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.
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.
Density functional theoryDensity-functional theory (DFT) is a computational quantum mechanical modelling method used in physics, chemistry and materials science to investigate the electronic structure (or nuclear structure) (principally the ground state) of many-body systems, in particular atoms, molecules, and the condensed phases. Using this theory, the properties of a many-electron system can be determined by using functionals, i.e. functions of another function. In the case of DFT, these are functionals of the spatially dependent electron density.
Dynamical systemIn mathematics, a dynamical system is a system in which a function describes the time dependence of a point in an ambient space, such as in a parametric curve. Examples include the mathematical models that describe the swinging of a clock pendulum, the flow of water in a pipe, the random motion of particles in the air, and the number of fish each springtime in a lake. The most general definition unifies several concepts in mathematics such as ordinary differential equations and ergodic theory by allowing different choices of the space and how time is measured.
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.
Dynamical systems theoryDynamical systems theory is an area of mathematics used to describe the behavior of complex dynamical systems, usually by employing differential equations or difference equations. When differential equations are employed, the theory is called continuous dynamical systems. From a physical point of view, continuous dynamical systems is a generalization of classical mechanics, a generalization where the equations of motion are postulated directly and are not constrained to be Euler–Lagrange equations of a least action principle.
SolidSolid is one of the four fundamental states of matter (the others being liquid, gas, and plasma). The molecules in a solid are closely packed together and contain the least amount of kinetic energy. A solid is characterized by structural rigidity (as in rigid bodies) and resistance to a force applied to the surface. Unlike a liquid, a solid object does not flow to take on the shape of its container, nor does it expand to fill the entire available volume like a gas.
Dynamical billiardsA dynamical billiard is a dynamical system in which a particle alternates between free motion (typically as a straight line) and specular reflections from a boundary. When the particle hits the boundary it reflects from it without loss of speed (i.e. elastic collisions). Billiards are Hamiltonian idealizations of the game of billiards, but where the region contained by the boundary can have shapes other than rectangular and even be multidimensional.
Amorphous solidIn condensed matter physics and materials science, an amorphous solid (or non-crystalline solid) is a solid that lacks the long-range order that is characteristic of a crystal. The terms "glass" and "glassy solid" are sometimes used synonymously with amorphous solid; however, these terms refer specifically to amorphous materials that undergo a glass transition. Examples of amorphous solids include glasses, metallic glasses, and certain types of plastics and polymers. The term comes from the Greek a ("without"), and morphé ("shape, form").
Electron densityElectron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either or . The density is determined, through definition, by the normalised -electron wavefunction which itself depends upon variables ( spatial and spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory.
Bulk cargoBulk cargo is commodity cargo that is transported unpackaged in large quantities. Bulk cargo refers to material in either liquid or granular, particulate form, as a mass of relatively small solids, such as petroleum/crude oil, grain, coal, or gravel. This cargo is usually dropped or poured, with a spout or shovel bucket, into a bulk carrier ship's hold, railroad car/railway wagon, or tanker truck/trailer/semi-trailer body. Smaller quantities can be boxed (or drummed) and palletised; cargo packaged in this manner is referred to as breakbulk cargo.
Bulk modulusThe bulk modulus ( or ) of a substance is a measure of the resistance of a substance to bulk compression. It is defined as the ratio of the infinitesimal pressure increase to the resulting relative decrease of the volume. Other moduli describe the material's response (strain) to other kinds of stress: the shear modulus describes the response to shear stress, and Young's modulus describes the response to normal (lengthwise stretching) stress. For a fluid, only the bulk modulus is meaningful.
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.
Measure-preserving dynamical systemIn mathematics, a measure-preserving dynamical system is an object of study in the abstract formulation of dynamical systems, and ergodic theory in particular. Measure-preserving systems obey the Poincaré recurrence theorem, and are a special case of conservative systems. They provide the formal, mathematical basis for a broad range of physical systems, and, in particular, many systems from classical mechanics (in particular, most non-dissipative systems) as well as systems in thermodynamic equilibrium.
Energy profile (chemistry)In theoretical chemistry, an energy profile is a theoretical representation of a chemical reaction or process as a single energetic pathway as the reactants are transformed into products. This pathway runs along the reaction coordinate, which is a parametric curve that follows the pathway of the reaction and indicates its progress; thus, energy profiles are also called reaction coordinate diagrams.
SimulationA simulation is the imitation of the operation of a real-world process or system over time. Simulations require the use of models; the model represents the key characteristics or behaviors of the selected system or process, whereas the simulation represents the evolution of the model over time. Often, computers are used to execute the simulation. Simulation is used in many contexts, such as simulation of technology for performance tuning or optimizing, safety engineering, testing, training, education, and video games.
Negative temperatureCertain systems can achieve negative thermodynamic temperature; that is, their temperature can be expressed as a negative quantity on the Kelvin or Rankine scales. This should be distinguished from temperatures expressed as negative numbers on non-thermodynamic Celsius or Fahrenheit scales, which are nevertheless higher than absolute zero. The absolute temperature (Kelvin) scale can be understood loosely as a measure of average kinetic energy. Usually, system temperatures are positive.
TemperatureTemperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied on various reference points and thermometric substances for definition. The most common scales are the Celsius scale with the unit symbol °C (formerly called centigrade), the Fahrenheit scale (°F), and the Kelvin scale (K), the latter being used predominantly for scientific purposes.
Bulk carrierA bulk carrier or bulker is a merchant ship specially designed to transport unpackaged bulk cargo—such as grain, coal, ore, steel coils, and cement—in its cargo holds. Since the first specialized bulk carrier was built in 1852, economic forces have led to increased size and sophistication of these ships. Today's bulk carriers are specially designed to maximize capacity, safety, efficiency, and durability. Today, bulk carriers make up 21 percent of the world's merchant fleets, and they range in size from single-hold mini-bulk carriers to mammoth ore ships able to carry 400,000 metric tons of deadweight (DWT).
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.
