Biological Computation
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Biological Computation
The concept of biological computation proposes that living organisms perform computations, and that as such, abstract ideas of information and computation may be key to understanding biology. As a field, biological computation can include the study of the systems biology computations performed by biota the design of algorithms inspired by the computational methods of biota, the design and engineering of manufactured computational devices using synthetic biology components and computer methods for the analysis of biological data, elsewhere called computational biology or bioinformatics. According to Dominique Chu, Mikhail Prokopenko, and J. Christian J. Ray, "the most important class of natural computers can be found in biological systems that perform computation on multiple levels. From molecular and cellular information processing networks to ecologies, economies and brains, life computes. Despite ubiquitous agreement on this fact going back as far as von Neumann automata and ...
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Organism
In biology, an organism () is any living system that functions as an individual entity. All organisms are composed of cells (cell theory). Organisms are classified by taxonomy into groups such as multicellular animals, plants, and fungi; or unicellular microorganisms such as protists, bacteria, and archaea. All types of organisms are capable of reproduction, growth and development, maintenance, and some degree of response to stimuli. Beetles, squids, tetrapods, mushrooms, and vascular plants are examples of multicellular organisms that differentiate specialized tissues and organs during development. A unicellular organism may be either a prokaryote or a eukaryote. Prokaryotes are represented by two separate domains – bacteria and archaea. Eukaryotic organisms are characterized by the presence of a membrane-bound cell nucleus and contain additional membrane-bound compartments called organelles (such as mitochondria in animals and plants ...
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McCulloch Pitts Neuron
An artificial neuron is a mathematical function conceived as a model of biological neurons, a neural network. Artificial neurons are elementary units in an artificial neural network. The artificial neuron receives one or more inputs (representing excitatory postsynaptic potentials and inhibitory postsynaptic potentials at neural dendrites) and sums them to produce an output (or , representing a neuron's action potential which is transmitted along its axon). Usually each input is separately weighted, and the sum is passed through a non-linear function known as an activation function or transfer function. The transfer functions usually have a sigmoid shape, but they may also take the form of other non-linear functions, piecewise linear functions, or step functions. They are also often monotonically increasing, continuous, differentiable and bounded. Non-monotonic, unbounded and oscillating activation functions with multiple zeros that outperform sigmoidal and ReLU like activatio ...
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Zero Player Game
A zero-player game or no-player game is a simulation game that has no sentient players. Types There are various different types of games that can be considered "zero-player". Determined by initial state A game that evolves as determined by its initial state, requiring no further input from humans is considered a zero-player game. Cellular automaton games that are determined by initial conditions including Conway's Game of Life are examples of this.' ''Progress Quest'' is another example, in the game the player sets up a artificial character, and afterwards the game plays itself with no further input from the player. '' Godville'' is a similar game that took inspiration from ''Progress Quest'', in the game the player is a god that can communicate with a non-player character hero, however the game can progress with no interaction from the player. Incremental games, sometimes called idle games, are games which do require some player intervention near the beginning however m ...
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Biological Computing
Biological computers use biologically derived molecules — such as DNA and/or proteins — to perform digital or real computations. The development of biocomputers has been made possible by the expanding new science of nanobiotechnology. The term nanobiotechnology can be defined in multiple ways; in a more general sense, nanobiotechnology can be defined as any type of technology that uses both nano-scale materials (i.e. materials having characteristic dimensions of 1-100 nanometers) and biologically based materials. A more restrictive definition views nanobiotechnology more specifically as the design and engineering of proteins that can then be assembled into larger, functional structures The implementation of nanobiotechnology, as defined in this narrower sense, provides scientists with the ability to engineer biomolecular systems specifically so that they interact in a fashion that can ultimately result in the computational functionality of a computer. Scientific background ...
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Artificial Neuron
An artificial neuron is a mathematical function conceived as a model of biological neurons, a neural network. Artificial neurons are elementary units in an artificial neural network. The artificial neuron receives one or more inputs (representing excitatory postsynaptic potentials and inhibitory postsynaptic potentials at neural dendrites) and sums them to produce an output (or , representing a neuron's action potential which is transmitted along its axon). Usually each input is separately weighted, and the sum is passed through a non-linear function known as an activation function or transfer function. The transfer functions usually have a sigmoid shape, but they may also take the form of other non-linear functions, piecewise linear functions, or step functions. They are also often monotonically increasing, continuous, differentiable and bounded. Non-monotonic, unbounded and oscillating activation functions with multiple zeros that outperform sigmoidal and ReLU like activ ...
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Neural Circuit
A neural circuit is a population of neurons interconnected by synapses to carry out a specific function when activated. Neural circuits interconnect to one another to form large scale brain networks. Biological neural networks have inspired the design of artificial neural networks, but artificial neural networks are usually not strict copies of their biological counterparts. Early study Early treatments of neural networks can be found in Herbert Spencer's ''Principles of Psychology'', 3rd edition (1872), Theodor Meynert's ''Psychiatry'' (1884), William James' ''Principles of Psychology'' (1890), and Sigmund Freud's Project for a Scientific Psychology (composed 1895). The first rule of neuronal learning was described by Hebb in 1949, in the Hebbian theory. Thus, Hebbian pairing of pre-synaptic and post-synaptic activity can substantially alter the dynamic characteristics of the synaptic connection and therefore either facilitate or inhibit signal transmission. In 1959, the ...
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Wetware Computer
A wetware computer is an organic computer (which can also be known as an artificial organic brain or a neurocomputer) composed of organic material " wetware" such as "living" neurons. Wetware computers composed of neurons are different than conventional computers because they are thought to be capable in a way of "thinking for themselves", because of the dynamic nature of neurons. While a wetware computer is still largely conceptual, there has been limited success with construction and prototyping, which has acted as a proof of the concept's realistic application to computing in the future. The most notable prototypes have stemmed from the research completed by biological engineer William Ditto during his time at the Georgia Institute of Technology. His work constructing a simple neurocomputer capable of basic addition from leech neurons in 1999 was a significant discovery for the concept. This research acted as a primary example driving interest in the creation of these artifi ...
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Interface (computing)
In computing, an interface is a shared boundary across which two or more separate components of a computer system exchange information. The exchange can be between software, computer hardware, peripheral devices, humans, and combinations of these. Some computer hardware devices, such as a touchscreen, can both send and receive data through the interface, while others such as a mouse or microphone may only provide an interface to send data to a given system. Hardware interfaces Hardware interfaces exist in many components, such as the various buses, storage devices, other I/O devices, etc. A hardware interface is described by the mechanical, electrical, and logical signals at the interface and the protocol for sequencing them (sometimes called signaling). See also: A standard interface, such as SCSI, decouples the design and introduction of computing hardware, such as I/O devices, from the design and introduction of other components of a computing system, thereby allow ...
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Mycelium
Mycelium (plural mycelia) is a root-like structure of a fungus consisting of a mass of branching, thread-like hyphae. Fungal colonies composed of mycelium are found in and on soil and many other substrates. A typical single spore germinates into a monokaryotic mycelium, which cannot reproduce sexually; when two compatible monokaryotic mycelia join and form a dikaryotic mycelium, that mycelium may form fruiting bodies such as mushrooms. A mycelium may be minute, forming a colony that is too small to see, or may grow to span thousands of acres as in ''Armillaria''. Through the mycelium, a fungus absorbs nutrients from its environment. It does this in a two-stage process. First, the hyphae secrete enzymes onto or into the food source, which break down biological polymers into smaller units such as monomers. These monomers are then absorbed into the mycelium by facilitated diffusion and active transport. Mycelia are vital in terrestrial and aquatic ecosystems for their role ...
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Basidiomycota
Basidiomycota () is one of two large divisions that, together with the Ascomycota, constitute the subkingdom Dikarya (often referred to as the "higher fungi") within the kingdom Fungi. Members are known as basidiomycetes. More specifically, Basidiomycota includes these groups: mushrooms, puffballs, stinkhorns, bracket fungi, other polypores, jelly fungi, boletes, chanterelles, earth stars, smuts, bunts, rusts, mirror yeasts, and ''Cryptococcus'', the human pathogenic yeast. Basidiomycota are filamentous fungi composed of hyphae (except for basidiomycota-yeast) and reproduce sexually via the formation of specialized club-shaped end cells called basidia that normally bear external meiospores (usually four). These specialized spores are called basidiospores. However, some Basidiomycota are obligate asexual reproducers. Basidiomycota that reproduce asexually (discussed below) can typically be recognized as members of this division by gross similarity to others, by the forma ...
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Time Complexity
In computer science, the time complexity is the computational complexity that describes the amount of computer time it takes to run an algorithm. Time complexity is commonly estimated by counting the number of elementary operations performed by the algorithm, supposing that each elementary operation takes a fixed amount of time to perform. Thus, the amount of time taken and the number of elementary operations performed by the algorithm are taken to be related by a constant factor. Since an algorithm's running time may vary among different inputs of the same size, one commonly considers the worst-case time complexity, which is the maximum amount of time required for inputs of a given size. Less common, and usually specified explicitly, is the average-case complexity, which is the average of the time taken on inputs of a given size (this makes sense because there are only a finite number of possible inputs of a given size). In both cases, the time complexity is generally expresse ...
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Travelling Salesman Problem
The travelling salesman problem (also called the travelling salesperson problem or TSP) asks the following question: "Given a list of cities and the distances between each pair of cities, what is the shortest possible route that visits each city exactly once and returns to the origin city?" It is an NP-hard problem in combinatorial optimization, important in theoretical computer science and operations research. The travelling purchaser problem and the vehicle routing problem are both generalizations of TSP. In the theory of computational complexity, the decision version of the TSP (where given a length ''L'', the task is to decide whether the graph has a tour of at most ''L'') belongs to the class of NP-complete problems. Thus, it is possible that the worst-case running time for any algorithm for the TSP increases superpolynomially (but no more than exponentially) with the number of cities. The problem was first formulated in 1930 and is one of the most intensively studi ...
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