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.
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.
Electric potentialThe electric potential (also called the electric field potential, potential drop, the electrostatic potential) is defined as the amount of work energy needed per unit of electric charge to move this charge from a reference point to the specific point in an electric field. More precisely, it is the energy per unit charge for a test charge that is so small that the disturbance of the field under consideration is negligible.
Molecular mechanicsMolecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Potassium channelPotassium channels are the most widely distributed type of ion channel found in virtually all organisms. They form potassium-selective pores that span cell membranes. Potassium channels are found in most cell types and control a wide variety of cell functions. Potassium channels function to conduct potassium ions down their electrochemical gradient, doing so both rapidly (up to the diffusion rate of K+ ions in bulk water) and selectively (excluding, most notably, sodium despite the sub-angstrom difference in ionic radius).
ElectrostaticsElectrostatics is a branch of physics that studies slow-moving or stationary electric charges. Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber, ἤλεκτρον (), was thus the source of the word 'electricity'. Electrostatic phenomena arise from the forces that electric charges exert on each other. Such forces are described by Coulomb's law.
Potential energyIn physics, potential energy is the energy held by an object because of its position relative to other objects, stresses within itself, its electric charge, or other factors. The term potential energy was introduced by the 19th-century Scottish engineer and physicist William Rankine, although it has links to the ancient Greek philosopher Aristotle's concept of potentiality. Common types of potential energy include the gravitational potential energy of an object, the elastic potential energy of an extended spring, and the electric potential energy of an electric charge in an electric field.
Ion channelIon channels are pore-forming membrane proteins that allow ions to pass through the channel pore. Their functions include establishing a resting membrane potential, shaping action potentials and other electrical signals by gating the flow of ions across the cell membrane, controlling the flow of ions across secretory and epithelial cells, and regulating cell volume. Ion channels are present in the membranes of all cells. Ion channels are one of the two classes of ionophoric proteins, the other being ion transporters.
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.
Electrostatic generatorAn electrostatic generator, or electrostatic machine, is an electrical generator that produces static electricity, or electricity at high voltage and low continuous current. The knowledge of static electricity dates back to the earliest civilizations, but for millennia it remained merely an interesting and mystifying phenomenon, without a theory to explain its behavior and often confused with magnetism.
Basis set (chemistry)In theoretical and computational chemistry, a basis set is a set of functions (called basis functions) that is used to represent the electronic wave function in the Hartree–Fock method or density-functional theory in order to turn the partial differential equations of the model into algebraic equations suitable for efficient implementation on a computer. The use of basis sets is equivalent to the use of an approximate resolution of the identity: the orbitals are expanded within the basis set as a linear combination of the basis functions , where the expansion coefficients are given by .
Electrostatic inductionElectrostatic induction, also known as "electrostatic influence" or simply "influence" in Europe and Latin America, is a redistribution of electric charge in an object that is caused by the influence of nearby charges. In the presence of a charged body, an insulated conductor develops a positive charge on one end and a negative charge on the other end. Induction was discovered by British scientist John Canton in 1753 and Swedish professor Johan Carl Wilcke in 1762.
Molecular modelA molecular model is a physical model of an atomistic system that represents molecules and their processes. They play an important role in understanding chemistry and generating and testing hypotheses. The creation of mathematical models of molecular properties and behavior is referred to as molecular modeling, and their graphical depiction is referred to as molecular graphics. The term, "molecular model" refer to systems that contain one or more explicit atoms (although solvent atoms may be represented implicitly) and where nuclear structure is neglected.
Electric potential energyElectric potential energy is a potential energy (measured in joules) that results from conservative Coulomb forces and is associated with the configuration of a particular set of point charges within a defined system. An object may be said to have electric potential energy by virtue of either its own electric charge or its relative position to other electrically charged objects. The term "electric potential energy" is used to describe the potential energy in systems with time-variant electric fields, while the term "electrostatic potential energy" is used to describe the potential energy in systems with time-invariant electric fields.
VoltageVoltage, also known as electric pressure, electric tension, or (electric) potential difference, is the difference in electric potential between two points. In a static electric field, it corresponds to the work needed per unit of charge to move a test charge between the two points. In the International System of Units (SI), the derived unit for voltage is named volt. The voltage between points can be caused by the build-up of electric charge (e.g., a capacitor), and from an electromotive force (e.g.
Electronic filterElectronic filters are a type of signal processing filter in the form of electrical circuits. This article covers those filters consisting of lumped electronic components, as opposed to distributed-element filters. That is, using components and interconnections that, in analysis, can be considered to exist at a single point. These components can be in discrete packages or part of an integrated circuit. Electronic filters remove unwanted frequency components from the applied signal, enhance wanted ones, or both.
Electrostatic dischargeElectrostatic discharge (ESD) is a sudden and momentary flow of electric current between two electrically charged objects caused by contact, an electrical short or dielectric breakdown. A buildup of static electricity can be caused by tribocharging or by electrostatic induction. The ESD occurs when differently-charged objects are brought close together or when the dielectric between them breaks down, often creating a visible spark.
Energy minimizationIn the field of computational chemistry, energy minimization (also called energy optimization, geometry minimization, or geometry optimization) is the process of finding an arrangement in space of a collection of atoms where, according to some computational model of chemical bonding, the net inter-atomic force on each atom is acceptably close to zero and the position on the potential energy surface (PES) is a stationary point (described later).
