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Screened Coulomb Potentials Implicit Solvent Model
SCP-ISM, or screened Coulomb potentials implicit solvent model, is a continuum approximation of solvent effects for use in computer simulations of biological macromolecules, such as proteins and nucleic acids, usually within the framework of molecular dynamics. It is based on the classic theory of polar liquids, as developed by Peter Debye and corrected by Lars Onsager to incorporate reaction field effects. The model can be combined with quantum chemical Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions ... calculations to formally derive a continuum model of solvent effects suitable for computer simulations of small and large molecular systems. External links An essay on SCP-ISMCHARMM website Molecular dynamics {{chem-software-stub ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvent
A solvent (s) (from the Latin '' solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for polar molecules and the most common solvent used by living things; all the ions and proteins in a cell are dissolved in water within the cell. The quantity of solute that can dissolve in a specific volume of solvent varies with temperature. Major uses of solvents are in paints, paint removers, inks, and dry cleaning. Specific uses for organic solvents are in dry cleaning (e.g. tetrachloroethylene); as paint thinners (toluene, turpentine); as nail polish removers and solvents of glue (acetone, methyl acetate, ethyl acetate); in spot removers (hexane, petrol ether); in detergents ( citrus terpenes); and in perfumes (ethanol). Solvents find various applications in chemical, pharmaceutical, oil, and gas industries, including in chemical syn ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computer Simulations
Computer simulation is the process of mathematical modelling, performed on a computer, which is designed to predict the behaviour of, or the outcome of, a real-world or physical system. The reliability of some mathematical models can be determined by comparing their results to the real-world outcomes they aim to predict. Computer simulations have become a useful tool for the mathematical modeling of many natural systems in physics (computational physics), astrophysics, climatology, chemistry, biology and manufacturing, as well as human systems in economics, psychology, social science, health care and engineering. Simulation of a system is represented as the running of the system's model. It can be used to explore and gain new insights into new technology and to estimate the performance of systems too complex for analytical solutions. Computer simulations are realized by running computer programs that can be either small, running almost instantly on small devices, or large ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biology
Biology is the scientific study of life. It is a natural science with a broad scope but has several unifying themes that tie it together as a single, coherent field. For instance, all organisms are made up of cells that process hereditary information encoded in genes, which can be transmitted to future generations. Another major theme is evolution, which explains the unity and diversity of life. Energy processing is also important to life as it allows organisms to move, grow, and reproduce. Finally, all organisms are able to regulate their own internal environments. Biologists are able to study life at multiple levels of organization, from the molecular biology of a cell to the anatomy and physiology of plants and animals, and evolution of populations.Based on definition from: Hence, there are multiple subdisciplines within biology, each defined by the nature of their research questions and the tools that they use. Like other scientists, biologists use the sc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Macromolecule
A macromolecule is a very large molecule important to biophysical processes, such as a protein or nucleic acid. It is composed of thousands of covalently bonded atoms. Many macromolecules are polymers of smaller molecules called monomers. The most common macromolecules in biochemistry are biopolymers (nucleic acids, proteins, and carbohydrates) and large non-polymeric molecules such as lipids, nanogels and macrocycles. Synthetic fibers and experimental materials such as carbon nanotubes are also examples of macromolecules. Definition The term ''macromolecule'' (''macro-'' + ''molecule'') was coined by Nobel laureate Hermann Staudinger in the 1920s, although his first relevant publication on this field only mentions ''high molecular compounds'' (in excess of 1,000 atoms). At that time the term ''polymer'', as introduced by Berzelius in 1832, had a different meaning from that of today: it simply was another form of isomerism for example with benzene and acetylene and had litt ... [...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 residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 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 peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residue ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nucleic Acid
Nucleic acids are biopolymers, macromolecules, essential to all known forms of life. They are composed of nucleotides, which are the monomers made of three components: a 5-carbon sugar, a phosphate group and a nitrogenous base. The two main classes of nucleic acids are deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). If the sugar is ribose, the polymer is RNA; if the sugar is the ribose derivative deoxyribose, the polymer is DNA. Nucleic acids are naturally occurring chemical compounds that serve as the primary information-carrying molecules in cells and make up the genetic material. Nucleic acids are found in abundance in all living things, where they create, encode, and then store information of every living cell of every life-form on Earth. In turn, they function to transmit and express that information inside and outside the cell nucleus to the interior operations of the cell and ultimately to the next generation of each living organism. The encoded information is ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular 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. The method is applied mostly in chemical physics, materials science, and biophysics. Because molecular systems typically consist of a vast number of particles, it is impossible to determine the properties of such complex systems analytically; MD simulation circumvents this problem by using numerical methods. However, long MD simulations are mathematically ill-conditioned, generating cumulative errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intermolecular Force
An intermolecular force (IMF) (or secondary force) is the force that mediates interaction between molecules, including the electromagnetic forces of attraction or repulsion which act between atoms and other types of neighbouring particles, e.g. atoms or ions. Intermolecular forces are weak relative to intramolecular forces – the forces which hold a molecule together. For example, the covalent bond, involving sharing electron pairs between atoms, is much stronger than the forces present between neighboring molecules. Both sets of forces are essential parts of force fields frequently used in molecular mechanics. The investigation of intermolecular forces starts from macroscopic observations which indicate the existence and action of forces at a molecular level. These observations include non-ideal-gas thermodynamic behavior reflected by virial coefficients, vapor pressure, viscosity, superficial tension, and absorption data. The first reference to the nature of microscopic forc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peter Debye
Peter Joseph William Debye (; ; March 24, 1884 – November 2, 1966) was a Dutch-American physicist and physical chemist, and Nobel laureate in Chemistry. Biography Early life Born Petrus Josephus Wilhelmus Debije in Maastricht, Netherlands, Debye enrolled in the Aachen University of Technology in 1901. In 1905, he completed his first degree in electrical engineering. He published his first paper, a mathematically elegant solution of a problem involving eddy currents, in 1907. At Aachen, he studied under the theoretical physicist Arnold Sommerfeld, who later claimed that his most important discovery was Peter Debye. In 1906, Sommerfeld received an appointment at Munich, Bavaria, and took Debye with him as his assistant. Debye got his Ph.D. with a dissertation on radiation pressure in 1908. In 1910, he derived the Planck radiation formula using a method which Max Planck agreed was simpler than his own. In 1911, when Albert Einstein took an appointment as a professor at Prague ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lars Onsager
Lars Onsager (November 27, 1903 – October 5, 1976) was a Norwegian-born American physical chemist and theoretical physicist. He held the Gibbs Professorship of Theoretical Chemistry at Yale University. He was awarded the Nobel Prize in Chemistry in 1968. Education and early life Lars Onsager was born in Kristiania (now Oslo), Norway. His father was a lawyer. After completing secondary school in Oslo, he attended the Norwegian Institute of Technology (NTH) in Trondheim, graduating as a chemical engineer in 1925. Career and research In 1925 he arrived at a correction to the Debye-Hückel theory of electrolytic solutions, to specify Brownian movement of ions in solution, and during 1926 published it. He traveled to Zürich, where Peter Debye was teaching, and confronted Debye, telling him his theory was wrong. He impressed Debye so much that he was invited to become Debye's assistant at the Eidgenössische Technische Hochschule (ETH), where he remained until 1928. Johns ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantum Chemistry
Quantum chemistry, also called molecular quantum mechanics, is a branch of physical chemistry focused on the application of quantum mechanics to chemical systems, particularly towards the quantum-mechanical calculation of electronic contributions to physical and chemical properties of Molecule, molecules, Material, materials, and solutions at the atomic level. These calculations include systematically applied approximations intended to make calculations computationally feasible while still capturing as much information about important contributions to the computed Wave function, wave functions as well as to observable properties such as structures, spectra, and thermodynamic properties. Quantum chemistry is also concerned with the computation of quantum effects on molecular dynamics and chemical kinetics. Chemists rely heavily on spectroscopy through which information regarding the Quantization (physics), quantization of energy on a molecular scale can be obtained. Common metho ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
