AMBER: AMBER (an acronym for Assisted Model Building with Energy Refinement) is a family of force fields for molecular dynamics of biomolecules originally developed by Peter Kollman's group at the University of California, San Francisco. AMBER is also the name for the molecular dynamics software package that simulates these force fields.Interval boundary element method: Interval boundary element method is classical boundary element method with the interval parameters.
Reaction coordinateOutline of water: The following outline is provided as an overview of and topical guide to water:Ice Ih: [showing details of an ice cube under magnification. Ice Ih is the form of ice commonly seen on Earth.Standard enthalpy of formation: The standard enthalpy of formation or standard heat of formation of a compound is the change of enthalpy during the formation of 1 mole of the compound from its constituent elements, with all substances in their standard states at 1 atmosphere (1 atm or 101.3 kPa).Database of protein conformational diversity: The Database of protein conformational diversity (PCDB) is a database of diversity of protein tertiary structures within protein domains as determined by X-ray crystallography. Proteins are inherently flexible and this database collects information on this subject for use in molecular research.Transmembrane domain: Transmembrane segment usually denotes a single transmembrane alpha helix of a transmembrane protein, also known as an integral protein.http://www.Principles of motion economy: The principles of motion economy form a set of rules and suggestions to improve the manual work in manufacturing and reduce fatigue and unnecessary movements by the worker, which can lead to the reduction in the work related trauma.Model lipid bilayer: A model lipid bilayer is any bilayer assembled in vitro, as opposed to the bilayer of natural cell membranes or covering various sub-cellular structures like the nucleus. A model bilayer can be made with either synthetic or natural lipids.Chronic solvent-induced encephalopathy: Chronic solvent induced encephalopathy (CSE) is a condition induced by long-term exposure to organic solvents, typically in the workplace, that lead to a wide variety of persisting sensorimotor polyneuropathies and neurobehavioral deficits even after solvent exposure has been removed. This syndrome can also be referred to as "psycho-organic syndrome", "organic solvent syndrome", "chronic painter's syndrome", "occupational solvent encephalopathy", "solvent intoxication", "toxic solvent syndrome", "painters disease", "psycho-organic syndrome", "chronic toxic encephalopathy", and "neurasthenic syndrome".Outline of biophysics: The following outline is provided as an overview of and topical guide to biophysics:FERM domain: In molecular biology, the FERM domain (F for 4.1 protein, E for ezrin, R for radixin and M for moesin) is a widespread protein module involved in localising proteins to the plasma membrane.DNA binding site: DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites are distinct from other binding sites in that (1) they are part of a DNA sequence (e.Phase problem: In physics the phase problem is the name given to the problem of loss of information concerning the phase that can occur when making a physical measurement. The name itself comes from the field of x-ray crystallography, where the phase problem has to be solved for the determination of a structure from diffraction data.Proximity ligation assay: Proximity ligation assay (in situ PLA) is a technology that extends the capabilities of traditional immunoassays to include direct detection of proteins, protein interactions and modifications with high specificity and sensitivity. Protein targets can be readily detected and localized with single molecule resolution and objectively quantified in unmodified cells and tissues.Knotted protein: Knotted proteins are proteins whose backbones entangle themselves in a knot. One can imagine pulling a protein chain from both termini, as though pulling a string from both ends.IlmeniteSHIFTCORProtein primary structure: The primary structure of a peptide or protein is the linear sequence of its amino acid structural units, and partly comprises its overall biomolecular structure. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end.Trapped ion quantum computer: A trapped ion quantum computer is one proposed approach to a large-scale quantum computer. Ions, or charged atomic particles, can be confined and suspended in free space using electromagnetic fields.Conditional quantum entropy: The conditional quantum entropy is an entropy measure used in quantum information theory. It is a generalization of the conditional entropy of classical information theory.Spin–lattice relaxation in the rotating frame: Spin–lattice relaxation in the rotating frame is the mechanism by which Mxy, the transverse component of the magnetization vector, exponentially decays towards its equilibrium value of zero, under the influence of a radio frequency (RF) field in nuclear magnetic resonance (NMR) and magnetic resonance imaging (MRI). It is characterized by the spin–lattice relaxation time constant in the rotating frame, T1ρ.Coles PhillipsNucleic acid structure: Nucleic acid structure refers to the structure of nucleic acids such as DNA and RNA. Chemically speaking, DNA and RNA are very similar.Ligand (biochemistry): In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. In protein-ligand binding, the ligand is usually a signal-triggering molecule binding to a site on a target protein.Membrane fluidity: In biology, membrane fluidity refers to the viscosity of the lipid bilayer of a cell membrane or a synthetic lipid membrane. Lipid packing can influence the fluidity of the membrane.SEA Native Peptide LigationPermissive temperature: The permissive temperature is the temperature at which a temperature sensitive mutant gene product takes on a normal, functional phenotype.http://www.Lattice protein: Lattice proteins are highly simplified computer models of proteins which are used to investigate protein folding.Clonal Selection Algorithm: In artificial immune systems, Clonal selection algorithms are a class of algorithms inspired by the clonal selection theory of acquired immunity that explains how B and T lymphocytes improve their response to antigens over time called affinity maturation. These algorithms focus on the Darwinian attributes of the theory where selection is inspired by the affinity of antigen-antibody interactions, reproduction is inspired by cell division, and variation is inspired by somatic hypermutation.Mass diffusivity: Diffusivity or diffusion coefficient is a proportionality constant between the molar flux due to molecular diffusion and the gradient in the concentration of the species (or the driving force for diffusion). Diffusivity is encountered in Fick's law and numerous other equations of physical chemistry.Burst kinetics: Burst kinetics is a form of enzyme kinetics that refers to an initial high velocity of enzymatic turnover when adding enzyme to substrate. This initial period of high velocity product formation is referred to as the "Burst Phase".Porosity: Porosity or void fraction is a measure of the void (i.e.Proton emissionMac OS X Server 1.0Egg lecithinElectron crystallography: Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM).Base pair: Base pairs (unit: bp), which form between specific nucleobases (also termed nitrogenous bases), are the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, Watson-Crick base pairs (guanine-cytosine and adenine-thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence.Silent mutation: Silent mutations are mutations in DNA that do not significantly alter the phenotype of the organism in which they occur. Silent mutations can occur in non-coding regions (outside of genes or within introns), or they may occur within exons.Matrix model: == Mathematics and physics ==Gramicidin SDenaturation midpoint: Assuming two-state protein folding, denaturation midpoint is defined as that temperature (Tm) or denaturant concentration (Cm) at which both the folded and unfolded states are equally populated at equilibrium. Tm is often determined using a thermal shift assay.Surface modification: Surface modification is the act of modifying the surface of a material by bringing physical, chemical or biological characteristics different from the ones originally found on the surface of a material.Ethyl groupDNA condensation: DNA condensation refers to the process of compacting DNA molecules in vitro or in vivo. Mechanistic details of DNA packing are essential for its functioning in the process of gene regulation in living systems.Temporal analysis of products: Temporal Analysis of Products (TAP), (TAP-2), (TAP-3) is an experimental technique for studyingMyoglobin: Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, specifically in the red blood cells.Chemically induced dimerization: Chemically Induced Dimerization (CID) is a biological mechanism in which two proteins bind only in the presence of a certain small molecule, enzyme or other dimerizing agent. Genetically engineered CID systems are used in biological research to control protein localization, to manipulate signalling pathways and to induce protein activation.Monte Carlo methods for option pricing: In mathematical finance, a Monte Carlo option model uses Monte Carlo methods Although the term 'Monte Carlo method' was coined by Stanislaw Ulam in the 1940s, some trace such methods to the 18th century French naturalist Buffon, and a question he asked about the results of dropping a needle randomly on a striped floor or table. See Buffon's needle.Inverse probability weighting: Inverse probability weighting is a statistical technique for calculating statistics standardized to a population different from that in which the data was collected. Study designs with a disparate sampling population and population of target inference (target population) are common in application.Twist compression tester: The Twist Compression Tester ("TCT") is a hydraulically operated bench-top apparatus used to evaluate the level of friction and/or wear between two materials under lubricated or non-lubricated conditions.Von Neumann regular ring: In mathematics, a von Neumann regular ring is a ring R such that for every a in R there exists an x in R such that . To avoid the possible confusion with the regular rings and regular local rings of commutative algebra (which are unrelated notions), von Neumann regular rings are also called absolutely flat rings, because these rings are characterized by the fact that every left module is flat.Diffractometer: A diffractometer (pronunciation: di-"frak-'tä-m&-t&r) is a measuring instrument for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (such as X-rays or neutrons) interacts with it.MIPModDB: MIPModDB is a database of comparative protein structure models of MIP (Major intrinsic proteins) family of proteins.Nanopore sequencing: Nanopore sequencing is a method under development since 1995 for determining the order in which nucleotides occur on a strand of DNA.Acid catalysis: In acid catalysis and base catalysis a chemical reaction is catalyzed by an acid or a base. The acid is the proton donor and the base is the proton acceptor.PSI Protein Classifier: PSI Protein Classifier is a program generalizing the results of both successive and independent iterations of the PSI-BLAST program. PSI Protein Classifier determines belonging of the found by PSI-BLAST proteins to the known families.RV coefficient: In statistics, the RV coefficientOctaneFerric uptake regulator family: In molecular biology, the ferric uptake regulator (FUR) family of proteins includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria.Moens–Korteweg equation: In biomechanics, the Moens–Korteweg equation models the relationship between wave speed or pulse wave velocity (PWV) and the incremental elastic modulus of the arterial wall or its distensibility. The equation was derived independently by Adriaan Isebree Moens and Diederik Korteweg.Kosmotropic: Co-solvents (in water solvent) are defined as kosmotropic (order-making) if they contribute to the stability and structure of water-water interactions. Kosmotropes cause water molecules to favorably interact, which also (in effect) stabilizes intramolecular interactions in macromolecules such as proteins.Stretch-activated ion channel: Stretch-activated or stretch-gated ion channels are ion channels which open their pores in response to mechanical deformation of a neuron's plasma membrane. Also see mechanosensitive ion channels and mechanosensitive channels, with which they may be synonymous.Specificity constant: In the field of biochemistry, the specificity constant (also called kinetic efficiency or k_{cat}/K_{M}), is a measure of how efficiently an enzyme converts substrates into products. A comparison of specificity constants can also be used as a measure of the preference of an enzyme for different substrates (i.Cell membraneDynamic strain aging: Although sometimes dynamic strain aging is used interchangeably with the Portevin–Le Chatelier effect (or serrated yielding), dynamic strain aging refers specifically to the microscopic mechanism that induces the Portevin–Le Chatelier effect. This strengthening mechanism is related to solid-solution strengthening and has been observed in a variety of fcc and bcc substitutional and interstitial alloys, metalloids like silicon, and ordered intermetallics within specific ranges of temperature and strain rate.HexaneTryptophan operon leaderNanosensors (company)Doxanthrine: Doxanthrine is a synthetic compound which is a potent and selective full agonist for the dopamine D1 receptor. Doxanthrine has been shown to be orally active in producing contralateral rotation in the 6-hydroxy-dopamine rat model of Parkinson's disease.Amyloid: Amyloids are insoluble fibrous protein [species|aggregates] sharing specific structural traits. They are insoluble and arise from at least 18 inappropriately folded versions of proteins and polypeptides present naturally in the body.Powder diffraction: Powder diffraction is a scientific technique using X-ray, neutron, or electron diffraction on powder or microcrystalline samples for structural characterization of materials.B.