1.
Java (software platform)
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Java is used in a wide variety of computing platforms from embedded devices and mobile phones to enterprise servers and supercomputers. While they are less common than standalone Java applications, Java applets run in secure, sandboxed environments to provide many features of native applications, in addition, several languages have been designed to run natively on the JVM, including Scala, Clojure and Apache Groovy. Java syntax borrows heavily from C and C++, but object-oriented features are modeled after Smalltalk, Java eschews certain low-level constructs such as pointers and has a very simple memory model where every object is allocated on the heap and all variables of object types are references. Memory management is handled through integrated automatic garbage collection performed by the JVM, on November 13,2006, Sun Microsystems made the bulk of its implementation of Java available under the GNU General Public License. The latest version is Java 8, the only supported version as of 2016, Oracle has announced that using older versions of their JVM implementation presents serious risks due to unresolved security issues. The Java platform is a suite of programs that facilitate developing and running programs written in the Java programming language. A Java platform will include an engine, a compiler. Java ME, Specifies several different sets of libraries for devices with limited storage, display and it is often used to develop applications for mobile devices, PDAs, TV set-top boxes, and printers. Java SE, For general-purpose use on desktop PCs, servers, Java EE, Java SE plus various APIs which are useful for multi-tier client–server enterprise applications. The Java platform consists of programs, each of which provides a portion of its overall capabilities. For example, the Java compiler, which converts Java source code into Java bytecode, is provided as part of the Java Development Kit, the Java Runtime Environment, complementing the JVM with a just-in-time compiler, converts intermediate bytecode into native machine code on the fly. The Java platform also includes a set of libraries. The heart of the Java platform is the concept of a machine that executes Java bytecode programs. This bytecode is the same no matter what hardware or operating system the program is running under, there is a JIT compiler within the Java Virtual Machine, or JVM. The JIT compiler translates the Java bytecode into native processor instructions at run-time, the use of bytecode as an intermediate language permits Java programs to run on any platform that has a virtual machine available. Since JRE version 1.2, Suns JVM implementation has included a just-in-time compiler instead of an interpreter, although Java programs are cross-platform or platform independent, the code of the Java Virtual Machines that execute these programs is not. Every supported operating platform has its own JVM, in most modern operating systems, a large body of reusable code is provided to simplify the programmers job. This code is provided as a set of dynamically loadable libraries that applications can call at runtime
2.
Chemistry
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Chemistry is a branch of physical science that studies the composition, structure, properties and change of matter. Chemistry is sometimes called the science because it bridges other natural sciences, including physics. For the differences between chemistry and physics see comparison of chemistry and physics, the history of chemistry can be traced to alchemy, which had been practiced for several millennia in various parts of the world. The word chemistry comes from alchemy, which referred to a set of practices that encompassed elements of chemistry, metallurgy, philosophy, astrology, astronomy, mysticism. An alchemist was called a chemist in popular speech, and later the suffix -ry was added to this to describe the art of the chemist as chemistry, the modern word alchemy in turn is derived from the Arabic word al-kīmīā. In origin, the term is borrowed from the Greek χημία or χημεία and this may have Egyptian origins since al-kīmīā is derived from the Greek χημία, which is in turn derived from the word Chemi or Kimi, which is the ancient name of Egypt in Egyptian. Alternately, al-kīmīā may derive from χημεία, meaning cast together, in retrospect, the definition of chemistry has changed over time, as new discoveries and theories add to the functionality of the science. The term chymistry, in the view of noted scientist Robert Boyle in 1661, in 1837, Jean-Baptiste Dumas considered the word chemistry to refer to the science concerned with the laws and effects of molecular forces. More recently, in 1998, Professor Raymond Chang broadened the definition of chemistry to mean the study of matter, early civilizations, such as the Egyptians Babylonians, Indians amassed practical knowledge concerning the arts of metallurgy, pottery and dyes, but didnt develop a systematic theory. Greek atomism dates back to 440 BC, arising in works by such as Democritus and Epicurus. In 50 BC, the Roman philosopher Lucretius expanded upon the theory in his book De rerum natura, unlike modern concepts of science, Greek atomism was purely philosophical in nature, with little concern for empirical observations and no concern for chemical experiments. Work, particularly the development of distillation, continued in the early Byzantine period with the most famous practitioner being the 4th century Greek-Egyptian Zosimos of Panopolis. He formulated Boyles law, rejected the four elements and proposed a mechanistic alternative of atoms. Before his work, though, many important discoveries had been made, the Scottish chemist Joseph Black and the Dutchman J. B. English scientist John Dalton proposed the theory of atoms, that all substances are composed of indivisible atoms of matter. Davy discovered nine new elements including the alkali metals by extracting them from their oxides with electric current, british William Prout first proposed ordering all the elements by their atomic weight as all atoms had a weight that was an exact multiple of the atomic weight of hydrogen. The inert gases, later called the noble gases were discovered by William Ramsay in collaboration with Lord Rayleigh at the end of the century, thereby filling in the basic structure of the table. Organic chemistry was developed by Justus von Liebig and others, following Friedrich Wöhlers synthesis of urea which proved that organisms were, in theory
3.
Linux
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Linux is a Unix-like computer operating system assembled under the model of free and open-source software development and distribution. The defining component of Linux is the Linux kernel, an operating system kernel first released on September 17,1991 by Linus Torvalds, the Free Software Foundation uses the name GNU/Linux to describe the operating system, which has led to some controversy. Linux was originally developed for computers based on the Intel x86 architecture. Because of the dominance of Android on smartphones, Linux has the largest installed base of all operating systems. Linux is also the operating system on servers and other big iron systems such as mainframe computers. It is used by around 2. 3% of desktop computers, the Chromebook, which runs on Chrome OS, dominates the US K–12 education market and represents nearly 20% of the sub-$300 notebook sales in the US. Linux also runs on embedded systems – devices whose operating system is built into the firmware and is highly tailored to the system. This includes TiVo and similar DVR devices, network routers, facility automation controls, televisions, many smartphones and tablet computers run Android and other Linux derivatives. The development of Linux is one of the most prominent examples of free, the underlying source code may be used, modified and distributed—commercially or non-commercially—by anyone under the terms of its respective licenses, such as the GNU General Public License. Typically, Linux is packaged in a known as a Linux distribution for both desktop and server use. Distributions intended to run on servers may omit all graphical environments from the standard install, because Linux is freely redistributable, anyone may create a distribution for any intended use. The Unix operating system was conceived and implemented in 1969 at AT&Ts Bell Laboratories in the United States by Ken Thompson, Dennis Ritchie, Douglas McIlroy, first released in 1971, Unix was written entirely in assembly language, as was common practice at the time. Later, in a key pioneering approach in 1973, it was rewritten in the C programming language by Dennis Ritchie, the availability of a high-level language implementation of Unix made its porting to different computer platforms easier. Due to an earlier antitrust case forbidding it from entering the computer business, as a result, Unix grew quickly and became widely adopted by academic institutions and businesses. In 1984, AT&T divested itself of Bell Labs, freed of the legal obligation requiring free licensing, the GNU Project, started in 1983 by Richard Stallman, has the goal of creating a complete Unix-compatible software system composed entirely of free software. Later, in 1985, Stallman started the Free Software Foundation, by the early 1990s, many of the programs required in an operating system were completed, although low-level elements such as device drivers, daemons, and the kernel were stalled and incomplete. Linus Torvalds has stated that if the GNU kernel had been available at the time, although not released until 1992 due to legal complications, development of 386BSD, from which NetBSD, OpenBSD and FreeBSD descended, predated that of Linux. Torvalds has also stated that if 386BSD had been available at the time, although the complete source code of MINIX was freely available, the licensing terms prevented it from being free software until the licensing changed in April 2000
4.
Unix
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Among these is Apples macOS, which is the Unix version with the largest installed base as of 2014. Many Unix-like operating systems have arisen over the years, of which Linux is the most popular, Unix was originally meant to be a convenient platform for programmers developing software to be run on it and on other systems, rather than for non-programmer users. The system grew larger as the system started spreading in academic circles, as users added their own tools to the system. Unix was designed to be portable, multi-tasking and multi-user in a time-sharing configuration and these concepts are collectively known as the Unix philosophy. By the early 1980s users began seeing Unix as a universal operating system. Under Unix, the system consists of many utilities along with the master control program. To mediate such access, the kernel has special rights, reflected in the division between user space and kernel space, the microkernel concept was introduced in an effort to reverse the trend towards larger kernels and return to a system in which most tasks were completed by smaller utilities. In an era when a standard computer consisted of a disk for storage and a data terminal for input and output. However, modern systems include networking and other new devices, as graphical user interfaces developed, the file model proved inadequate to the task of handling asynchronous events such as those generated by a mouse. In the 1980s, non-blocking I/O and the set of inter-process communication mechanisms were augmented with Unix domain sockets, shared memory, message queues, and semaphores. In microkernel implementations, functions such as network protocols could be moved out of the kernel, Multics introduced many innovations, but had many problems. Frustrated by the size and complexity of Multics but not by the aims and their last researchers to leave Multics, Ken Thompson, Dennis Ritchie, M. D. McIlroy, and J. F. Ossanna, decided to redo the work on a much smaller scale. The name Unics, a pun on Multics, was suggested for the project in 1970. Peter H. Salus credits Peter Neumann with the pun, while Brian Kernighan claims the coining for himself, in 1972, Unix was rewritten in the C programming language. Bell Labs produced several versions of Unix that are referred to as Research Unix. In 1975, the first source license for UNIX was sold to faculty at the University of Illinois Department of Computer Science, UIUC graduate student Greg Chesson was instrumental in negotiating the terms of this license. During the late 1970s and early 1980s, the influence of Unix in academic circles led to adoption of Unix by commercial startups, including Sequent, HP-UX, Solaris, AIX. In the late 1980s, AT&T Unix System Laboratories and Sun Microsystems developed System V Release 4, in the 1990s, Unix-like systems grew in popularity as Linux and BSD distributions were developed through collaboration by a worldwide network of programmers
5.
Ribbon diagram
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Ribbon diagrams, also known as Richardson Diagrams, are 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone, α-helices are shown as coiled ribbons or thick tubes, β-strands as arrows, and lines or thin tubes for non-repetitive coils or loops. The direction of the chain is shown locally by the arrows. Ribbon diagrams are simple, yet powerful, in expressing the visual basics of a molecular structure, as well as the TIM ribbon drawing at the right, other hand-drawn examples are for prealbumin, flavodoxin, and Cu, Zn superoxide dismutase. In 1982, Arthur M. Lesk and co-workers first enabled automatic generation of ribbon diagrams through an implementation that uses Protein Data Bank files as input. This conceptually simple algorithm fit cubic polynomial B-spline curves to the peptide planes, most modern graphics systems provide either B-splines or Hermite splines as a basic drawing primitive. One type of spline implementation passes through each Cα guide point, producing an exact, both hand-drawn and most computer ribbons are smoothed over about 4 successive guide points, to produce a more visually pleasing and understandable representation. One popular program used for drawing ribbon diagrams is Molscript, Molscript utilizes Hermite splines to create coordinates for coils, turns, strands and helices. The curve passes through all its control points guided by direction vectors, the program was built on the basis of traditional molecular graphics by Arthur M. Lesk, Karl Hardman, and John Priestle. Jmol is an open-source Java-based viewer for browsing molecular structures on the web, other graphics programs such as DeepView and MolMol also produce ribbon images. KiNG is the Java-based successor to Mage
6.
Web browser
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A web browser is a software application for retrieving, presenting and traversing information resources on the World Wide Web. An information resource is identified by a Uniform Resource Identifier that may be a web page, image, hyperlinks present in resources enable users easily to navigate their browsers to related resources. Although browsers are primarily intended to use the World Wide Web, the most popular web browsers are Google Chrome, Microsoft Edge, Safari, Opera and Firefox. The first web browser was invented in 1990 by Sir Tim Berners-Lee, Berners-Lee is the director of the World Wide Web Consortium, which oversees the Webs continued development, and is also the founder of the World Wide Web Foundation. His browser was called WorldWideWeb and later renamed Nexus, the first commonly available web browser with a graphical user interface was Erwise. The development of Erwise was initiated by Robert Cailliau, andreesens browser sparked the internet boom of the 1990s. The introduction of Mosaic in 1993 – one of the first graphical web browsers – led to an explosion in web use, Microsoft responded with its Internet Explorer in 1995, also heavily influenced by Mosaic, initiating the industrys first browser war. Bundled with Windows, Internet Explorer gained dominance in the web browser market, Internet Explorer usage share peaked at over 95% by 2002. Opera debuted in 1996, it has never achieved widespread use and it is also available on several other embedded systems, including Nintendos Wii video game console. In 1998, Netscape launched what was to become the Mozilla Foundation in an attempt to produce a competitive browser using the open source software model, as of August 2011, Firefox has a 28% usage share. Apples Safari had its first beta release in January 2003, as of April 2011, the most recent major entrant to the browser market is Chrome, first released in September 2008. Chromes take-up has increased year by year, by doubling its usage share from 8% to 16% by August 2011. This increase seems largely to be at the expense of Internet Explorer, in December 2011, Chrome overtook Internet Explorer 8 as the most widely used web browser but still had lower usage than all versions of Internet Explorer combined. Chromes user-base continued to grow and in May 2012, Chromes usage passed the usage of all versions of Internet Explorer combined, by April 2014, Chromes usage had hit 45%. Internet Explorer was deprecated in Windows 10, with Microsoft Edge replacing it as the web browser. The ways that web browser makers fund their development costs has changed over time, the first web browser, WorldWideWeb, was a research project. In addition to being freeware, Netscape Navigator and Opera were also sold commercially, Internet Explorer, on the other hand, was bundled free with the Windows operating system, and therefore it was funded partly by the sales of Windows to computer manufacturers and direct to users. Internet Explorer also used to be available for the Mac, in this respect, IE may have contributed to Windows and Microsoft applications sales in another way, through lock-in to Microsofts browser
7.
3D computer graphics
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Such images may be stored for viewing later or displayed in real-time. 3D computer graphics rely on many of the same algorithms as 2D computer vector graphics in the wire-frame model, 3D computer graphics are often referred to as 3D models. Apart from the graphic, the model is contained within the graphical data file. However, there are differences, a 3D model is the representation of any three-dimensional object. A model is not technically a graphic until it is displayed, a model can be displayed visually as a two-dimensional image through a process called 3D rendering or used in non-graphical computer simulations and calculations. With 3D printing, 3D models are rendered into a 3D physical representation of the model. William Fetter was credited with coining the term computer graphics in 1961 to describe his work at Boeing, 3D computer graphics software began appearing for home computers in the late 1970s. The earliest known example is 3D Art Graphics, a set of 3D computer graphics effects, written by Kazumasa Mitazawa, models can also be produced procedurally or via physical simulation. Basically, a 3D model is formed from points called vertices that define the shape, a polygon is an area formed from at least three vertexes. A polygon of n points is an n-gon, the overall integrity of the model and its suitability to use in animation depend on the structure of the polygons. Before rendering into an image, objects must be out in a scene. This defines spatial relationships between objects, including location and size, Animation refers to the temporal description of an object. These techniques are used in combination. As with animation, physical simulation also specifies motion, rendering converts a model into an image either by simulating light transport to get photo-realistic images, or by applying an art style as in non-photorealistic rendering. The two basic operations in realistic rendering are transport and scattering and this step is usually performed using 3D computer graphics software or a 3D graphics API. Altering the scene into a form for rendering also involves 3D projection. There are a multitude of websites designed to help, educate, some are managed by software developers and content providers, but there are standalone sites as well. These communities allow for members to seek advice, post tutorials, not all computer graphics that appear 3D are based on a wireframe model
8.
Molecule
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A molecule is an electrically neutral group of two or more atoms held together by chemical bonds. Molecules are distinguished from ions by their lack of electrical charge, however, in quantum physics, organic chemistry, and biochemistry, the term molecule is often used less strictly, also being applied to polyatomic ions. In the kinetic theory of gases, the molecule is often used for any gaseous particle regardless of its composition. According to this definition, noble gas atoms are considered molecules as they are in fact monoatomic molecules. A molecule may be homonuclear, that is, it consists of atoms of one element, as with oxygen, or it may be heteronuclear. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic bonds, are not considered single molecules. Molecules as components of matter are common in organic substances and they also make up most of the oceans and atmosphere. Also, no typical molecule can be defined for ionic crystals and covalent crystals, the theme of repeated unit-cellular-structure also holds for most condensed phases with metallic bonding, which means that solid metals are also not made of molecules. In glasses, atoms may also be together by chemical bonds with no presence of any definable molecule. The science of molecules is called molecular chemistry or molecular physics, in practice, however, this distinction is vague. In molecular sciences, a molecule consists of a system composed of two or more atoms. Polyatomic ions may sometimes be thought of as electrically charged molecules. The term unstable molecule is used for very reactive species, i. e, according to Merriam-Webster and the Online Etymology Dictionary, the word molecule derives from the Latin moles or small unit of mass. Molecule – extremely minute particle, from French molécule, from New Latin molecula, diminutive of Latin moles mass, a vague meaning at first, the vogue for the word can be traced to the philosophy of Descartes. The definition of the molecule has evolved as knowledge of the structure of molecules has increased, earlier definitions were less precise, defining molecules as the smallest particles of pure chemical substances that still retain their composition and chemical properties. Molecules are held together by covalent bonding or ionic bonding. Several types of non-metal elements exist only as molecules in the environment, for example, hydrogen only exists as hydrogen molecule. A molecule of a compound is made out of two or more elements, a covalent bond is a chemical bond that involves the sharing of electron pairs between atoms
9.
Ball-and-stick model
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In chemistry, the ball-and-stick model is a molecular model of a chemical substance which is to display both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods which represent the bonds, double and triple bonds are usually represented by two or three curved rods, respectively. The chemical element of each atom is often indicated by the spheres color, in a ball-and-stick model, the radius of the spheres is usually much smaller than the rod lengths, in order to provide a clearer view of the atoms and bonds throughout the model. As a consequence, the model does not provide an insight about the space occupied by the model. Ball-and-stick models can be physical artifacts or virtual computer models, the former are usually built from molecular modeling kits, consisting of a number of helical springs or rods made of flexible plastic, and a number of plastic balls with pre-drilled holes. The sphere colors commonly follow the CPK coloring, some university courses on chemistry require students to buy such models as learning material. In 1865, German chemist August Wilhelm von Hofmann was the first to make stick-and-ball molecular models and he used such models in lecture at the Royal Institution of Great Britain. Specialist companies manufacture kits and models to order, one of the earlier companies was Woosters at Bottisham, Cambridgeshire, UK. Besides tetrahedral, trigonal and octahedral holes, there were all-purpose balls with 24 holes and these models allowed rotation about the single rod bonds, which could be both an advantage and a disadvantage. The approximate scale was 5 cm per ångström, but was not consistent over all elements, the Beevers Miniature Models company in Edinburgh produced small models using PMMA balls and stainless steel rods. In these models, the use of individually drilled balls with precise bond angles and bond lengths enabled large crystal structures to be created in a light. Figure 3 shows a cell of ruby in this style
10.
Streptavidin
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Streptavidin /ˌstrɛpˈtævɪdɪn/ is a 52.8 kDa protein purified from the bacterium Streptomyces avidinii. Streptavidin homo-tetramers have a high affinity for biotin. With a dissociation constant on the order of ≈10−14 mol/L, the binding of biotin to streptavidin is one of the strongest non-covalent interactions known in nature, the crystal structure of streptavidin with biotin bound was reported by two groups in 1989. The structure was solved using multi wavelength anomalous diffraction by Hendrickson et al. at Columbia University, duPont Central Research and Development Department. As of September 2016, there are 167 structures deposited in the Protein Data Bank, see this link for a complete list. The secondary structure of a monomer is composed of eight antiparallel β-strands. A biotin binding-site is located at one end of each β-barrel, four identical streptavidin monomers associate to give streptavidin’s tetrameric quaternary structure. The biotin binding-site in each barrel consists of residues from the interior of the barrel, in this way, each subunit contributes to the binding site on the neighboring subunit, and so the tetramer can also be considered a dimer of functional dimers. The numerous crystal structures of the complex have shed light on the origins of the remarkable affinity. Firstly, there is high shape complementarity between the pocket and biotin. Secondly, there is a network of hydrogen bonds formed to biotin when in the binding site. There are eight hydrogen bonds directly made to residues in the site, involving residues Asn23, Tyr43, Ser27, Ser45, Asn49, Ser88, Thr90. There is also a shell of hydrogen bonding involving residues that interact with the first shell residues. However, the streptavidin-biotin affinity exceeds that which would be predicted from the bonding interactions alone. In particular, the pocket is lined with conserved tryptophan residues, most attempts at mutating streptavidin result in a lowered biotin-binding affinity, which is to be expected in such a highly optimised system. However, a recently engineered mutant of streptavidin, named traptavidin, was found to have more than ten-fold slower biotin dissociation and this decreased dissociation rate was accompanied by a two-fold decrease in the association rate. Among the most common uses are the purification or detection of various biomolecules, the strong streptavidin-biotin bond can be used to attach various biomolecules to one another or onto a solid support. Harsh conditions are needed to break the interaction, which often denatures the protein of interest being purified
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