electrons in a molecule, ion or solid metal that are not associated with a single atom or a covalent bond. The term delocalization is general and can have slightly different meanings in different fields: In organic chemistry, it refers to resonance in conjugated systems and aromatic compounds. In solid-state physics, it refers to free electrons that facilitate electrical conduction. In quantum chemistry, it refers to molecular orbital electrons that have extended over several adjacent atoms.
Nonlinear opticsNonlinear optics (NLO) is the branch of optics that describes the behaviour of light in nonlinear media, that is, media in which the polarization density P responds non-linearly to the electric field E of the light. The non-linearity is typically observed only at very high light intensities (when the electric field of the light is >108 V/m and thus comparable to the atomic electric field of ~1011 V/m) such as those provided by lasers. Above the Schwinger limit, the vacuum itself is expected to become nonlinear.
Diffraction-limited systemIn optics, any optical instrument or system a microscope, telescope, or camera has a principal limit to its resolution due to the physics of diffraction. An optical instrument is said to be diffraction-limited if it has reached this limit of resolution performance. Other factors may affect an optical system's performance, such as lens imperfections or aberrations, but these are caused by errors in the manufacture or calculation of a lens, whereas the diffraction limit is the maximum resolution possible for a theoretically perfect, or ideal, optical system.
Electron-beam lithographyElectron-beam lithography (often abbreviated as e-beam lithography, EBL) is the practice of scanning a focused beam of electrons to draw custom shapes on a surface covered with an electron-sensitive film called a resist (exposing). The electron beam changes the solubility of the resist, enabling selective removal of either the exposed or non-exposed regions of the resist by immersing it in a solvent (developing). The purpose, as with photolithography, is to create very small structures in the resist that can subsequently be transferred to the substrate material, often by etching.
