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.
Quantum mechanicsQuantum mechanics is a fundamental theory in physics that provides a description of the physical properties of nature at the scale of atoms and subatomic particles. It is the foundation of all quantum physics including quantum chemistry, quantum field theory, quantum technology, and quantum information science. Classical physics, the collection of theories that existed before the advent of quantum mechanics, describes many aspects of nature at an ordinary (macroscopic) scale, but is not sufficient for describing them at small (atomic and subatomic) scales.
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.
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.
Interpretations of quantum mechanicsAn interpretation of quantum mechanics is an attempt to explain how the mathematical theory of quantum mechanics might correspond to experienced reality. Although quantum mechanics has held up to rigorous and extremely precise tests in an extraordinarily broad range of experiments, there exist a number of contending schools of thought over their interpretation. These views on interpretation differ on such fundamental questions as whether quantum mechanics is deterministic or stochastic, local or non-local, which elements of quantum mechanics can be considered real, and what the nature of measurement is, among other matters.
Mathematical formulation of quantum mechanicsThe mathematical formulations of quantum mechanics are those mathematical formalisms that permit a rigorous description of quantum mechanics. This mathematical formalism uses mainly a part of functional analysis, especially Hilbert spaces, which are a kind of linear space. Such are distinguished from mathematical formalisms for physics theories developed prior to the early 1900s by the use of abstract mathematical structures, such as infinite-dimensional Hilbert spaces (L2 space mainly), and operators on these spaces.
Nuclear magnetic resonance quantum computerNuclear magnetic resonance quantum computing (NMRQC) is one of the several proposed approaches for constructing a quantum computer, that uses the spin states of nuclei within molecules as qubits. The quantum states are probed through the nuclear magnetic resonances, allowing the system to be implemented as a variation of nuclear magnetic resonance spectroscopy. NMR differs from other implementations of quantum computers in that it uses an ensemble of systems, in this case molecules, rather than a single pure state.
Measurement in quantum mechanicsIn quantum physics, a measurement is the testing or manipulation of a physical system to yield a numerical result. A fundamental feature of quantum theory is that the predictions it makes are probabilistic. The procedure for finding a probability involves combining a quantum state, which mathematically describes a quantum system, with a mathematical representation of the measurement to be performed on that system. The formula for this calculation is known as the Born rule.
Quantum computingA quantum computer is a computer that exploits quantum mechanical phenomena. At small scales, physical matter exhibits properties of both particles and waves, and quantum computing leverages this behavior, specifically quantum superposition and entanglement, using specialized hardware that supports the preparation and manipulation of quantum states. Classical physics cannot explain the operation of these quantum devices, and a scalable quantum computer could perform some calculations exponentially faster than any modern "classical" computer.
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.
Molecular design softwareMolecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g
Relational quantum mechanicsRelational quantum mechanics (RQM) is an interpretation of quantum mechanics which treats the state of a quantum system as being observer-dependent, that is, the state is the relation between the observer and the system. This interpretation was first delineated by Carlo Rovelli in a 1994 preprint, and has since been expanded upon by a number of theorists. It is inspired by the key idea behind special relativity, that the details of an observation depend on the reference frame of the observer, and uses some ideas from Wheeler on quantum information.
Quantum chemistryQuantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions to physical and chemical properties of molecules, materials, and solutions at the atomic level. These calculations include systematically applied approximations intended to make calculations computationally feasible while still capturing as much information about important contributions to the computed wave functions as well as to observable properties such as structures, spectra, and thermodynamic properties.
Quantum tunnellingIn physics, quantum tunnelling, barrier penetration, or simply tunnelling is a quantum mechanical phenomenon in which an object such as an electron or atom passes through a potential energy barrier that, according to classical mechanics, the object does not have sufficient energy to enter or surmount. Tunneling is a consequence of the wave nature of matter, where the quantum wave function describes the state of a particle or other physical system, and wave equations such as the Schrödinger equation describe their behavior.
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.
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.
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.
Introduction to quantum mechanicsQuantum mechanics is the study of matter and its interactions with energy on the scale of atomic and subatomic particles. By contrast, classical physics explains matter and energy only on a scale familiar to human experience, including the behavior of astronomical bodies such as the moon. Classical physics is still used in much of modern science and technology. However, towards the end of the 19th century, scientists discovered phenomena in both the large (macro) and the small (micro) worlds that classical physics could not explain.
Water modelIn computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
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.
