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.
Gibbs free energyIn thermodynamics, the Gibbs free energy (or Gibbs energy as the recommended name; symbol ) is a thermodynamic potential that can be used to calculate the maximum amount of work, other than pressure-volume work, that may be performed by a thermodynamically closed system at constant temperature and pressure. It also provides a necessary condition for processes such as chemical reactions that may occur under these conditions. The Gibbs free energy is expressed as where p is pressure, T is the temperature, U is the internal energy, V is volume, H is the enthalpy, and S is the entropy.
Work (thermodynamics)Thermodynamic work is one of the principal processes by which a thermodynamic system can interact with its surroundings and exchange energy. This exchange results in externally measurable macroscopic forces on the system's surroundings, which can cause mechanical work, to lift a weight, for example, or cause changes in electromagnetic, or gravitational variables. The surroundings also can perform work on a thermodynamic system, which is measured by an opposite sign convention.
Activation energyIn chemistry and physics, activation energy is the minimum amount of energy that must be provided for compounds to result in a chemical reaction. The activation energy (Ea) of a reaction is measured in joules per mole (J/mol), kilojoules per mole (kJ/mol) or kilocalories per mole (kcal/mol). Activation energy can be thought of as the magnitude of the potential barrier (sometimes called the energy barrier) separating minima of the potential energy surface pertaining to the initial and final thermodynamic state.
Helmholtz free energyIn thermodynamics, the Helmholtz free energy (or Helmholtz energy) is a thermodynamic potential that measures the useful work obtainable from a closed thermodynamic system at a constant temperature (isothermal). The change in the Helmholtz energy during a process is equal to the maximum amount of work that the system can perform in a thermodynamic process in which temperature is held constant. At constant temperature, the Helmholtz free energy is minimized at equilibrium.
Ensemble (mathematical physics)In physics, specifically statistical mechanics, an ensemble (also statistical ensemble) is an idealization consisting of a large number of virtual copies (sometimes infinitely many) of a system, considered all at once, each of which represents a possible state that the real system might be in. In other words, a statistical ensemble is a set of systems of particles used in statistical mechanics to describe a single system. The concept of an ensemble was introduced by J. Willard Gibbs in 1902.
Isochoric processIn thermodynamics, an isochoric process, also called a constant-volume process, an isovolumetric process, or an isometric process, is a thermodynamic process during which the volume of the closed system undergoing such a process remains constant. An isochoric process is exemplified by the heating or the cooling of the contents of a sealed, inelastic container: The thermodynamic process is the addition or removal of heat; the isolation of the contents of the container establishes the closed system; and the inability of the container to deform imposes the constant-volume condition.
Surface energyIn surface science, surface free energy (also interfacial free energy or surface energy) quantifies the disruption of intermolecular bonds that occurs when a surface is created. In solid-state physics, surfaces must be intrinsically less energetically favorable than the bulk of the material (the atoms on the surface have more energy compared with the atoms in the bulk), otherwise there would be a driving force for surfaces to be created, removing the bulk of the material (see sublimation).
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.
State functionIn the thermodynamics of equilibrium, a state function, function of state, or point function for a thermodynamic system is a mathematical function relating several state variables or state quantities (that describe equilibrium states of a system) that depend only on the current equilibrium thermodynamic state of the system (e.g. gas, liquid, solid, crystal, or emulsion), not the path which the system has taken to reach that state. A state function describes equilibrium states of a system, thus also describing the type of system.
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.
Thermodynamic free energyIn thermodynamics, the thermodynamic free energy is one of the state functions of a thermodynamic system (the others being internal energy, enthalpy, entropy, etc.). The change in the free energy is the maximum amount of work that the system can perform in a process at constant temperature, and its sign indicates whether the process is thermodynamically favorable or forbidden. Since free energy usually contains potential energy, it is not absolute but depends on the choice of a zero point.
Generalized coordinatesIn analytical mechanics, generalized coordinates are a set of parameters used to represent the state of a system in a configuration space. These parameters must uniquely define the configuration of the system relative to a reference state. The generalized velocities are the time derivatives of the generalized coordinates of the system. The adjective "generalized" distinguishes these parameters from the traditional use of the term "coordinate" to refer to Cartesian coordinates.
Potential energy surfaceA potential energy surface (PES) describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates; if there is only one coordinate, the surface is called a potential energy curve or . An example is the Morse/Long-range potential. It is helpful to use the analogy of a landscape: for a system with two degrees of freedom (e.g.
Thermodynamic temperatureThermodynamic temperature is a quantity defined in thermodynamics as distinct from kinetic theory or statistical mechanics. Historically, thermodynamic temperature was defined by Lord Kelvin in terms of a macroscopic relation between thermodynamic work and heat transfer as defined in thermodynamics, but the kelvin was redefined by international agreement in 2019 in terms of phenomena that are now understood as manifestations of the kinetic energy of free motion of microscopic particles such as atoms, molecules, and electrons.
Molecular orbital theoryIn chemistry, molecular orbital theory (MO theory or MOT) is a method for describing the electronic structure of molecules using quantum mechanics. It was proposed early in the 20th century. In molecular orbital theory, electrons in a molecule are not assigned to individual chemical bonds between atoms, but are treated as moving under the influence of the atomic nuclei in the whole molecule. Quantum mechanics describes the spatial and energetic properties of electrons as molecular orbitals that surround two or more atoms in a molecule and contain valence electrons between atoms.
Surface tensionSurface tension is the tendency of liquid surfaces at rest to shrink into the minimum surface area possible. Surface tension is what allows objects with a higher density than water such as razor blades and insects (e.g. water striders) to float on a water surface without becoming even partly submerged. At liquid–air interfaces, surface tension results from the greater attraction of liquid molecules to each other (due to cohesion) than to the molecules in the air (due to adhesion). There are two primary mechanisms in play.
Molecular geometryMolecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that determine the position of each atom. Molecular geometry influences several properties of a substance including its reactivity, polarity, phase of matter, color, magnetism and biological activity. The angles between bonds that an atom forms depend only weakly on the rest of molecule, i.
Multi-configurational self-consistent fieldMulti-configurational self-consistent field (MCSCF) is a method in quantum chemistry used to generate qualitatively correct reference states of molecules in cases where Hartree–Fock and density functional theory are not adequate (e.g., for molecular ground states which are quasi-degenerate with low-lying excited states or in bond-breaking situations). It uses a linear combination of configuration state functions (CSF), or configuration determinants, to approximate the exact electronic wavefunction of an atom or molecule.
Mollusc shellThe mollusc (or mollusk) shell is typically a calcareous exoskeleton which encloses, supports and protects the soft parts of an animal in the phylum Mollusca, which includes snails, clams, tusk shells, and several other classes. Not all shelled molluscs live in the sea; many live on the land and in freshwater. The ancestral mollusc is thought to have had a shell, but this has subsequently been lost or reduced on some families, such as the squid, octopus, and some smaller groups such as the caudofoveata and solenogastres.
