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.
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.
Goldstone bosonIn particle and condensed matter physics, Goldstone bosons or Nambu–Goldstone bosons (NGBs) are bosons that appear necessarily in models exhibiting spontaneous breakdown of continuous symmetries. They were discovered by Yoichiro Nambu in particle physics within the context of the BCS superconductivity mechanism, and subsequently elucidated by Jeffrey Goldstone, and systematically generalized in the context of quantum field theory. In condensed matter physics such bosons are quasiparticles and are known as Anderson–Bogoliubov modes.
Spontaneous symmetry breakingSpontaneous symmetry breaking is a spontaneous process of symmetry breaking, by which a physical system in a symmetric state spontaneously ends up in an asymmetric state. In particular, it can describe systems where the equations of motion or the Lagrangian obey symmetries, but the lowest-energy vacuum solutions do not exhibit that same symmetry. When the system goes to one of those vacuum solutions, the symmetry is broken for perturbations around that vacuum even though the entire Lagrangian retains that symmetry.
Symmetry breakingIn physics, symmetry breaking is a phenomenon where a disordered but symmetric state collapses into an ordered, but less symmetric state. This collapse is often one of many possible bifurcations that a particle can take as it approaches a lower energy state. Due to the many possibilities, an observer may assume the result of the collapse to be arbitrary. This phenomenon is fundamental to quantum field theory (QFT), and further, contemporary understandings of physics.
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.
Symmetry (physics)In physics, a symmetry of a physical system is a physical or mathematical feature of the system (observed or intrinsic) that is preserved or remains unchanged under some transformation. A family of particular transformations may be continuous (such as rotation of a circle) or discrete (e.g., reflection of a bilaterally symmetric figure, or rotation of a regular polygon). Continuous and discrete transformations give rise to corresponding types of symmetries.
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.
Symmetry in quantum mechanicsSymmetries in quantum mechanics describe features of spacetime and particles which are unchanged under some transformation, in the context of quantum mechanics, relativistic quantum mechanics and quantum field theory, and with applications in the mathematical formulation of the standard model and condensed matter physics. In general, symmetry in physics, invariance, and conservation laws, are fundamentally important constraints for formulating physical theories and models.
Time translation symmetryTime translation symmetry or temporal translation symmetry (TTS) is a mathematical transformation in physics that moves the times of events through a common interval. Time translation symmetry is the law that the laws of physics are unchanged (i.e. invariant) under such a transformation. Time translation symmetry is a rigorous way to formulate the idea that the laws of physics are the same throughout history. Time translation symmetry is closely connected, via the Noether theorem, to conservation of energy.
T-symmetryT-symmetry or time reversal symmetry is the theoretical symmetry of physical laws under the transformation of time reversal, Since the second law of thermodynamics states that entropy increases as time flows toward the future, in general, the macroscopic universe does not show symmetry under time reversal. In other words, time is said to be non-symmetric, or asymmetric, except for special equilibrium states when the second law of thermodynamics predicts the time symmetry to hold.
Magnetic coreA magnetic core is a piece of magnetic material with a high magnetic permeability used to confine and guide magnetic fields in electrical, electromechanical and magnetic devices such as electromagnets, transformers, electric motors, generators, inductors, magnetic recording heads, and magnetic assemblies. It is made of ferromagnetic metal such as iron, or ferrimagnetic compounds such as ferrites. The high permeability, relative to the surrounding air, causes the magnetic field lines to be concentrated in the core material.
Van der Waals forceIn molecular physics, the van der Waals force is a distance-dependent interaction between atoms or molecules. Unlike ionic or covalent bonds, these attractions do not result from a chemical electronic bond; they are comparatively weak and therefore more susceptible to disturbance. The van der Waals force quickly vanishes at longer distances between interacting molecules. Named after Dutch physicist Johannes Diderik van der Waals, the van der Waals force plays a fundamental role in fields as diverse as supramolecular chemistry, structural biology, polymer science, nanotechnology, surface science, and condensed matter physics.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Condensed matter physicsCondensed matter physics is the field of physics that deals with the macroscopic and microscopic physical properties of matter, especially the solid and liquid phases which arise from electromagnetic forces between atoms. More generally, the subject deals with condensed phases of matter: systems of many constituents with strong interactions among them. More exotic condensed phases include the superconducting phase exhibited by certain materials at extremely low cryogenic temperature, the ferromagnetic and antiferromagnetic phases of spins on crystal lattices of atoms, and the Bose–Einstein condensate found in ultracold atomic systems.
Intermolecular forceAn intermolecular force (IMF) (or secondary force) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules.
Magnetic circuitA magnetic circuit is made up of one or more closed loop paths containing a magnetic flux. The flux is usually generated by permanent magnets or electromagnets and confined to the path by magnetic cores consisting of ferromagnetic materials like iron, although there may be air gaps or other materials in the path. Magnetic circuits are employed to efficiently channel magnetic fields in many devices such as electric motors, generators, transformers, relays, lifting electromagnets, SQUIDs, galvanometers, and magnetic recording heads.
