Stochastic simulationA stochastic simulation is a simulation of a system that has variables that can change stochastically (randomly) with individual probabilities. Realizations of these random variables are generated and inserted into a model of the system. Outputs of the model are recorded, and then the process is repeated with a new set of random values. These steps are repeated until a sufficient amount of data is gathered. In the end, the distribution of the outputs shows the most probable estimates as well as a frame of expectations regarding what ranges of values the variables are more or less likely to fall in.
Protein tertiary structureProtein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.
Absolute configurationAbsolute configuration refers to the spatial arrangement of atoms within a chiral molecular entity (or group) and its resultant stereochemical description. Absolute configuration is typically relevant in organic molecules where carbon is bonded to four different substituents. This type of construction creates two possible enantiomers. Absolute configuration uses a set of rules to describe the relative positions of each bond around the chiral center atom.
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 biologyMolecular biology məˈlɛkjʊlər is the study of chemical and physical structure of biological macromolecules. It is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena—uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology.
GasGas is one of the four fundamental states of matter. The others are solid, liquid, and plasma. A pure gas may be made up of individual atoms (e.g. a noble gas like neon), elemental molecules made from one type of atom (e.g. oxygen), or compound molecules made from a variety of atoms (e.g. carbon dioxide). A gas mixture, such as air, contains a variety of pure gases. What distinguishes a gas from liquids and solids is the vast separation of the individual gas particles.
Phase transitionIn chemistry, thermodynamics, and other related fields, a phase transition (or phase change) is the physical process of transition between one state of a medium and another. Commonly the term is used to refer to changes among the basic states of matter: solid, liquid, and gas, and in rare cases, plasma. A phase of a thermodynamic system and the states of matter have uniform physical properties. During a phase transition of a given medium, certain properties of the medium change as a result of the change of external conditions, such as temperature or pressure.
Phase diagramA phase diagram in physical chemistry, engineering, mineralogy, and materials science is a type of chart used to show conditions (pressure, temperature, volume, etc.) at which thermodynamically distinct phases (such as solid, liquid or gaseous states) occur and coexist at equilibrium. Common components of a phase diagram are lines of equilibrium or phase boundaries, which refer to lines that mark conditions under which multiple phases can coexist at equilibrium. Phase transitions occur along lines of equilibrium.
Protein domainIn molecular biology, a protein domain is a region of a protein's polypeptide chain that is self-stabilizing and that folds independently from the rest. Each domain forms a compact folded three-dimensional structure. Many proteins consist of several domains, and a domain may appear in a variety of different proteins. Molecular evolution uses domains as building blocks and these may be recombined in different arrangements to create proteins with different functions.
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.
