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Zimm–Bragg Model
In statistical mechanics, the Zimm–Bragg model is a helix-coil transition model that describes helix-coil transitions of macromolecules, usually polymer chains. Most models provide a reasonable approximation of the fractional helicity of a given polypeptide; the Zimm–Bragg model differs by incorporating the ease of propagation (self-replication) with respect to nucleation. It is named for co-discoverers Bruno H. Zimm and J. K. Bragg. Helix-coil transition models Helix-coil transition models assume that polypeptides are linear chains composed of interconnected segments. Further, models group these sections into two broad categories: ''coils'', random conglomerations of disparate unbound pieces, are represented by the letter 'C', and ''helices'', ordered states where the chain has assumed a structure stabilized by hydrogen bonding, are represented by the letter 'H'. Thus, it is possible to loosely represent a macromolecule as a string such as CCCCHCCHCHHHHHCHCCC and so forth. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Mechanics
In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. Sometimes called statistical physics or statistical thermodynamics, its applications include many problems in a wide variety of fields such as biology, neuroscience, computer science Computer science is the study of computation, information, and automation. Computer science spans Theoretical computer science, theoretical disciplines (such as algorithms, theory of computation, and information theory) to Applied science, ..., information theory and sociology. Its main purpose is to clarify the properties of matter in aggregate, in terms of physical laws governing atomic motion. Statistical mechanics arose out of the development of classical thermodynamics, a field for which it was successful in explaining macroscopic physical properties—such as temperature, pressure, and heat capacity—in terms of microscop ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metabolic reactions, DNA replication, Cell signaling, responding to stimuli, providing Cytoskeleton, structure to cells and Fibrous protein, organisms, and Intracellular transport, transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the Nucleic acid sequence, nucleotide sequence of their genes, and which usually results in protein folding into a specific Protein structure, 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called pep ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Mechanics
In physics, statistical mechanics is a mathematical framework that applies statistical methods and probability theory to large assemblies of microscopic entities. Sometimes called statistical physics or statistical thermodynamics, its applications include many problems in a wide variety of fields such as biology, neuroscience, computer science Computer science is the study of computation, information, and automation. Computer science spans Theoretical computer science, theoretical disciplines (such as algorithms, theory of computation, and information theory) to Applied science, ..., information theory and sociology. Its main purpose is to clarify the properties of matter in aggregate, in terms of physical laws governing atomic motion. Statistical mechanics arose out of the development of classical thermodynamics, a field for which it was successful in explaining macroscopic physical properties—such as temperature, pressure, and heat capacity—in terms of microscop ... [...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 th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lifson–Roig Model
In polymer science, the Lifson–Roig model is a helix-coil transition model applied to the alpha helix- random coil transition of polypeptides; it is a refinement of the Zimm–Bragg model that recognizes that a polypeptide alpha helix is only stabilized by a hydrogen bond only once three consecutive residues have adopted the helical conformation. To consider three consecutive residues each with two states (helix and coil), the Lifson–Roig model uses a 4x4 transfer matrix instead of the 2x2 transfer matrix of the Zimm–Bragg model, which considers only two consecutive residues. However, the simple nature of the coil state allows this to be reduced to a 3x3 matrix for most applications. The Zimm–Bragg and Lifson–Roig models are but the first two in a series of analogous transfer-matrix methods in polymer science that have also been applied to nucleic acids and branched polymers. The transfer-matrix approach is especially elegant for homopolymers, since the statistical mec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Helix
An alpha helix (or α-helix) is a sequence of amino acids in a protein that are twisted into a coil (a helix). The alpha helix is the most common structural arrangement in the Protein secondary structure, secondary structure of proteins. It is also the most extreme type of local structure, and it is the local structure that is most easily predicted from a sequence of amino acids. The alpha helix has a right-handed helix conformation in which every backbone amino, N−H group hydrogen bonds to the backbone carbonyl, C=O group of the amino acid that is four residue (biochemistry), residues earlier in the protein sequence. Other names The alpha helix is also commonly called a: * Pauling–Corey–Branson α-helix (from the names of three scientists who described its structure) * 3.613-helix because there are 3.6 amino acids in one ring, with 13 atoms being involved in the ring formed by the hydrogen bond (starting with amidic hydrogen and ending with carbonyl oxygen) Discovery ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Glycine
Glycine (symbol Gly or G; ) is an amino acid that has a single hydrogen atom as its side chain. It is the simplest stable amino acid. Glycine is one of the proteinogenic amino acids. It is encoded by all the codons starting with GG (GGU, GGC, GGA, GGG). Glycine disrupts the formation of alpha-helices in secondary protein structure. Its small side chain causes it to favor random coils instead. Glycine is also an inhibitory neurotransmitter – interference with its release within the spinal cord (such as during a '' Clostridium tetani'' infection) can cause spastic paralysis due to uninhibited muscle contraction. It is the only achiral proteinogenic amino acid. It can fit into both hydrophilic and hydrophobic environments, due to its minimal side chain of only one hydrogen atom. History and etymology Glycine was discovered in 1820 by French chemist Henri Braconnot when he hydrolyzed gelatin by boiling it with sulfuric acid. He originally called it "sugar of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Leucine
Leucine (symbol Leu or L) is an essential amino acid that is used in the biosynthesis of proteins. Leucine is an α-amino acid, meaning it contains an α-amino group (which is in the protonated −NH3+ form under biological conditions), an α-Carboxylic acid, carboxylic acid group (which is in the deprotonated −COO− form under biological conditions), and a side chain Isobutyl, isobutyl group, making it a Chemical polarity, non-polar Aliphatic compound, aliphatic amino acid. It is Essential amino acid, essential in humans, meaning the body cannot synthesize it; it must be obtained from the diet. Human dietary sources are foods that contain protein, such as meats, dairy products, soy products, and beans and other legumes. It is genetic code, encoded by the codons UUA, UUG, CUU, CUC, CUA, and CUG. Leucine is named after the Greek language, Greek word for "white": ''λευκός'' (''leukós'', "white"), after its common appearance as a white powder, a property it shares with many ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proline
Proline (symbol Pro or P) is an organic acid classed as a proteinogenic amino acid (used in the biosynthesis of proteins), although it does not contain the amino group but is rather a secondary amine. The secondary amine nitrogen is in the protonated form (NH2+) under biological conditions, while the carboxyl group is in the deprotonated −COO− form. The "side chain" from the α carbon connects to the nitrogen forming a pyrrolidine loop, classifying it as a aliphatic amino acid. It is non-essential in humans, meaning the body can synthesize it from the non-essential amino acid L-glutamate. It is encoded by all the codons starting with CC (CCU, CCC, CCA, and CCG). Proline is the only proteinogenic amino acid which is a secondary amine, as the nitrogen atom is attached both to the α-carbon and to a chain of three carbons that together form a five-membered ring. History and etymology Proline was first isolated in 1900 by Richard Willstätter who obtained the amino a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Transfer-matrix Method (statistical Mechanics)
In statistical mechanics, the transfer-matrix method is a mathematical technique which is used to write the partition function into a simpler form. It was introduced in 1941 by Hans Kramers and Gregory Wannier. In many one dimensional lattice models, the partition function is first written as an ''n''-fold summation over each possible microstate, and also contains an additional summation of each component's contribution to the energy of the system within each microstate. Overview Higher-dimensional models contain even more summations. For systems with more than a few particles, such expressions can quickly become too complex to work out directly, even by computer. Instead, the partition function can be rewritten in an equivalent way. The basic idea is to write the partition function in the form : \mathcal = \mathbf_0 \cdot \left\ \cdot \mathbf_ where v0 and v''N''+1 are vectors of dimension ''p'' and the ''p'' × ''p'' matrices W''k'' are the so-called transfer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Phase Transition
In physics, chemistry, and other related fields like biology, 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 State of matter, states of matter: solid, liquid, and gas, and in rare cases, plasma (physics), plasma. A phase of a thermodynamic system and the states of matter have uniform physical property, 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. This can be a discontinuous change; for example, a liquid may become gas upon heating to its boiling point, resulting in an abrupt change in volume. The identification of the external conditions at which a transformation occurs defines the phase transition point. Types of phase transition States of matter Phase transitions commonly refer to when a substance tran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rudolf Peierls
Sir Rudolf Ernst Peierls, (; ; 5 June 1907 – 19 September 1995) was a German-born British physicist who played a major role in Tube Alloys, Britain's nuclear weapon programme, as well as the subsequent Manhattan Project, the combined Allied nuclear bomb programme. His 1996 obituary in ''Physics Today'' described him as "a major player in the drama of the eruption of nuclear physics into world affairs". Peierls studied physics at the University of Berlin, at the University of Munich under Arnold Sommerfeld, the University of Leipzig under Werner Heisenberg, and ETH Zurich under Wolfgang Pauli. After receiving his DPhil from Leipzig in 1929, he became an assistant to Pauli in Zurich. In 1932, he was awarded a Rockefeller Fellowship, which he used to study in Rome under Enrico Fermi, and then at the Cavendish Laboratory at the University of Cambridge under Ralph H. Fowler. Because of his Jewish background, he elected to not return home after Adolf Hitler's rise to power in 1 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
