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.
Neutron scatteringNeutron scattering, the irregular dispersal of free neutrons by matter, can refer to either the naturally occurring physical process itself or to the man-made experimental techniques that use the natural process for investigating materials. The natural/physical phenomenon is of elemental importance in nuclear engineering and the nuclear sciences. Regarding the experimental technique, understanding and manipulating neutron scattering is fundamental to the applications used in crystallography, physics, physical chemistry, biophysics, and materials research.
Molecular machineMolecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes.
Molecular motorMolecular motors are natural (biological) or artificial molecular machines that are the essential agents of movement in living organisms. In general terms, a motor is a device that consumes energy in one form and converts it into motion or mechanical work; for example, many protein-based molecular motors harness the chemical free energy released by the hydrolysis of ATP in order to perform mechanical work. In terms of energetic efficiency, this type of motor can be superior to currently available man-made motors.
Neutron spin echoNeutron spin echo spectroscopy is an inelastic neutron scattering technique invented by Ferenc Mezei in the 1970s, and developed in collaboration with John Hayter. In recognition of his work and in other areas, Mezei was awarded the first Walter Haelg Prize in 1999. In magnetic resonance, a spin echo is the refocusing of spin magnetisation by a pulse of resonant electromagnetic radiation. The spin echo spectrometer possesses an extremely high energy resolution (roughly one part in 100,000).
Protein–protein interactionProtein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.
Molecular propellerMolecular propeller is a molecule that can propel fluids when rotated, due to its special shape that is designed in analogy to macroscopic propellers: it has several molecular-scale blades attached at a certain pitch angle around the circumference of a shaft, aligned along the rotational axis. The molecular propellers designed in the group of Prof. Petr Král from the University of Illinois at Chicago have their blades formed by planar aromatic molecules and the shaft is a carbon nanotube.
Deep inelastic scatteringIn particle physics, deep inelastic scattering is the name given to a process used to probe the insides of hadrons (particularly the baryons, such as protons and neutrons), using electrons, muons and neutrinos. It was first attempted in the 1960s and 1970s and provided the first convincing evidence of the reality of quarks, which up until that point had been considered by many to be a purely mathematical phenomenon. It is an extension of Rutherford scattering to much higher energies of the scattering particle and thus to much finer resolution of the components of the nuclei.
Molecular physicsMolecular physics is the study of the physical properties of molecules and molecular dynamics. The field overlaps significantly with physical chemistry, chemical physics, and quantum chemistry. It is often considered as a sub-field of atomic, molecular, and optical physics. Research groups studying molecular physics are typically designated as one of these other fields. Molecular physics addresses phenomena due to both molecular structure and individual atomic processes within molecules.
ScatteringScattering is a term used in physics to describe a wide range of physical processes where moving particles or radiation of some form, such as light or sound, are forced to deviate from a straight trajectory by localized non-uniformities (including particles and radiation) in the medium through which they pass. In conventional use, this also includes deviation of reflected radiation from the angle predicted by the law of reflection.
Ab initio quantum chemistry methodsAb initio quantum chemistry methods are computational chemistry methods based on quantum chemistry. The term ab initio was first used in quantum chemistry by Robert Parr and coworkers, including David Craig in a semiempirical study on the excited states of benzene. The background is described by Parr. Ab initio means "from first principles" or "from the beginning", implying that the only inputs into an ab initio calculation are physical constants.
Non-covalent interactionIn chemistry, a non-covalent interaction differs from a covalent bond in that it does not involve the sharing of electrons, but rather involves more dispersed variations of electromagnetic interactions between molecules or within a molecule. The chemical energy released in the formation of non-covalent interactions is typically on the order of 1–5 kcal/mol (1000–5000 calories per 6.02 molecules). Non-covalent interactions can be classified into different categories, such as electrostatic, π-effects, van der Waals forces, and hydrophobic effects.
Cation–π interactionCation–π interaction is a noncovalent molecular interaction between the face of an electron-rich π system (e.g. benzene, ethylene, acetylene) and an adjacent cation (e.g. Li+, Na+). This interaction is an example of noncovalent bonding between a monopole (cation) and a quadrupole (π system). Bonding energies are significant, with solution-phase values falling within the same order of magnitude as hydrogen bonds and salt bridges.
Binding siteIn biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may include other proteins (resulting in a protein-protein interaction), enzyme substrates, second messengers, hormones, or allosteric modulators. The binding event is often, but not always, accompanied by a conformational change that alters the protein's function.
Neutron diffractionNeutron diffraction or elastic neutron scattering is the application of neutron scattering to the determination of the atomic and/or magnetic structure of a material. A sample to be examined is placed in a beam of thermal or cold neutrons to obtain a diffraction pattern that provides information of the structure of the material. The technique is similar to X-ray diffraction but due to their different scattering properties, neutrons and X-rays provide complementary information: X-Rays are suited for superficial analysis, strong x-rays from synchrotron radiation are suited for shallow depths or thin specimens, while neutrons having high penetration depth are suited for bulk samples.
BackscatterIn physics, backscatter (or backscattering) is the reflection of waves, particles, or signals back to the direction from which they came. It is usually a diffuse reflection due to scattering, as opposed to specular reflection as from a mirror, although specular backscattering can occur at normal incidence with a surface. Backscattering has important applications in astronomy, photography, and medical ultrasonography. The opposite effect is forward scatter, e.g. when a translucent material like a cloud diffuses sunlight, giving soft light.
Perturbation theoryIn mathematics and applied mathematics, perturbation theory comprises methods for finding an approximate solution to a problem, by starting from the exact solution of a related, simpler problem. A critical feature of the technique is a middle step that breaks the problem into "solvable" and "perturbative" parts. In perturbation theory, the solution is expressed as a power series in a small parameter . The first term is the known solution to the solvable problem. Successive terms in the series at higher powers of usually become smaller.
Atomic, molecular, and optical physicsAtomic, molecular, and optical physics (AMO) is the study of matter–matter and light–matter interactions, at the scale of one or a few atoms and energy scales around several electron volts. The three areas are closely interrelated. AMO theory includes classical, semi-classical and quantum treatments. Typically, the theory and applications of emission, absorption, scattering of electromagnetic radiation (light) from excited atoms and molecules, analysis of spectroscopy, generation of lasers and masers, and the optical properties of matter in general, fall into these categories.
Electron scatteringElectron scattering occurs when electrons are displaced from their original trajectory. This is due to the electrostatic forces within matter interaction or, if an external magnetic field is present, the electron may be deflected by the Lorentz force. This scattering typically happens with solids such as metals, semiconductors and insulators; and is a limiting factor in integrated circuits and transistors.
Perturbation theory (quantum mechanics)In quantum mechanics, perturbation theory is a set of approximation schemes directly related to mathematical perturbation for describing a complicated quantum system in terms of a simpler one. The idea is to start with a simple system for which a mathematical solution is known, and add an additional "perturbing" Hamiltonian representing a weak disturbance to the system. If the disturbance is not too large, the various physical quantities associated with the perturbed system (e.g.
