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.
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.
Version controlIn software engineering, version control (also known as revision control, source control, or source code management) is a class of systems responsible for managing changes to computer programs, documents, large web sites, or other collections of information. Version control is a component of software configuration management. Changes are usually identified by a number or letter code, termed the "revision number", "revision level", or simply "revision". For example, an initial set of files is "revision 1".
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).
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.
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.
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.
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 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.
Distributed version controlIn software development, distributed version control (also known as distributed revision control) is a form of version control in which the complete codebase, including its full history, is mirrored on every developer's computer. Compared to centralized version control, this enables automatic management branching and merging, speeds up most operations (except pushing and pulling), improves the ability to work offline, and does not rely on a single location for backups.
Photoreceptor proteinPhotoreceptor proteins are light-sensitive proteins involved in the sensing and response to light in a variety of organisms. Some examples are rhodopsin in the photoreceptor cells of the vertebrate retina, phytochrome in plants, and bacteriorhodopsin and bacteriophytochromes in some bacteria. They mediate light responses as varied as visual perception, phototropism and phototaxis, as well as responses to light-dark cycles such as circadian rhythm and other photoperiodisms including control of flowering times in plants and mating seasons in animals.
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.
Quantum wellA quantum well is a potential well with only discrete energy values. The classic model used to demonstrate a quantum well is to confine particles, which were initially free to move in three dimensions, to two dimensions, by forcing them to occupy a planar region. The effects of quantum confinement take place when the quantum well thickness becomes comparable to the de Broglie wavelength of the carriers (generally electrons and holes), leading to energy levels called "energy subbands", i.e.
OptogeneticsOptogenetics is a biological technique to control the activity of neurons or other cell types with light. This is achieved by expression of light-sensitive ion channels, pumps or enzymes specifically in the target cells. On the level of individual cells, light-activated enzymes and transcription factors allow precise control of biochemical signaling pathways. In systems neuroscience, the ability to control the activity of a genetically defined set of neurons has been used to understand their contribution to decision making, learning, fear memory, mating, addiction, feeding, and locomotion.
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.
Crystal oscillatorA crystal oscillator is an electronic oscillator circuit that uses a piezoelectric crystal as a frequency-selective element. The oscillator frequency is often used to keep track of time, as in quartz wristwatches, to provide a stable clock signal for digital integrated circuits, and to stabilize frequencies for radio transmitters and receivers. The most common type of piezoelectric resonator used is a quartz crystal, so oscillator circuits incorporating them became known as crystal oscillators.
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.
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.
Quantum Zeno effectThe quantum Zeno effect (also known as the Turing paradox) is a feature of quantum-mechanical systems allowing a particle's time evolution to be slowed down by measuring it frequently enough with respect to some chosen measurement setting. Sometimes this effect is interpreted as "a system cannot change while you are watching it". One can "freeze" the evolution of the system by measuring it frequently enough in its known initial state.
Injection lockingInjection locking and injection pulling are the frequency effects that can occur when a harmonic oscillator is disturbed by a second oscillator operating at a nearby frequency. When the coupling is strong enough and the frequencies near enough, the second oscillator can capture the first oscillator, causing it to have essentially identical frequency as the second. This is injection locking. When the second oscillator merely disturbs the first but does not capture it, the effect is called injection pulling.
