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Biological Computer
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 backgroun ...
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Proteins
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues ...
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Chemically Induced Dimerization
Chemically Induced Dimerization (CID) is a biological mechanism in which two proteins bind only in the presence of a certain small molecule, enzyme or other dimerizing agent. Genetically engineered CID systems are used in biological research to control protein localization, to manipulate signalling pathways and to induce protein activation. History The first small molecule CID system was developed in 1993 and used FK1012, a derivative of the drug tacrolimus (FK506), to induce homo-dimerization of FKBP. This system was used ''in vivo'' to induce binding between cell surface receptors which could not bind in the normal way because they lacked the transmembrane and extracellular domain. Addition of FK1012 to the cells caused signal transduction. Chemically induced dimerization systems Applications CID has been used for a number of applications in biomedical research. In most applications each dimerizing protein is expressed as part of a fusion construct with other proteins of inter ...
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Logic Family
In computer engineering, a logic family is one of two related concepts: * A logic family of monolithic digital integrated circuit devices is a group of electronic logic gates constructed using one of several different designs, usually with compatible logic levels and power supply characteristics within a family. Many logic families were produced as individual components, each containing one or a few related basic logical functions, which could be used as "building-blocks" to create systems or as so-called "glue" to interconnect more complex integrated circuits. * A logic family may also be a set of techniques used to implement logic within VLSI integrated circuits such as central processors, memories, or other complex functions. Some such logic families use static techniques to minimize design complexity. Other such logic families, such as domino logic, use clocked dynamic techniques to minimize size, power consumption and delay. Before the widespread use of integrated circuits, ...
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Data Storage Device
Data storage is the recording (storing) of information (data) in a storage medium. Handwriting, phonographic recording, magnetic tape, and optical discs are all examples of storage media. Biological molecules such as RNA and DNA are considered by some as data storage. Recording may be accomplished with virtually any form of energy. Electronic data storage requires electrical power to store and retrieve data. Data storage in a digital, machine-readable medium is sometimes called ''digital data''. Computer data storage is one of the core functions of a general-purpose computer. Electronic documents can be stored in much less space than paper documents. Barcodes and magnetic ink character recognition (MICR) are two ways of recording machine-readable data on paper. Recording media A recording medium is a physical material that holds information. Newly created information is distributed and can be stored in four storage media–print, film, magnetic, and optical–and seen or ...
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Transcriptor
A transcriptor is a transistor-like device composed of DNA and RNA rather than a semiconducting material such as silicon. Prior to its invention in 2013, the transcriptor was considered an important component to build biological computers. Background To function, a modern computer needs three different capabilities: It must be able to store information, transmit information between components, and possess a basic system of logic. Prior to March 2013, scientists had successfully demonstrated the ability to store and transmit data using biological components made of proteins and DNA. Simple two-terminal logic gates had been demonstrated, but required multiple layers of inputs and thus were impractical due to scaling difficulties. Invention and description On March 28, 2013, a team of bioengineers from Stanford University led by Drew Endy announced that they had created the biological equivalent of a transistor, which they named a "transcriptor". That is, they created a thr ...
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Transistor
upright=1.4, gate (G), body (B), source (S) and drain (D) terminals. The gate is separated from the body by an insulating layer (pink). A transistor is a semiconductor device used to Electronic amplifier, amplify or electronic switch, switch electrical signals and electrical power, power. The transistor is one of the basic building blocks of modern electronics. It is composed of semiconductor material, usually with at least three terminals for connection to an electronic circuit. A voltage or current applied to one pair of the transistor's terminals controls the current through another pair of terminals. Because the controlled (output) power can be higher than the controlling (input) power, a transistor can amplify a signal. Some transistors are packaged individually, but many more are found embedded in integrated circuits. Austro-Hungarian physicist Julius Edgar Lilienfeld proposed the concept of a field-effect transistor in 1926, but it was not possible to actually constru ...
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Drew Endy
Andrew (Drew) David Endy (born 1970) is a synthetic biologist and tenured associate professor of bioengineering at Stanford University, California. Education and Work History Endy received his PhD from Dartmouth College in 1997 for his work on genetic engineering using T7 phage. Endy was a junior fellow for 3 years and later an Assistant Professor of Biological Engineering at MIT, from 2002-2008. In 2008, Endy moved to Stanford University, where he currently serves as an Associate Professor of Bioengineering. Research With Thomas Knight, Gerald Jay Sussman, Randy Rettberg, and others at MIT, Endy worked on synthetic biology and the engineering of standardized biological components, devices, and parts, collectively known as BioBricks.From the cells up
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Stanford University
Stanford University, officially Leland Stanford Junior University, is a private research university in Stanford, California. The campus occupies , among the largest in the United States, and enrolls over 17,000 students. Stanford is considered among the most prestigious universities in the world. Stanford was founded in 1885 by Leland and Jane Stanford in memory of their only child, Leland Stanford Jr., who had died of typhoid fever at age 15 the previous year. Leland Stanford was a U.S. senator and former governor of California who made his fortune as a railroad tycoon. The school admitted its first students on October 1, 1891, as a coeducational and non-denominational institution. Stanford University struggled financially after the death of Leland Stanford in 1893 and again after much of the campus was damaged by the 1906 San Francisco earthquake. Following World War II, provost of Stanford Frederick Terman inspired and supported faculty and graduates' entrepreneu ...
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Binary Numeral System
A binary number is a number expressed in the base-2 numeral system or binary numeral system, a method of mathematical expression which uses only two symbols: typically "0" (zero) and "1" ( one). The base-2 numeral system is a positional notation with a radix of 2. Each digit is referred to as a bit, or binary digit. Because of its straightforward implementation in digital electronic circuitry using logic gates, the binary system is used by almost all modern computers and computer-based devices, as a preferred system of use, over various other human techniques of communication, because of the simplicity of the language and the noise immunity in physical implementation. History The modern binary number system was studied in Europe in the 16th and 17th centuries by Thomas Harriot, Juan Caramuel y Lobkowitz, and Gottfried Leibniz. However, systems related to binary numbers have appeared earlier in multiple cultures including ancient Egypt, China, and India. Leibniz was specifica ...
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Tom Knight (scientist)
Tom Knight is an American synthetic biologist and computer engineer, who was formerly a senior research scientist at the MIT Computer Science and Artificial Intelligence Laboratory, a part of the MIT School of Engineering. He now works at the synthetic biology company Ginkgo Bioworks, which he cofounded in 2008. Work in electrical engineering and computer science Tom Knight arrived at MIT when he was fourteen. Even though he only started his undergraduate studies at the regular age of 18, he took classes in computer programming and organic chemistry during high school because he lived close to the university. He built early hardware such as ARPANET interfaces for host #6 on the network, some of the first bitmapped displays, the ITS time sharing system, Lisp machines (he was also instrumental in releasing a version of the operating system for the Lisp machine under a BSD license), the Connection Machine, and parallel symbolic processing computer systems. In 1967 Knight ...
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Logic
Logic is the study of correct reasoning. It includes both formal and informal logic. Formal logic is the science of deductively valid inferences or of logical truths. It is a formal science investigating how conclusions follow from premises in a topic-neutral way. When used as a countable noun, the term "a logic" refers to a logical formal system that articulates a proof system. Formal logic contrasts with informal logic, which is associated with informal fallacies, critical thinking, and argumentation theory. While there is no general agreement on how formal and informal logic are to be distinguished, one prominent approach associates their difference with whether the studied arguments are expressed in formal or informal languages. Logic plays a central role in multiple fields, such as philosophy, mathematics, computer science, and linguistics. Logic studies arguments, which consist of a set of premises together with a conclusion. Premises and conclusions are usually un ...
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