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.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
AtomAn atom is a particle that consists of a nucleus of protons and neutrons surrounded by a cloud of electrons. The atom is the basic particle of the chemical elements, and the chemical elements are distinguished from each other by the number of protons that are in their atoms. For example, any atom that contains 11 protons is sodium, and any atom that contains 29 protons is copper. The number of neutrons defines the isotope of the element. Atoms are extremely small, typically around 100 picometers across.
Interatomic potentialInteratomic potentials are mathematical functions to calculate the potential energy of a system of atoms with given positions in space. Interatomic potentials are widely used as the physical basis of molecular mechanics and molecular dynamics simulations in computational chemistry, computational physics and computational materials science to explain and predict materials properties.
Hydrogen-like atomA hydrogen-like atom (or hydrogenic atom) is any atom or ion with a single valence electron. These atoms are isoelectronic with hydrogen. Examples of hydrogen-like atoms include, but are not limited to, hydrogen itself, all alkali metals such as Rb and Cs, singly ionized alkaline earth metals such as Ca+ and Sr+ and other ions such as He+, Li2+, and Be3+ and isotopes of any of the above. A hydrogen-like atom includes a positively charged core consisting of the atomic nucleus and any core electrons as well as a single valence electron.
Rydberg atomA Rydberg atom is an excited atom with one or more electrons that have a very high principal quantum number, n. The higher the value of n, the farther the electron is from the nucleus, on average. Rydberg atoms have a number of peculiar properties including an exaggerated response to electric and magnetic fields, long decay periods and electron wavefunctions that approximate, under some conditions, classical orbits of electrons about the nuclei.
Ionization energyIn physics and chemistry, ionization energy (IE) (American English spelling), ionisation energy (British English spelling) is the minimum energy required to remove the most loosely bound electron of an isolated gaseous atom, positive ion, or molecule. The first ionization energy is quantitatively expressed as X(g) + energy ⟶ X+(g) + e− where X is any atom or molecule, X+ is the resultant ion when the original atom was stripped of a single electron, and e− is the removed electron.
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Fragmentation (computing)In computer storage, fragmentation is a phenomenon in which storage space, main storage or secondary storage, is used inefficiently, reducing capacity or performance and often both. The exact consequences of fragmentation depend on the specific system of storage allocation in use and the particular form of fragmentation. In many cases, fragmentation leads to storage space being "wasted", and in that case the term also refers to the wasted space itself.
Cluster decayCluster decay, also named heavy particle radioactivity, heavy ion radioactivity or heavy cluster decay, is a rare type of nuclear decay in which an atomic nucleus emits a small "cluster" of neutrons and protons, more than in an alpha particle, but less than a typical binary fission fragment. Ternary fission into three fragments also produces products in the cluster size. The loss of protons from the parent nucleus changes it to the nucleus of a different element, the daughter, with a mass number Ad = A − Ae and atomic number Zd = Z − Ze, where Ae = Ne + Ze.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Energy levelA quantum mechanical system or particle that is bound—that is, confined spatially—can only take on certain discrete values of energy, called energy levels. This contrasts with classical particles, which can have any amount of energy. The term is commonly used for the energy levels of the electrons in atoms, ions, or molecules, which are bound by the electric field of the nucleus, but can also refer to energy levels of nuclei or vibrational or rotational energy levels in molecules.
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.
Ion implantationIon implantation is a low-temperature process by which ions of one element are accelerated into a solid target, thereby changing the physical, chemical, or electrical properties of the target. Ion implantation is used in semiconductor device fabrication and in metal finishing, as well as in materials science research. The ions can alter the elemental composition of the target (if the ions differ in composition from the target) if they stop and remain in the target.
Bohr modelIn atomic physics, the Bohr model or Rutherford–Bohr model of the atom, presented by Niels Bohr and Ernest Rutherford in 1913, consists of a small, dense nucleus surrounded by orbiting electrons. It is analogous to the structure of the Solar System, but with attraction provided by electrostatic force rather than gravity, and with the electron energies quantized (assuming only discrete values).
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.
Impact eventAn impact event is a collision between astronomical objects causing measurable effects. Impact events have physical consequences and have been found to regularly occur in planetary systems, though the most frequent involve asteroids, comets or meteoroids and have minimal effect. When large objects impact terrestrial planets such as the Earth, there can be significant physical and biospheric consequences, though atmospheres mitigate many surface impacts through atmospheric entry.
File system fragmentationIn computing, file system fragmentation, sometimes called file system aging, is the tendency of a to lay out the contents of non-continuously to allow in-place modification of their contents. It is a special case of data fragmentation. File system fragmentation negatively impacts seek time in spinning storage media, which is known to hinder throughput. Fragmentation can be remedied by re-organizing files and free space back into contiguous areas, a process called defragmentation.
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.
NanoclusterNanoclusters are atomically precise, crystalline materials most often existing on the 0-2 nanometer scale. They are often considered kinetically stable intermediates that form during the synthesis of comparatively larger materials such as semiconductor and metallic nanocrystals. The majority of research conducted to study nanoclusters has focused on characterizing their crystal structures and understanding their role in the nucleation and growth mechanisms of larger materials.
