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.
Rate equationIn chemistry, the rate law or rate equation for a chemical reaction is a mathematical equation that links the rate of forward reaction with the concentrations or pressures of the reactants and constant parameters (normally rate coefficients and partial reaction orders). For many reactions, the initial rate is given by a power law such as where [\mathrm{A}] and [\mathrm{B}] express the concentration of the species \mathrm{A} and \mathrm{B}, usually in moles per liter (molarity, M).
Graphical user interfaceThe graphical user interface, or GUI (ˌdʒi:juːˈaɪ or ˈɡu:i ), is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicators such as primary notation, instead of text-based UIs, typed command labels or text navigation. GUIs were introduced in reaction to the perceived steep learning curve of command-line interfaces (CLIs), which require commands to be typed on a computer keyboard. The actions in a GUI are usually performed through direct manipulation of the graphical elements.
User interfaceIn the industrial design field of human–computer interaction, a user interface (UI) is the space where interactions between humans and machines occur. The goal of this interaction is to allow effective operation and control of the machine from the human end, while the machine simultaneously feeds back information that aids the operators' decision-making process. Examples of this broad concept of user interfaces include the interactive aspects of computer operating systems, hand tools, heavy machinery operator controls and process controls.
History of the graphical user interfaceThe history of the graphical user interface, understood as the use of graphic icons and a pointing device to control a computer, covers a five-decade span of incremental refinements, built on some constant core principles. Several vendors have created their own windowing systems based on independent code, but with basic elements in common that define the WIMP "window, icon, menu and pointing device" paradigm. There have been important technological achievements, and enhancements to the general interaction in small steps over previous systems.
Chemical kineticsChemical kinetics, also known as reaction kinetics, is the branch of physical chemistry that is concerned with understanding the rates of chemical reactions. It is different from chemical thermodynamics, which deals with the direction in which a reaction occurs but in itself tells nothing about its rate. Chemical kinetics includes investigations of how experimental conditions influence the speed of a chemical reaction and yield information about the reaction's mechanism and transition states, as well as the construction of mathematical models that also can describe the characteristics of a chemical reaction.
Enzyme kineticsEnzyme kinetics is the study of the rates of enzyme-catalysed chemical reactions. In enzyme kinetics, the reaction rate is measured and the effects of varying the conditions of the reaction are investigated. Studying an enzyme's kinetics in this way can reveal the catalytic mechanism of this enzyme, its role in metabolism, how its activity is controlled, and how a drug or a modifier (inhibitor or activator) might affect the rate. An enzyme (E) is typically a protein molecule that promotes a reaction of another molecule, its substrate (S).
Zooming user interfaceIn computing, a zooming user interface or zoomable user interface (ZUI, pronounced zoo-ee) is a graphical environment where users can change the scale of the viewed area in order to see more detail or less, and browse through different documents. A ZUI is a type of graphical user interface (GUI). Information elements appear directly on an infinite virtual desktop (usually created using vector graphics), instead of in windows. Users can pan across the virtual surface in two dimensions and zoom into objects of interest.
User interface designUser interface (UI) design or user interface engineering is the design of user interfaces for machines and software, such as computers, home appliances, mobile devices, and other electronic devices, with the focus on maximizing usability and the user experience. In computer or software design, user interface (UI) design primarily focuses on information architecture. It is the process of building interfaces that clearly communicates to the user what's important. UI design refers to graphical user interfaces and other forms of interface design.
Graphical widgetA graphical widget (also graphical control element or control) in a graphical user interface is an element of interaction, such as a button or a scroll bar. Controls are software components that a computer user interacts with through direct manipulation to read or edit information about an application. User interface libraries such as Windows Presentation Foundation, Qt, GTK, and Cocoa, contain a collection of controls and the logic to render these.
Tangible user interfaceA tangible user interface (TUI) is a user interface in which a person interacts with digital information through the physical environment. The initial name was Graspable User Interface, which is no longer used. The purpose of TUI development is to empower collaboration, learning, and design by giving physical forms to digital information, thus taking advantage of the human ability to grasp and manipulate physical objects and materials.
Internal energyThe internal energy of a thermodynamic system is the energy contained within it, measured as the quantity of energy necessary to bring the system from its standard internal state to its present internal state of interest, accounting for the gains and losses of energy due to changes in its internal state, including such quantities as magnetization. It excludes the kinetic energy of motion of the system as a whole and the potential energy of position of the system as a whole, with respect to its surroundings and external force fields.
Law of mass actionIn chemistry, the law of mass action is the proposition that the rate of the chemical reaction is directly proportional to the product of the activities or concentrations of the reactants. It explains and predicts behaviors of solutions in dynamic equilibrium. Specifically, it implies that for a chemical reaction mixture that is in equilibrium, the ratio between the concentration of reactants and products is constant.
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.
Biomolecular structureBiomolecular structure is the intricate folded, three-dimensional shape that is formed by a molecule of protein, DNA, or RNA, and that is important to its function. The structure of these molecules may be considered at any of several length scales ranging from the level of individual atoms to the relationships among entire protein subunits. This useful distinction among scales is often expressed as a decomposition of molecular structure into four levels: primary, secondary, tertiary, and quaternary.
Intrinsically disordered proteinsIn molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins.
Thermodynamic free energyIn thermodynamics, the thermodynamic free energy is one of the state functions of a thermodynamic system (the others being internal energy, enthalpy, entropy, etc.). The change in the free energy is the maximum amount of work that the system can perform in a process at constant temperature, and its sign indicates whether the process is thermodynamically favorable or forbidden. Since free energy usually contains potential energy, it is not absolute but depends on the choice of a zero point.
Relaxation (physics)In the physical sciences, relaxation usually means the return of a perturbed system into equilibrium. Each relaxation process can be categorized by a relaxation time τ. The simplest theoretical description of relaxation as function of time t is an exponential law exp(−t/τ) (exponential decay). Let the homogeneous differential equation: model damped unforced oscillations of a weight on a spring. The displacement will then be of the form . The constant T () is called the relaxation time of the system and the constant μ is the quasi-frequency.
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.
Nucleic acid structure predictionNucleic acid structure prediction is a computational method to determine secondary and tertiary nucleic acid structure from its sequence. Secondary structure can be predicted from one or several nucleic acid sequences. Tertiary structure can be predicted from the sequence, or by comparative modeling (when the structure of a homologous sequence is known).
