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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 calculations to formally derive a continuum model of solvent effects suitable for computer simulations of small and large molecular systems. The model is included in the CHARMM Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CH ... molecular mechanics code. References External links An essay on SCP-ISMCHARMM website Molecular d ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Continuum Approximation
Continuum (: continua or continuums) theories or models explain variation as involving gradual quantitative transitions without abrupt changes or discontinuities. In contrast, categorical theories or models explain variation using qualitatively different states. In physics In physics, for example, the space-time continuum model describes space and time as part of the same continuum rather than as separate entities. A spectrum in physics, such as the electromagnetic spectrum, is often termed as either continuous (with energy at all wavelengths) or discrete (energy at only certain wavelengths). In contrast, quantum mechanics uses quanta, certain defined amounts (i.e. categorical amounts) which are distinguished from continuous amounts. In mathematics and philosophy A good introduction to the philosophical issues involved is John Lane Bell's essay in the ''Stanford Encyclopedia of Philosophy''. A significant divide is provided by the law of excluded middle. It determin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvent
A solvent (from the Latin language, Latin ''wikt:solvo#Latin, solvō'', "loosen, untie, solve") is a substance that dissolves a solute, resulting in a Solution (chemistry), solution. A solvent is usually a liquid but can also be a solid, a gas, or a supercritical fluid. Water is a solvent for Chemical polarity#Polarity of molecules, polar molecules, and the most common solvent used by living things; all the ions and proteins in a Cell (biology), cell are dissolved in water within the cell. Major uses of solvents are in paints, paint removers, inks, and dry cleaning. Specific uses for Organic compound, 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 (D-limonene, citrus terpenes); and in perfumes (ethanol). Solvents find various applications in chemical, pharmaceutical, oil, and gas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computer Simulations
Computer simulation is the running of a mathematical model on a computer, the model being designed to represent 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-scale p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Biology
Biology is the scientific study of life and living organisms. It is a broad natural science that encompasses a wide range of fields and unifying principles that explain the structure, function, growth, History of life, origin, evolution, and distribution of life. Central to biology are five fundamental themes: the cell (biology), cell as the basic unit of life, genes and heredity as the basis of inheritance, evolution as the driver of biological diversity, energy transformation for sustaining life processes, and the maintenance of internal stability (homeostasis). Biology examines life across multiple biological organisation, levels of organization, from molecules and cells to organisms, populations, and ecosystems. Subdisciplines include molecular biology, physiology, ecology, evolutionary biology, developmental biology, and systematics, among others. Each of these fields applies a range of methods to investigate biological phenomena, including scientific method, observation, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Macromolecule
A macromolecule is a "molecule of high relative molecular mass, the structure of which essentially comprises the multiple repetition of units derived, actually or conceptually, from molecules of low relative molecular mass." Polymers are physical examples of macromolecules. Common macromolecules are biopolymers (nucleic acids, proteins, and carbohydrates). and polyolefins (polyethylene) and polyamides (nylon). Synthetic macromolecules Many macromolecules are synthetic polymers (plastics, synthetic fibers, and synthetic rubber. Polyethylene is produced on a particularly large scale such that ethylene is the primary product in the chemical industry. Macromolecules in nature * Proteins are polymers of amino acids joined by peptide bonds. * DNA and RNA are polymers of nucleotides joined by phosphodiester bonds. These nucleotides consist of a phosphate group, a sugar ( ribose in the case of RNA, deoxyribose in the case of DNA), and a nucleotide base (either adenine, guan ... [...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] |
Nucleic Acid
Nucleic acids are large biomolecules that are crucial in all cells and viruses. They are composed of nucleotides, which are the monomer components: a pentose, 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 deoxyribose, a variant of ribose, the polymer is DNA. Nucleic acids are chemical compounds that are found in nature. They carry information in cells and make up genetic material. These acids are very common in all living things, where they create, encode, and store information in every living cell of every outline of life forms, life-form on Earth. In turn, they send and express that information inside and outside the cell nucleus. From the inner workings of the cell to the young of a living thing, they contain and provide information via the nucleic acid sequence. This gives the RNA and DNA their unmistakable 'la ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Dynamics
Molecular dynamics (MD) is a computer simulation method for analyzing the Motion (physics), 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 dynamics (mechanics), dynamic "evolution" of the system. In the most common version, the trajectory, trajectories of atoms and molecules are determined by Numerical integration, numerically solving Newton's laws of motion, Newton's equations of motion for a system of interacting particles, where Force (physics), forces between the particles and their potential energy, potential energies are often calculated using interatomic potentials or molecular mechanics, molecular mechanical Force field (chemistry), 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 analyt ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Intermolecular Force
An intermolecular force (IMF; also 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 first reference to the nature of microscopic forces is found in Alexis Clairaut's work ''Théorie de la figure de la Terre,'' published in Paris in 1743. Other scientists who have contributed to the investigation of microscopic forces include: Laplace, Gauss, Maxwell, Boltzmann and Pauling. Attractive intermolecular forces are categorized into the following ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peter Debye
Peter Joseph William Debye ( ; born Petrus Josephus Wilhelmus Debije, ; March 24, 1884 – November 2, 1966) was a Dutch-American physicist and physical chemist, and Nobel laureate in Chemistry. Biography Early life Born 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 profes ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Lars Onsager
Lars Onsager (November 27, 1903 – October 5, 1976) was a Norwegian 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, Norwegian Institute of Technology (NTH) in Trondheim, graduating as a chemical engineering, chemical engineer in 1925. While there he worked through ''A Course of Modern Analysis'', which was instrumental in his later work. Career and research In 1925 he arrived at a correction to the Debye–Hückel equation, Debye-Hückel theory of electrolyte, electrolytic Solution (chemistry), solutions, to specify Brownian movement of ions in solution, and during 1926 published it. He traveled to Zürich, where Peter Debye was teaching, and ... [...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 Thermodynamics, 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
