Molecular dynamicsMolecular 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.
Organic horticultureOrganic horticulture is the science and art of growing fruits, vegetables, flowers, or ornamental plants by following the essential principles of organic agriculture in soil building and conservation, pest management, and heirloom variety preservation. The Latin words hortus (garden plant) and cultura (culture) together form horticulture, classically defined as the culture or growing of garden plants. Horticulture is also sometimes defined simply as "agriculture minus the plough".
Organic farmingOrganic farming, also known as ecological farming or biological farming, is an agricultural system that uses fertilizers of organic origin such as compost manure, green manure, and bone meal and places emphasis on techniques such as crop rotation and companion planting. It originated early in the 20th century in reaction to rapidly changing farming practices. Certified organic agriculture accounts for globally, with over half of that total in Australia. Organic farming continues to be developed by various organizations today.
Abalone (molecular mechanics)Abalone is a general purpose molecular dynamics and molecular graphics program for simulations of bio-molecules in a periodic boundary conditions in explicit (flexible SPC water model) or in implicit water models. Mainly designed to simulate the protein folding and DNA-ligand complexes in AMBER force field. 3D molecular graphics Automatic Force Field generator for bioelements: H, C, N, O Building and editing chemical structures Library of building blocks Force fields: Assisted Model Building with Energy Re
Organic chemistryOrganic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms. Study of structure determines their structural formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior.
Reaction mechanismIn chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical reaction occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction.
Organic certificationOrganic certification is a certification process for producers of organic food and other organic agricultural products, in the European Union more commonly known as ecological or biological products. In general, any business directly involved in food production can be certified, including seed suppliers, farmers, food processors, retailers and restaurants. A lesser known counterpart is certification for organic textiles (or organic clothing) that includes certification of textile products made from organically grown fibres.
Organic foodOrganic food, ecological food, or biological food are foods and drinks produced by methods complying with the standards of organic farming. Standards vary worldwide, but organic farming features practices that cycle resources, promote ecological balance, and conserve biodiversity. Organizations regulating organic products may restrict the use of certain pesticides and fertilizers in the farming methods used to produce such products. Organic foods are typically not processed using irradiation, industrial solvents, or synthetic food additives.
Conformational isomerismIn chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers.
Computational scienceComputational science, also known as scientific computing, technical computing or scientific computation (SC), is a division of science that uses advanced computing capabilities to understand and solve complex physical problems. This includes Algorithms (numerical and non-numerical): mathematical models, computational models, and computer simulations developed to solve sciences (e.
Outline of organic gardening and farmingThe following outline is provided as an overview of and topical guide to organic gardening and farming: Organic farming – alternative agricultural system that relies on fertilizers of organic origin such as compost, manure, green manure, and bone meal and places emphasis on techniques such as crop rotation and companion planting. Biological pest control, mixed cropping and the fostering of insect predators are encouraged. Organic standards, in general, are intended to enable the use of naturally occurring compounds while restricting or strongly limiting the use of manufactured substances.
Docking (molecular)In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.
Electronic correlationElectronic correlation is the interaction between electrons in the electronic structure of a quantum system. The correlation energy is a measure of how much the movement of one electron is influenced by the presence of all other electrons. Within the Hartree–Fock method of quantum chemistry, the antisymmetric wave function is approximated by a single Slater determinant. Exact wave functions, however, cannot generally be expressed as single determinants.
Potential energy surfaceA potential energy surface (PES) describes the energy of a system, especially a collection of atoms, in terms of certain parameters, normally the positions of the atoms. The surface might define the energy as a function of one or more coordinates; if there is only one coordinate, the surface is called a potential energy curve or . An example is the Morse/Long-range potential. It is helpful to use the analogy of a landscape: for a system with two degrees of freedom (e.g.
Organic reactionOrganic reactions are chemical reactions involving organic compounds. The basic organic chemistry reaction types are addition reactions, elimination reactions, substitution reactions, pericyclic reactions, rearrangement reactions, photochemical reactions and redox reactions. In organic synthesis, organic reactions are used in the construction of new organic molecules. The production of many man-made chemicals such as drugs, plastics, food additives, fabrics depend on organic reactions.
TemperatureTemperature is a physical quantity that expresses quantitatively the perceptions of hotness and coldness. Temperature is measured with a thermometer. Thermometers are calibrated in various temperature scales that historically have relied on various reference points and thermometric substances for definition. The most common scales are the Celsius scale with the unit symbol °C (formerly called centigrade), the Fahrenheit scale (°F), and the Kelvin scale (K), the latter being used predominantly for scientific purposes.
Force field (chemistry)In the context of chemistry and molecular modelling, a force field is a computational method that is used to estimate the forces between atoms within molecules and also between molecules. More precisely, the force field refers to the functional form and parameter sets used to calculate the potential energy of a system of atoms or coarse-grained particles in molecular mechanics, molecular dynamics, or Monte Carlo simulations. The parameters for a chosen energy function may be derived from experiments in physics and chemistry, calculations in quantum mechanics, or both.
Pericyclic reactionIn organic chemistry, a pericyclic reaction is the type of organic reaction wherein the transition state of the molecule has a cyclic geometry, the reaction progresses in a concerted fashion, and the bond orbitals involved in the reaction overlap in a continuous cycle at the transition state. Pericyclic reactions stand in contrast to linear reactions, encompassing most organic transformations and proceeding through an acyclic transition state, on the one hand and coarctate reactions, which proceed through a doubly cyclic, concerted transition state on the other hand.
Elimination reactionAn elimination reaction is a type of organic reaction in which two substituents are removed from a molecule in either a one- or two-step mechanism. The one-step mechanism is known as the E2 reaction, and the two-step mechanism is known as the E1 reaction. The numbers refer not to the number of steps in the mechanism, but rather to the kinetics of the reaction: E2 is bimolecular (second-order) while E1 is unimolecular (first-order). In cases where the molecule is able to stabilize an anion but possesses a poor leaving group, a third type of reaction, E1CB, exists.
Coarse-grained modelingCoarse-grained modeling, coarse-grained models, aim at simulating the behaviour of complex systems using their coarse-grained (simplified) representation. Coarse-grained models are widely used for molecular modeling of biomolecules at various granularity levels. A wide range of coarse-grained models have been proposed. They are usually dedicated to computational modeling of specific molecules: proteins, nucleic acids, lipid membranes, carbohydrates or water.
