Mathematical optimizationMathematical optimization (alternatively spelled optimisation) or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries.
Pontryagin's maximum principlePontryagin's maximum principle is used in optimal control theory to find the best possible control for taking a dynamical system from one state to another, especially in the presence of constraints for the state or input controls. It states that it is necessary for any optimal control along with the optimal state trajectory to solve the so-called Hamiltonian system, which is a two-point boundary value problem, plus a maximum condition of the control Hamiltonian.
Multiple sequence alignmentMultiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.
Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Hamiltonian (control theory)The Hamiltonian is a function used to solve a problem of optimal control for a dynamical system. It can be understood as an instantaneous increment of the Lagrangian expression of the problem that is to be optimized over a certain time period. Inspired by—but distinct from—the Hamiltonian of classical mechanics, the Hamiltonian of optimal control theory was developed by Lev Pontryagin as part of his maximum principle. Pontryagin proved that a necessary condition for solving the optimal control problem is that the control should be chosen so as to optimize the Hamiltonian.
Reinforcement learningReinforcement learning (RL) is an area of machine learning concerned with how intelligent agents ought to take actions in an environment in order to maximize the notion of cumulative reward. Reinforcement learning is one of three basic machine learning paradigms, alongside supervised learning and unsupervised learning. Reinforcement learning differs from supervised learning in not needing labelled input/output pairs to be presented, and in not needing sub-optimal actions to be explicitly corrected.
Rotating disk electrodeIn analytical chemistry, a rotating disk electrode (RDE) is a working electrode used in three-electrode systems for hydrodynamic voltammetry. The electrode rotates during experiments, inducing a flux of analyte to the electrode. These working electrodes are used in electrochemical studies when investigating reaction mechanisms related to redox chemistry, among other chemical phenomena. The more complex rotating ring-disk electrode can be used as a rotating disk electrode if the ring is left inactive during the experiment.
Hydrodynamic voltammetryIn analytical chemistry, hydrodynamic voltammetry is a form of voltammetry in which the analyte solution flows relative to a working electrode. In many voltammetry techniques, the solution is intentionally left still to allow diffusion-controlled mass transfer. When a solution is made to flow, through stirring or some other physical mechanism, it is very important to the technique to achieve a very controlled flux or mass transfer in order to obtain predictable results.
Operations researchOperations research (operational research) (U.S. Air Force Specialty Code: Operations Analysis), often shortened to the initialism OR, is a discipline that deals with the development and application of analytical methods to improve decision-making. The term management science is occasionally used as a synonym. Employing techniques from other mathematical sciences, such as modeling, statistics, and optimization, operations research arrives at optimal or near-optimal solutions to decision-making problems.
Structural alignmentStructural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.
