XOR gateXOR gate (sometimes EOR, or EXOR and pronounced as Exclusive OR) is a digital logic gate that gives a true (1 or HIGH) output when the number of true inputs is odd. An XOR gate implements an exclusive or () from mathematical logic; that is, a true output results if one, and only one, of the inputs to the gate is true. If both inputs are false (0/LOW) or both are true, a false output results. XOR represents the inequality function, i.e., the output is true if the inputs are not alike otherwise the output is false.
Quantum logic gateIn quantum computing and specifically the quantum circuit model of computation, a quantum logic gate (or simply quantum gate) is a basic quantum circuit operating on a small number of qubits. They are the building blocks of quantum circuits, like classical logic gates are for conventional digital circuits. Unlike many classical logic gates, quantum logic gates are reversible. It is possible to perform classical computing using only reversible gates.
Allosteric regulationIn biochemistry, allosteric regulation (or allosteric control) is the regulation of an enzyme by binding an effector molecule at a site other than the enzyme's active site. The site to which the effector binds is termed the allosteric site or regulatory site. Allosteric sites allow effectors to bind to the protein, often resulting in a conformational change and/or a change in protein dynamics. Effectors that enhance the protein's activity are referred to as allosteric activators, whereas those that decrease the protein's activity are called allosteric inhibitors.
NAND gateIn digital electronics, a NAND gate (NOT-AND) is a logic gate which produces an output which is false only if all its inputs are true; thus its output is complement to that of an AND gate. A LOW (0) output results only if all the inputs to the gate are HIGH (1); if any input is LOW (0), a HIGH (1) output results. A NAND gate is made using transistors and junction diodes. By De Morgan's laws, a two-input NAND gate's logic may be expressed as =+, making a NAND gate equivalent to inverters followed by an OR gate.
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.
Conformational changeProtein dynamics In biochemistry, a conformational change is a change in the shape of a macromolecule, often induced by environmental factors. A macromolecule is usually flexible and dynamic. Its shape can change in response to changes in its environment or other factors; each possible shape is called a conformation, and a transition between them is called a conformational change. Factors that may induce such changes include temperature, pH, voltage, light in chromophores, concentration of ions, phosphorylation, or the binding of a ligand.
Logic gateA logic gate is an idealized or physical device that performs a Boolean function, a logical operation performed on one or more binary inputs that produces a single binary output. Depending on the context, the term may refer to an ideal logic gate, one that has, for instance, zero rise time and unlimited fan-out, or it may refer to a non-ideal physical device (see ideal and real op-amps for comparison). In the real world, the primary way of building logic gates uses diodes or transistors acting as electronic switches.
Molecular machineMolecular machines are a class of molecules typically described as an assembly of a discrete number of molecular components intended to produce mechanical movements in response to specific stimuli, mimicking macromolecular devices such as switches and motors. Naturally occurring or biological molecular machines are responsible for vital living processes such as DNA replication and ATP synthesis. Kinesins and ribosomes are examples of molecular machines, and they often take the form of multi-protein complexes.
OR gateThe OR gate is a digital logic gate that implements logical disjunction. The OR gate returns true if any of its inputs are true; otherwise it returns false. The input and output states are normally represented by different voltage levels. Any OR gate can be constructed with two or more inputs. It outputs a 1 if any of these inputs are 1, or outputs a 0 only if all inputs are 0. The inputs and outputs are binary digits ("bits") which have two possible logical states.
Binding siteIn biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may include other proteins (resulting in a protein-protein interaction), enzyme substrates, second messengers, hormones, or allosteric modulators. The binding event is often, but not always, accompanied by a conformational change that alters the protein's function.
AND gateThe AND gate is a basic digital logic gate that implements logical conjunction (∧) from mathematical logic - AND gate behaves according to the truth table. A HIGH output (1) results only if all the inputs to the AND gate are HIGH (1). If not all inputs to the AND gate are HIGH, LOW output results. The function can be extended to any number of inputs. There are three symbols for AND gates: the American (ANSI or 'military') symbol and the IEC ('European' or 'rectangular') symbol, as well as the deprecated DIN symbol.
Protein structureProtein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers - specifically polypeptides - formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a residue, which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond.
Active siteIn biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the binding site, and residues that catalyse a reaction of that substrate, the catalytic site. Although the active site occupies only ~10–20% of the volume of an enzyme, it is the most important part as it directly catalyzes the chemical reaction.
Inverter (logic gate)In digital logic, an inverter or NOT gate is a logic gate which implements logical negation. It outputs a bit opposite of the bit that is put into it. The bits are typically implemented as two differing voltage levels. The NOT gate outputs a zero when given a one, and a one when given a zero. Hence, it inverts its inputs. Colloquially, this inversion of bits is called "flipping" bits. As with all binary logic gates, other pairs of symbols such as true and false, or high and low may be used in lieu of one and zero.
XNOR gateThe XNOR gate (sometimes ENOR, EXNOR or NXOR and pronounced as Exclusive NOR) is a digital logic gate whose function is the logical complement of the Exclusive OR (XOR) gate. It is equivalent to the logical connective () from mathematical logic, also known as the material biconditional. The two-input version implements logical equality, behaving according to the truth table to the right, and hence the gate is sometimes called an "equivalence gate". A high output (1) results if both of the inputs to the gate are the same.
Fredkin gateThe Fredkin gate (also CSWAP gate and conservative logic gate) is a computational circuit suitable for reversible computing, invented by Edward Fredkin. It is universal, which means that any logical or arithmetic operation can be constructed entirely of Fredkin gates. The Fredkin gate is a circuit or device with three inputs and three outputs that transmits the first bit unchanged and swaps the last two bits if, and only if, the first bit is 1. The basic Fredkin gate is a controlled swap gate that maps three inputs (C, I1, I2) onto three outputs (C, O1, O2).
Protein dynamicsProteins are generally thought to adopt unique structures determined by their amino acid sequences. However, proteins are not strictly static objects, but rather populate ensembles of (sometimes similar) conformations. Transitions between these states occur on a variety of length scales (tenths of Å to nm) and time scales (ns to s), and have been linked to functionally relevant phenomena such as allosteric signaling and enzyme catalysis.
Intrinsically disordered proteinsIn molecular biology, an intrinsically disordered protein (IDP) is a protein that lacks a fixed or ordered three-dimensional structure, typically in the absence of its macromolecular interaction partners, such as other proteins or RNA. IDPs range from fully unstructured to partially structured and include random coil, molten globule-like aggregates, or flexible linkers in large multi-domain proteins. They are sometimes considered as a separate class of proteins along with globular, fibrous and membrane proteins.
Systems biologySystems biology is the computational and mathematical analysis and modeling of complex biological systems. It is a biology-based interdisciplinary field of study that focuses on complex interactions within biological systems, using a holistic approach (holism instead of the more traditional reductionism) to biological research. Particularly from the year 2000 onwards, the concept has been used widely in biology in a variety of contexts.
Diode logicDiode logic (or diode-resistor logic) constructs AND and OR logic gates with diodes and resistors. An active device (vacuum tubes in early computers, then transistors in diode–transistor logic) is additionally required to provide logical inversion (NOT) for functional completeness and amplification for voltage level restoration, which diode logic alone can't provide. Since voltage levels weaken with each diode logic stage, multiple stages can't easily be cascaded, limiting diode logic's usefulness.
