Implicit solvationImplicit solvation (sometimes termed continuum solvation) is a method to represent solvent as a continuous medium instead of individual “explicit” solvent molecules, most often used in molecular dynamics simulations and in other applications of molecular mechanics. The method is often applied to estimate free energy of solute-solvent interactions in structural and chemical processes, such as folding or conformational transitions of proteins, DNA, RNA, and polysaccharides, association of biological macromolecules with ligands, or transport of drugs across biological membranes.
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.
Water modelIn computational chemistry, a water model is used to simulate and thermodynamically calculate water clusters, liquid water, and aqueous solutions with explicit solvent. The models are determined from quantum mechanics, molecular mechanics, experimental results, and these combinations. To imitate a specific nature of molecules, many types of models have been developed. In general, these can be classified by the following three points; (i) the number of interaction points called site, (ii) whether the model is rigid or flexible, (iii) whether the model includes polarization effects.
Molecular mechanicsMolecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms.
Problem solvingProblem solving is the process of achieving a goal by overcoming obstacles, a frequent part of most activities. Problems in need of solutions range from simple personal tasks (e.g. how to turn on an appliance) to complex issues in business and technical fields. The former is an example of simple problem solving (SPS) addressing one issue, whereas the latter is complex problem solving (CPS) with multiple interrelated obstacles.
Molecular modellingMolecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.
Dimensionality reductionDimensionality reduction, or dimension reduction, is the transformation of data from a high-dimensional space into a low-dimensional space so that the low-dimensional representation retains some meaningful properties of the original data, ideally close to its intrinsic dimension. Working in high-dimensional spaces can be undesirable for many reasons; raw data are often sparse as a consequence of the curse of dimensionality, and analyzing the data is usually computationally intractable (hard to control or deal with).
Molecular orbitalIn chemistry, a molecular orbital (ɒrbədl) is a mathematical function describing the location and wave-like behavior of an electron in a molecule. This function can be used to calculate chemical and physical properties such as the probability of finding an electron in any specific region. The terms atomic orbital and molecular orbital were introduced by Robert S. Mulliken in 1932 to mean one-electron orbital wave functions. At an elementary level, they are used to describe the region of space in which a function has a significant amplitude.
Molecular biologyMolecular biology məˈlɛkjʊlər is the study of chemical and physical structure of biological macromolecules. It is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena—uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology.
Creative problem-solvingCreative problem-solving (CPS) is the mental process of searching for an original and previously unknown solution to a problem. To qualify, the solution must be novel and reached independently. The creative problem-solving process was originally developed by Alex Osborn and Sid Parnes. Creative problem solving (CPS) is a way of using creativity to develop new ideas and solutions to problems. The process is based on separating divergent and convergent thinking styles, so that one can focus one's mind on creating at the first stage, and then evaluating at the second stage.
Computational chemistryComputational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form.
Global optimizationGlobal optimization is a branch of applied mathematics and numerical analysis that attempts to find the global minima or maxima of a function or a set of functions on a given set. It is usually described as a minimization problem because the maximization of the real-valued function is equivalent to the minimization of the function . Given a possibly nonlinear and non-convex continuous function with the global minima and the set of all global minimizers in , the standard minimization problem can be given as that is, finding and a global minimizer in ; where is a (not necessarily convex) compact set defined by inequalities .
Osmotic pressureOsmotic pressure is the minimum pressure which needs to be applied to a solution to prevent the inward flow of its pure solvent across a semipermeable membrane. It is also defined as the measure of the tendency of a solution to take in its pure solvent by osmosis. Potential osmotic pressure is the maximum osmotic pressure that could develop in a solution if it were separated from its pure solvent by a semipermeable membrane. Osmosis occurs when two solutions containing different concentrations of solute are separated by a selectively permeable membrane.
Chemical equilibriumIn a chemical reaction, chemical equilibrium is the state in which both the reactants and products are present in concentrations which have no further tendency to change with time, so that there is no observable change in the properties of the system. This state results when the forward reaction proceeds at the same rate as the reverse reaction. The reaction rates of the forward and backward reactions are generally not zero, but they are equal. Thus, there are no net changes in the concentrations of the reactants and products.
NanoclusterNanoclusters are atomically precise, crystalline materials most often existing on the 0-2 nanometer scale. They are often considered kinetically stable intermediates that form during the synthesis of comparatively larger materials such as semiconductor and metallic nanocrystals. The majority of research conducted to study nanoclusters has focused on characterizing their crystal structures and understanding their role in the nucleation and growth mechanisms of larger materials.
Nonlinear dimensionality reductionNonlinear dimensionality reduction, also known as manifold learning, refers to various related techniques that aim to project high-dimensional data onto lower-dimensional latent manifolds, with the goal of either visualizing the data in the low-dimensional space, or learning the mapping (either from the high-dimensional space to the low-dimensional embedding or vice versa) itself. The techniques described below can be understood as generalizations of linear decomposition methods used for dimensionality reduction, such as singular value decomposition and principal component analysis.
Molecular engineeringMolecular engineering is an emerging field of study concerned with the design and testing of molecular properties, behavior and interactions in order to assemble better materials, systems, and processes for specific functions. This approach, in which observable properties of a macroscopic system are influenced by direct alteration of a molecular structure, falls into the broader category of “bottom-up” design.
OsmosisOsmosis (ɒzˈmoʊsɪs, ɒs-) is the spontaneous net movement or diffusion of solvent molecules through a selectively-permeable membrane from a region of high water potential (region of lower solute concentration) to a region of low water potential (region of higher solute concentration), in the direction that tends to equalize the solute concentrations on the two sides. It may also be used to describe a physical process in which any solvent moves across a selectively permeable membrane (permeable to the solvent, but not the solute) separating two solutions of different concentrations.
Open clusterAn open cluster is a type of star cluster made of tens to a few thousand stars that were formed from the same giant molecular cloud and have roughly the same age. More than 1,100 open clusters have been discovered within the Milky Way galaxy, and many more are thought to exist. They are loosely bound by mutual gravitational attraction and become disrupted by close encounters with other clusters and clouds of gas as they orbit the Galactic Center.
MoleculeA molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and molecule is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.
