Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically. == History == Prior to the use of computer graphics in representing molecular structure, Robert Corey and Linus Pauling developed a system for representing atoms or groups of atoms from hard wood on a scale of 1 inch = 1 angstrom connected by a clamping device to maintain the molecular configuration. These early models also established the CPK coloring scheme that is still used today to differentiate the different types of atoms in molecular models (e.g. carbon = black, oxygen = red, nitrogen = blue, etc). This early model was improved upon in 1966 by W.L. Koltun and are now known as Corey-Pauling-Koltun (CPK) models. The earliest efforts to produce models of molecular structure was done by Project MAC using wire-frame models displayed on a cathode ray tube in the mid 1960s. In 1965, Carroll Johnson distributed the Oak Ridge thermal ellipsoid plot (ORTEP) that visualized molecules as a ball-and-stick model with lines representing the bonds between atoms and ellipsoids to represent the probability of thermal motion. Thermal ellipsoid plots quickly became the de facto standard used in the display of X-ray crystallography data, and are still in wide use today. The first practical use of molecular graphics was a simple display of the protein myoglobin using a wireframe representation in 1966 by Cyrus Levinthal and Robert Langridge working at Project MAC. Among the milestones in high-performance molecular graphics was the work of Nelson Max in "realistic" rendering of macromolecules using reflecting spheres. Initially much of the technology concentrated on high-performance 3D graphics. During the 1970s, methods for displaying 3D graphics using cathode ray tubes were developed using continuous tone computer graphics in combination with electro-optic shutter viewing devices. The first devices used an active shutter 3D system, generating different perspective views for the left and right channel to provide the illusion of three-dimensional viewing. Stereoscopic viewing glasses were designed using lead lanthanum zirconate titanate (PLZT) ceramics as electronically controlled shutter elements. Active 3D glasses require batteries and work in concert with the display to actively change the presentation by the lenses to the wearer's eyes. Many modern 3D glasses use a passive, polarized 3D system that enables the wearer to visualize 3D effects based on their own perception. Passive 3D glasses are more common today since they are less expensive. The requirements of macromolecular crystallography also drove molecular graphics because the traditional techniques of physical model-building could not scale. The first two protein structures solved by molecular graphics without the aid of the Richards' Box were built with Stan Swanson's program FIT on the Vector General graphics display in the laboratory of Edgar Meyer at Texas A&M University: First Marge Legg in Al Cotton's lab at A&M solved a second, higher-resolution structure of staph. nuclease (1975) and then Jim Hogle solved the structure of monoclinic lysozyme in 1976. A full year passed before other graphics systems were used to replace the Richards' Box for modelling into density in 3-D. Alwyn Jones' FRODO program (and later "O") were developed to overlay the molecular electron density determined from X-ray crystallography and the hypothetical molecular structure. === Timeline === == Types == === Ball-and-stick models === In the ball-and-stick model, atoms are drawn as small sphered connected by rods representing the chemical bonds between them. === Space-filling models === In the space-filling model, atoms are drawn as solid spheres to suggest the space they occupy, in proportion to their van der Waals radii. Atoms that share a bond overlap with each other. === Surfaces === In some models, the surface of the molecule is approximated and shaded to represent a physical property of the molecule, such as electronic charge density. === Ribbon diagrams === Ribbon diagrams are schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon shows the overall path and organization of the protein backbone in 3D, and serves as a visual framework on which to hang details of the full atomic structure, such as the balls for the oxygen atoms bound to the active site of myoglobin in the adjacent image. 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 non-repetitive coils or loops as lines or thin tubes. The direction of the polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon.
Supertoroid
In geometry and computer graphics, a supertoroid or supertorus is usually understood to be a family of doughnut-like surfaces (technically, a topological torus) whose shape is defined by mathematical formulas similar to those that define the superellipsoids. The plural of "supertorus" is either supertori or supertoruses. The family was described and named by Alan Barr in 1994. Barr's supertoroids have been fairly popular in computer graphics as a convenient model for many objects, such as smooth frames for rectangular things. One quarter of a supertoroid can provide a smooth and seamless 90-degree joint between two superquadric cylinders. However, they are not algebraic surfaces (except in special cases). == Formulas == Alan Barr's supertoroids are defined by parametric equations similar to the trigonometric equations of the torus, except that the sine and cosine terms are raised to arbitrary powers. Namely, the generic point P(u, v) of the surface is given by P ( u , v ) = ( X ( u , v ) Y ( u , v ) Z ( u , v ) ) = ( ( a + C u s ) C v t ( b + C u s ) S v t S u s ) {\displaystyle P(u,v)=\left({\begin{array}{c}X(u,v)\\Y(u,v)\\Z(u,v)\end{array}}\right)=\left({\begin{array}{c}(a+C_{u}^{s})C_{v}^{t}\\(b+C_{u}^{s})S_{v}^{t}\\S_{u}^{s}\end{array}}\right)} where C θ ε = sgn ( cos θ ) | cos θ | ε , S θ ε = sgn ( sin θ ) | sin θ | ε , {\displaystyle {\begin{aligned}C_{\theta }^{\varepsilon }&=\operatorname {sgn} (\cos \theta )\,\left|\,\cos \theta \,\right|^{\varepsilon },\\S_{\theta }^{\varepsilon }&=\operatorname {sgn} (\sin \theta )\ \left|\,\sin \theta \ \right|^{\varepsilon },\end{aligned}}} sgn is the sign function, and the parameters u, v range from 0 to 360 degrees (0 to 2π radians). In these formulas, the parameter s > 0 controls the "squareness" of the vertical sections, t > 0 controls the squareness of the horizontal sections, and a, b ≥ 1 are the major radii in the x and y directions. With s = t = 1 and a = b = R one obtains the ordinary torus with major radius R and minor radius 1, with the center at the origin and rotational symmetry about the z-axis. In general, the supertorus defined as above spans the intervals: − ( a + 1 ) ≤ x ≤ + ( a + 1 ) − ( b + 1 ) ≤ y ≤ + ( b + 1 ) − 1 ≤ z ≤ + 1 {\displaystyle {\begin{array}{rcccl}-(a+1)&\leq &x&\leq &+(a+1)\\[4pt]-(b+1)&\leq &y&\leq &+(b+1)\\[4pt]-1&\leq &z&\leq &+1\end{array}}} The whole shape is symmetric about the planes x = 0, y = 0, and z = 0. The hole runs in the z direction and spans the intervals − ( a − 1 ) ≤ x ≤ + ( a − 1 ) − ( b − 1 ) ≤ y ≤ + ( b − 1 ) − ∞ ≤ z ≤ + ∞ {\displaystyle {\begin{array}{rcccl}-(a-1)&\leq &x&\leq &+(a-1)\\[4pt]-(b-1)&\leq &y&\leq &+(b-1)\\[4pt]-\infty &\leq &z&\leq &+\infty \end{array}}} A curve of constant u on this surface is a horizontal Lamé curve with exponent 2 t , {\displaystyle {\tfrac {2}{t}},} scaled in x and y and displaced in z. A curve of constant v, projected on the plane x = 0 or y = 0, is a Lamé curve with exponent 2 s , {\displaystyle {\tfrac {2}{s}},} scaled and horizontally shifted. If v = 0, the curve is planar and spans the intervals: a − 1 ≤ x ≤ a + 1 − 1 ≤ z ≤ + 1 {\displaystyle {\begin{array}{rcccl}a-1&\leq &x&\leq &a+1\\[4pt]-1&\leq &z&\leq &+1\end{array}}} and similarly if v = 90°, 180°, 270°. The curve is also planar if a = b. In general, if a ≠ b and v is not a multiple of 90 degrees, the curve of constant v will not be planar; and, conversely, a vertical plane section of the supertorus will not be a Lamé curve. The basic supertoroid shape defined above is often modified by non-uniform scaling to yield supertoroids of specific width, length, and vertical thickness. == Plotting code == The following GNU Octave code generates plots of a supertorus:
Anderson's rule (computer science)
In the field of computer security, Anderson's rule refers to a principle formulated by Ross J. Anderson: systems that handle sensitive personal information involve a trilemma of security, functionality, and scale, of which you can choose any two. A system that has information on many data subjects and to which many people require access is hard to secure unless its functionality is severely restricted. If it has rich functionality, you may have to restrict the number of people with access, or accept that some information will leak.
Color gradient
In color science, a color gradient (also known as a color ramp or a color progression) specifies a range of position-dependent colors, usually used to fill a region. In assigning colors to a set of values, a gradient is a continuous colormap, a type of color scheme. In computer graphics, the term swatch has come to mean a palette of active colors. == Definitions == Color gradient is a set of colors arranged in a linear order (ordered) A continuous colormap is a curve through a colorspace === Strict definition === A colormap is a function which associate a real value r with point c in color space C {\displaystyle C} f : [ r m i n , r m a x ] ⊂ R → C {\displaystyle f:[r_{min},r_{max}]\subset \mathbf {R} \to C} which is defined by: a colorspace C an increasing sequence of sampling points r 0 < . . . < r m ∈ [ r m i n , r m a x ] {\displaystyle r_{0}<... Computer Graphics: Principles and Practice is a textbook written by James D. Foley, Andries van Dam, Steven K. Feiner, John Hughes, Morgan McGuire, David F. Sklar, and Kurt Akeley and published by Addison–Wesley. First published in 1982 as Fundamentals of Interactive Computer Graphics, it is widely considered a classic standard reference book on the topic of computer graphics. It is sometimes known as the bible of computer graphics (due to its size). == Editions == === First Edition === The first edition, published in 1982 and titled Fundamentals of Interactive Computer Graphics, discussed the SGP library, which was based on ACM's SIGGRAPH CORE 1979 graphics standard, and focused on 2D vector graphics. === Second Edition === The second edition, published 1990, was completely rewritten and covered 2D and 3D raster and vector graphics, user interfaces, geometric modeling, anti-aliasing, advanced rendering algorithms and an introduction to animation. The SGP library was replaced by SRGP (Simple Raster Graphics Package), a library for 2D raster primitives and interaction handling, and SPHIGS (Simple PHIGS), a library for 3D primitives, which were specifically written for the book. === Second Edition in C === In the second edition in C, published in 1995, all examples were converted from Pascal to C. New implementations for the SRGP and SPHIGS graphics packages in C were also provided. === Third Edition === A third edition covering modern GPU architecture was released in July 2013. Examples in the third edition are written in C++, C#, WPF, GLSL, OpenGL, G3D, or pseudocode. == Awards == The book has won a Front Line Award (Hall of Fame) in 1998. Tradeshift is a cloud based business network and platform for purchase-to-pay automation, supply chain payments, marketplaces, virtual cards and supply chain financing. Its 2018 round of funding, led by Goldman Sachs, raised US$250 million at a valuation of $1.1 billion, giving the company unicorn status. Tradeshift is headquartered in San Francisco, California and has offices in London, Copenhagen, Bucharest and Kuala Lumpur. Tradeshift has reprocessed over $1 trillion USD through transactions on its network. == History == Tradeshift was founded in 2010 by Christian Lanng, Mikkel Hippe Brun, and Gert Sylvest. Inspiration for Tradeshift came after they created the world's first large scale peer-to-peer infrastructure for an e-business called NemHandel. The founders also had leading roles (Governing board member, Technical Director) in the European Commission project PEPPOL inside the European Union. In 2010, the Tradeshift platform launched in May in Copenhagen. Tradeshift won the European Startup Awards in the category of "Best Business or Enterprise Startup." In 2011, Tradeshift made its app marketplace available. In 2012, Tradeshift moved their headquarters from Copenhagen to San Francisco. In 2013, Tradeshift opened an R&D center in Suzhou, China. Tradeshift opened an additional office in London. And LATAM e-invoicing capabilities were added through partnership with Invoiceware. In 2014, Tradeshift expanded with offices in Tokyo, Paris, and Munich. The EU Commission officially approved the Universal Business Language (UBL) data format – a format Tradeshift supports – as eligible for referencing in tenders from public administrations. In 2015, Tradeshift won the Circulars "Digital Disruptor" Award at the WEF conference in Davos, Switzerland. Tradeshift also acquired product information management company Merchantry, and launched e-procurement and supplier risk management solutions. In 2016, Tradeshift acquired Hyper Travel and secured a $75 million series-D round funding. In 2017, Tradeshift acquired IBX Business Network and launches Tradeshift Ada. In 2018, Tradeshift secured a $250 million series-E round funding. and launched Blockchain Payments, the latter as part of Tradeshift Pay. In December 2018 Tradeshift acquired Babelway, an online B2B integration platform. The acquisition added three new office locations to Tradeshift (Salt Lake City, Louvain-la-neuve, Belgium, Cairo Egypt). In Q3 2018, Tradeshift reported year-over-year revenue growth of 400%, new bookings growth of 284%, and gross merchandise volume (GMV) growth of 262%. New total contract value also grew by US$47 million. Additionally, it added 27 new customers including Hertz, Shiseido, ECU and multiple Fortune 500 companies. In July 2023, HSBC and Tradeshift announced an agreement to launch a new, jointly owned business focused on the development of embedded finance solutions and financial services apps. As part of the agreement, HSBC made a $35 million investment into Tradeshift and joined its board. The agreement was part of a funding round which is expected to raise a minimum of $70 million from HSBC and other investors. The new joint venture will allow HSBC and Tradeshift to deploy a range of digital solutions across Tradeshift and other platforms. This includes payment and fintech services embedded into trade, e-commerce and marketplace experiences. In September 2023, CEO Lanng was fired for "gross misconduct on multiple grounds," including "allegations of sexual assault and harassment." Tradeshift was alleged to have fired his accuser after she complained to the company's human resources department, its co-founders and members of its board of directors about his abuse. == Financials == The company's valuation as of May 2018 was $1.1 billion. Tradeshift is now considered a unicorn, and, according to Bloomberg, will not need any further funding. Jan 14, 2020, Tradeshift announced that they had raised $240 million in Series F finance. == Acquisitions == In 2015, Tradeshift acquired product information management company Merchantry. Merchantry is a retail product information management (PIM) software for multi-vendor ecommerce retailers. In 2016, Tradeshift acquired Hyper Travel. Hyper Travel is a travel management service that allows customers to access travel agents via its native messaging apps, SMS, and email. In 2017, Tradeshift acquired IBX Group. In 2018, Tradeshift acquired Babelway, an online B2B integration platform. Starlight is a software product originally developed at Pacific Northwest National Laboratory and now by Future Point Systems. It is an advanced visual analysis environment. In addition to using information visualization to show the importance of individual pieces of data by showing how they relate to one another, it also contains a small suite of tools useful for collaboration and data sharing, as well as data conversion, processing, augmentation and loading. The software, originally developed for the intelligence community, allows users to load data from XML files, databases, RSS feeds, web services, HTML files, Microsoft Word, PowerPoint, Excel, CSV, Adobe PDF, TXT files, etc. and analyze it with a variety of visualizations and tools. The system integrates structured, unstructured, geospatial, and multimedia data, offering comparisons of information at multiple levels of abstraction, simultaneously and in near real-time. In addition Starlight allows users to build their own named entity-extractors using a combination of algorithms, targeted normalization lists and regular expressions in the Starlight Data Engineer (SDE). As an example, Starlight might be used to look for correlations in a database containing records about chemical spills. An analyst could begin by grouping records according to the cause of the spill to reveal general trends. Sorting the data a second time, they could apply different colors based on related details such as the company responsible, age of equipment or geographic location. Maps and photographs could be integrated into the display, making it even easier to recognize connections among multiple variables. Starlight has been deployed to both the Iraq and Afghanistan wars and used on a number of large-scale projects. PNNL began developing Starlight in the mid-1990s, with funding from the Land Information Warfare Agency, a part of the Army Intelligence and Security Command and continued developed at the laboratory with funding from the NSA and the CIA. Starlight integrates visual representations of reports, radio transcripts, radar signals, maps and other information. The software system was recently honored with an R&D 100 Award for technical innovation. In 2006 Future Point Systems, a Silicon Valley startup, acquired rights to jointly develop and distribute the Starlight product in cooperation with the Pacific Northwest National Laboratory. The software is now also used outside of the military/intelligence communities in a number of commercial environments.Computer Graphics: Principles and Practice
Tradeshift
Starlight Information Visualization System