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Periodic Boundary Conditions
Periodic boundary conditions (PBCs) are a set of boundary conditions which are often chosen for approximating a large (infinite) system by using a small part called a ''unit cell''. PBCs are often used in computer simulations and mathematical models. The topology of two-dimensional PBC is equal to that of a ''world map'' of some video games; the geometry of the unit cell satisfies perfect two-dimensional tiling, and when an object passes through one side of the unit cell, it re-appears on the opposite side with the same velocity. In topological terms, the space made by two-dimensional PBCs can be thought of as being mapped onto a torus (compactification). The large systems approximated by PBCs consist of an infinite number of unit cells. In computer simulations, one of these is the original simulation box, and others are copies called ''images''. During the simulation, only the properties of the original simulation box need to be recorded and propagated. The ''minimum-image conventi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phonon
In physics, a phonon is a collective excitation in a periodic, Elasticity (physics), elastic arrangement of atoms or molecules in condensed matter physics, condensed matter, specifically in solids and some liquids. A type of quasiparticle, a phonon is an excited state in the quantum mechanical Quantization (physics), quantization of the mode of vibration, modes of vibrations for elastic structures of interacting particles. Phonons can be thought of as quantized sound waves, similar to photons as quantized light waves. The study of phonons is an important part of condensed matter physics. They play a major role in many of the physical properties of condensed matter systems, such as thermal conductivity and electrical conductivity, as well as in models of neutron scattering and related effects. The concept of phonons was introduced in 1932 by Soviet Union, Soviet physicist Igor Tamm. The name ''phonon'' comes from the Ancient Greek language, Greek word (), which translates to ''so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Orthorhombic
In crystallography, the orthorhombic crystal system is one of the 7 crystal systems. Orthorhombic lattices result from stretching a cubic lattice along two of its orthogonal pairs by two different factors, resulting in a rectangular prism with a rectangular base (''a'' by ''b'') and height (''c''), such that ''a'', ''b'', and ''c'' are distinct. All three bases intersect at 90° angles, so the three lattice vectors remain mutually orthogonal. Bravais lattices There are four orthorhombic Bravais lattices: primitive orthorhombic, base-centered orthorhombic, body-centered orthorhombic, and face-centered orthorhombic. For the base-centered orthorhombic lattice, the primitive cell has the shape of a right rhombic prism;See , row oC, column Primitive, where the cell parameters are given as a1 = a2, α = β = 90° it can be constructed because the two-dimensional centered rectangular base layer can also be described with primitive rhombic axes. Note that the length a of the primit ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvation Shell
A solvation shell or solvation sheath is the solvent interface of any chemical compound or biomolecule that constitutes the solute. When the solvent is water it is called a hydration shell or hydration sphere. The number of solvent molecules surrounding each unit of solute is called the hydration number of the solute. A classic example is when water molecules arrange around a metal ion. If the metal ion is a cation, the electronegative oxygen atom of the water molecule would be attracted electrostatically to the positive charge on the metal ion. The result is a solvation shell of water molecules that surround the ion. This shell can be several molecules thick, dependent upon the charge of the ion, its distribution and spatial dimensions. A number of molecules of solvent are involved in the solvation shell around anions and cations from a dissolved salt in a solvent. Metal ions in aqueous solutions form metal aquo complexes. This number can be determined by various methods like c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Random Coil
In polymer chemistry, a random coil is a conformation of polymers where the monomer subunits are oriented randomly while still being bonded to adjacent units. It is not one specific shape, but a statistical distribution of shapes for all the chains in a population of macromolecules. The conformation's name is derived from the idea that, in the absence of specific, stabilizing interactions, a polymer backbone will "sample" all possible conformations randomly. Many unbranched, linear homopolymers — in solution, or above their melting temperatures — assume (approximate) random coils. Random walk model: The Gaussian chain There are an enormous number of different ways in which a chain can be curled around in a relatively compact shape, like an unraveling ball of twine with much open space, and comparatively few ways it can be more or less stretched out. So, if each conformation has an equal probability or statistical weight, chains are much more likely to be ball-like than ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Native State
In biochemistry, the native state of a protein or nucleic acid is its properly folded and/or assembled form, which is operative and functional. The native state of a biomolecule may possess all four levels of biomolecular structure, with the secondary through quaternary structure being formed from weak interactions along the covalently-bonded backbone. This is in contrast to the denatured state, in which these weak interactions are disrupted, leading to the loss of these forms of structure and retaining only the biomolecule's primary structure. Biochemistry Proteins While all protein molecules begin as simple unbranched chains of amino acids, once completed they assume highly specific three-dimensional shapes. That ultimate shape, known as tertiary structure, is the folded shape that possesses a minimum of free energy. It is a protein's tertiary, folded structure that makes it capable of performing its biological function. In fact, shape changes in proteins are the primary ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Folding
Protein folding is the physical process by which a protein chain is translated to its native three-dimensional structure, typically a "folded" conformation by which the protein becomes biologically functional. Via an expeditious and reproducible process, a polypeptide folds into its characteristic three-dimensional structure from a random coil. Each protein exists first as an unfolded polypeptide or random coil after being translated from a sequence of mRNA to a linear chain of amino acids. At this stage the polypeptide lacks any stable (long-lasting) three-dimensional structure (the left hand side of the first figure). As the polypeptide chain is being synthesized by a ribosome, the linear chain begins to fold into its three-dimensional structure. Folding of many proteins begins even during translation of the polypeptide chain. Amino acids interact with each other to produce a well-defined three-dimensional structure, the folded protein (the right hand side of the figure), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ferroelectricity
Ferroelectricity is a characteristic of certain materials that have a spontaneous electric polarization that can be reversed by the application of an external electric field. All ferroelectrics are also piezoelectric and pyroelectric, with the additional property that their natural electrical polarization is reversible. The term is used in analogy to ferromagnetism, in which a material exhibits a permanent magnetic moment. Ferromagnetism was already known when ferroelectricity was discovered in 1920 in Rochelle salt by Joseph Valasek.See and Thus, the prefix ''ferro'', meaning iron, was used to describe the property despite the fact that most ferroelectric materials do not contain iron. Materials that are both ferroelectric ''and'' ferromagnetic are known as multiferroics. Polarization When most materials are electrically polarized, the polarization induced, ''P'', is almost exactly proportional to the applied external electric field ''E''; so the polarization is a linear fun ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pyroelectricity
Pyroelectricity (from the two Greek words ''pyr'' meaning fire, and electricity) is a property of certain crystals which are naturally electrically polarized and as a result contain large electric fields. Pyroelectricity can be described as the ability of certain materials to generate a temporary voltage when they are heated or cooled. The change in temperature modifies the positions of the atoms slightly within the crystal structure, such that the polarization of the material changes. This polarization change gives rise to a voltage across the crystal. If the temperature stays constant at its new value, the pyroelectric voltage gradually disappears due to leakage current. The leakage can be due to electrons moving through the crystal, ions moving through the air, or current leaking through a voltmeter attached across the crystal. Explanation Pyroelectric charge in minerals develops on the opposite faces of asymmetric crystals. The direction in which the propagation of the char ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dipoles
In physics, a dipole () is an electromagnetic phenomenon which occurs in two ways: *An electric dipole deals with the separation of the positive and negative electric charges found in any electromagnetic system. A simple example of this system is a pair of charges of equal magnitude but opposite sign separated by some typically small distance. (A permanent electric dipole is called an electret.) *A magnetic dipole is the closed circulation of an electric current system. A simple example is a single loop of wire with constant current through it. A bar magnet is an example of a magnet with a permanent magnetic dipole moment. Dipoles, whether electric or magnetic, can be characterized by their dipole moment, a vector quantity. For the simple electric dipole, the electric dipole moment points from the negative charge towards the positive charge, and has a magnitude equal to the strength of each charge times the separation between the charges. (To be precise: for the definition of t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ionic Strength
The ionic strength of a solution is a measure of the concentration of ions in that solution. Ionic compounds, when dissolved in water, dissociate into ions. The total electrolyte concentration in solution will affect important properties such as the dissociation constant or the solubility of different salts. One of the main characteristics of a solution with dissolved ions is the ionic strength. Ionic strength can be molar (mol/L solution) or molal (mol/kg solvent) and to avoid confusion the units should be stated explicitly. The concept of ionic strength was first introduced by Lewis and Randall in 1921 while describing the activity coefficients of strong electrolytes. Quantifying ionic strength The molar ionic strength, ''I'', of a solution is a function of the concentration of ''all'' ions present in that solution. :I = \begin\frac\end\sum_^ c_i z_i^ where one half is because we are including both cations and anions, ''c''i is the molar concentration of ion i (M, mol/L), ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Counterion
160px, Polystyrene sulfonate, a cation-exchange resin, is typically supplied with as the counterion.">cation-exchange_resin.html" ;"title="Polystyrene sulfonate, a cation-exchange resin">Polystyrene sulfonate, a cation-exchange resin, is typically supplied with as the counterion. In chemistry, a counterion (sometimes written as "counter ion", pronounced as such) is the ion that accompanies an Ionic compound, ionic species in order to maintain Electric charge, electric neutrality. In table salt (NaCl, also known as sodium chloride) the sodium ion (positively charged) is the counterion for the chloride ion (negatively charged) and vice versa. A counterion will be more commonly referred to as an anion or a cation, depending on whether it is negatively or positively charged. Thus, the counterion to an anion will be a cation, and vice versa. In biochemistry, counterions are generally vaguely defined. Depending on their charge, proteins are associated with a variety of smaller ani ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
