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.
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.
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.
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.
Electronic correlationElectronic correlation is the interaction between electrons in the electronic structure of a quantum system. The correlation energy is a measure of how much the movement of one electron is influenced by the presence of all other electrons. Within the Hartree–Fock method of quantum chemistry, the antisymmetric wave function is approximated by a single Slater determinant. Exact wave functions, however, cannot generally be expressed as single determinants.
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.
Harmonic oscillatorIn classical mechanics, a harmonic oscillator is a system that, when displaced from its equilibrium position, experiences a restoring force F proportional to the displacement x: where k is a positive constant. If F is the only force acting on the system, the system is called a simple harmonic oscillator, and it undergoes simple harmonic motion: sinusoidal oscillations about the equilibrium point, with a constant amplitude and a constant frequency (which does not depend on the amplitude).
OscillationOscillation is the repetitive or periodic variation, typically in time, of some measure about a central value (often a point of equilibrium) or between two or more different states. Familiar examples of oscillation include a swinging pendulum and alternating current. Oscillations can be used in physics to approximate complex interactions, such as those between atoms.
Frequency responseIn signal processing and electronics, the frequency response of a system is the quantitative measure of the magnitude and phase of the output as a function of input frequency. The frequency response is widely used in the design and analysis of systems, such as audio and control systems, where they simplify mathematical analysis by converting governing differential equations into algebraic equations.
ChannelrhodopsinChannelrhodopsins are a subfamily of retinylidene proteins (rhodopsins) that function as light-gated ion channels. They serve as sensory photoreceptors in unicellular green algae, controlling phototaxis: movement in response to light. Expressed in cells of other organisms, they enable light to control electrical excitability, intracellular acidity, calcium influx, and other cellular processes (see optogenetics). Channelrhodopsin-1 (ChR1) and Channelrhodopsin-2 (ChR2) from the model organism Chlamydomonas reinhardtii are the first discovered channelrhodopsins.
Impulse responseIn signal processing and control theory, the impulse response, or impulse response function (IRF), of a dynamic system is its output when presented with a brief input signal, called an impulse (δ(t)). More generally, an impulse response is the reaction of any dynamic system in response to some external change. In both cases, the impulse response describes the reaction of the system as a function of time (or possibly as a function of some other independent variable that parameterizes the dynamic behavior of the system).
Linear systemIn systems theory, a linear system is a mathematical model of a system based on the use of a linear operator. Linear systems typically exhibit features and properties that are much simpler than the nonlinear case. As a mathematical abstraction or idealization, linear systems find important applications in automatic control theory, signal processing, and telecommunications. For example, the propagation medium for wireless communication systems can often be modeled by linear systems.
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.
SolventA solvent (from the Latin solvō, "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for polar molecules and the most common solvent used by living things; all the ions and proteins in a cell are dissolved in water within the cell. Major uses of solvents are in paints, paint removers, inks, and dry cleaning. Specific uses for organic solvents are in dry cleaning (e.
Linear regressionIn statistics, linear regression is a linear approach for modelling the relationship between a scalar response and one or more explanatory variables (also known as dependent and independent variables). The case of one explanatory variable is called simple linear regression; for more than one, the process is called multiple linear regression. This term is distinct from multivariate linear regression, where multiple correlated dependent variables are predicted, rather than a single scalar variable.
Quantum stateIn quantum physics, a quantum state is a mathematical entity that embodies the knowledge of a quantum system. Quantum mechanics specifies the construction, evolution, and measurement of a quantum state. The result is a quantum mechanical prediction for the system represented by the state. Knowledge of the quantum state together with the quantum mechanical rules for the system's evolution in time exhausts all that can be known about a quantum system. Quantum states may be defined in different ways for different kinds of systems or problems.
Van der Pol oscillatorIn the study of dynamical systems, the van der Pol oscillator (named for Dutch physicist Balthasar van der Pol) is a non-conservative, oscillating system with non-linear damping. It evolves in time according to the second-order differential equation where x is the position coordinate—which is a function of the time t—and μ is a scalar parameter indicating the nonlinearity and the strength of the damping. The Van der Pol oscillator was originally proposed by the Dutch electrical engineer and physicist Balthasar van der Pol while he was working at Philips.
Aqueous solutionAn aqueous solution is a solution in which the solvent is water. It is mostly shown in chemical equations by appending (aq) to the relevant chemical formula. For example, a solution of table salt, or sodium chloride (NaCl), in water would be represented as . The word aqueous (which comes from aqua) means pertaining to, related to, similar to, or dissolved in, water. As water is an excellent solvent and is also naturally abundant, it is a ubiquitous solvent in chemistry.
Linear filterLinear filters process time-varying input signals to produce output signals, subject to the constraint of linearity. In most cases these linear filters are also time invariant (or shift invariant) in which case they can be analyzed exactly using LTI ("linear time-invariant") system theory revealing their transfer functions in the frequency domain and their impulse responses in the time domain. Real-time implementations of such linear signal processing filters in the time domain are inevitably causal, an additional constraint on their transfer functions.
Wave packetIn physics, a wave packet (also known as a wave train or wave group) is a short burst of localized wave action that travels as a unit, outlined by an envelope. A wave packet can be analyzed into, or can be synthesized from, a potentially-infinite set of component sinusoidal waves of different wavenumbers, with phases and amplitudes such that they interfere constructively only over a small region of space, and destructively elsewhere.
