Metabolic engineeringMetabolic engineering is the practice of optimizing genetic and regulatory processes within cells to increase the cell's production of a certain substance. These processes are chemical networks that use a series of biochemical reactions and enzymes that allow cells to convert raw materials into molecules necessary for the cell's survival. Metabolic engineering specifically seeks to mathematically model these networks, calculate a yield of useful products, and pin point parts of the network that constrain the production of these products.
Reversible reactionA reversible reaction is a reaction in which the conversion of reactants to products and the conversion of products to reactants occur simultaneously. \mathit aA{} + \mathit bB \mathit cC{} + \mathit dD A and B can react to form C and D or, in the reverse reaction, C and D can react to form A and B. This is distinct from a reversible process in thermodynamics. Weak acids and bases undergo reversible reactions. For example, carbonic acid: H2CO3 (l) + H2O(l) ⇌ HCO3−(aq) + H3O+(aq).
Biological networkA biological network is a method of representing systems as complex sets of binary interactions or relations between various biological entities. In general, networks or graphs are used to capture relationships between entities or objects. A typical graphing representation consists of a set of nodes connected by edges. As early as 1736 Leonhard Euler analyzed a real-world issue known as the Seven Bridges of Königsberg, which established the foundation of graph theory. From the 1930's-1950's the study of random graphs were developed.
Protein–protein interactionProtein–protein interactions (PPIs) are physical contacts of high specificity established between two or more protein molecules as a result of biochemical events steered by interactions that include electrostatic forces, hydrogen bonding and the hydrophobic effect. Many are physical contacts with molecular associations between chains that occur in a cell or in a living organism in a specific biomolecular context. Proteins rarely act alone as their functions tend to be regulated.
Half-reactionIn chemistry, a half reaction (or half-cell reaction) is either the oxidation or reduction reaction component of a redox reaction. A half reaction is obtained by considering the change in oxidation states of individual substances involved in the redox reaction. Often, the concept of half reactions is used to describe what occurs in an electrochemical cell, such as a Galvanic cell battery. Half reactions can be written to describe both the metal undergoing oxidation (known as the anode) and the metal undergoing reduction (known as the cathode).
Network medicineNetwork medicine is the application of network science towards identifying, preventing, and treating diseases. This field focuses on using network topology and network dynamics towards identifying diseases and developing medical drugs. Biological networks, such as protein-protein interactions and metabolic pathways, are utilized by network medicine. Disease networks, which map relationships between diseases and biological factors, also play an important role in the field.
Derived categoryIn mathematics, the derived category D(A) of an A is a construction of homological algebra introduced to refine and in a certain sense to simplify the theory of derived functors defined on A. The construction proceeds on the basis that the of D(A) should be chain complexes in A, with two such chain complexes considered isomorphic when there is a chain map that induces an isomorphism on the level of homology of the chain complexes. Derived functors can then be defined for chain complexes, refining the concept of hypercohomology.
Concerted reactionIn chemistry, a concerted reaction is a chemical reaction in which all bond breaking and bond making occurs in a single step. Reactive intermediates or other unstable high energy intermediates are not involved. Concerted reaction rates tend not to depend on solvent polarity ruling out large buildup of charge in the transition state. The reaction is said to progress through a concerted mechanism as all bonds are formed and broken in concert. Pericyclic reactions, the S_N2 reaction, and some rearrangements - such as the Claisen rearrangement - are concerted reactions.
Biochemical cascadeA biochemical cascade, also known as a signaling cascade or signaling pathway, is a series of chemical reactions that occur within a biological cell when initiated by a stimulus. This stimulus, known as a first messenger, acts on a receptor that is transduced to the cell interior through second messengers which amplify the signal and transfer it to effector molecules, causing the cell to respond to the initial stimulus. Most biochemical cascades are series of events, in which one event triggers the next, in a linear fashion.
Chemical thermodynamicsChemical thermodynamics is the study of the interrelation of heat and work with chemical reactions or with physical changes of state within the confines of the laws of thermodynamics. Chemical thermodynamics involves not only laboratory measurements of various thermodynamic properties, but also the application of mathematical methods to the study of chemical questions and the spontaneity of processes. The structure of chemical thermodynamics is based on the first two laws of thermodynamics.
Automated reasoningIn computer science, in particular in knowledge representation and reasoning and metalogic, the area of automated reasoning is dedicated to understanding different aspects of reasoning. The study of automated reasoning helps produce computer programs that allow computers to reason completely, or nearly completely, automatically. Although automated reasoning is considered a sub-field of artificial intelligence, it also has connections with theoretical computer science and philosophy.
Derived functorIn mathematics, certain functors may be derived to obtain other functors closely related to the original ones. This operation, while fairly abstract, unifies a number of constructions throughout mathematics. It was noted in various quite different settings that a short exact sequence often gives rise to a "long exact sequence". The concept of derived functors explains and clarifies many of these observations. Suppose we are given a covariant left exact functor F : A → B between two A and B.
