The Avogadro project has developed an advanced molecule editor and visualizer designed for crossplatform use in computational chemistry, molecular modeling.MMU offers various engineering courses in Biotechnology, Civil Engineering, Electrical Engineering, Computer Science Engineering etc.Apply now for admissions A directory listing of nanotechnology business programs, by location.Aim Atoms In Molecules Software Developer' title='Aim Atoms In Molecules Software Developer' />Microfluidics A general overview.Microfluidics can be divided in many branches among which we can cite Continuous flow microfluidics.A continuous flow is a constant, regular, continued flow.Continuous flow microfluidics allow to manipulate the continuous flow of liquid through microchannels thanks to devices such as external pressure pumps or integrated mechanical micropumps.Continuous flow processes are used in a wide range of applications like in bioanalytical, chemical, energy and environmental fields.Digital microfluidics.Also called droplet microfluidics or emulsion science, digital microfluidics is one of the main application fields of microfluidics.It enables to manipulate autonomous droplets on a substrate using electro wetting.This allows to generate and control uniform, reproducible droplets over the experiments parameters.Droplets generation can be used in a large range of applications like in synthesis of nanoparticles, single cell analysis, and encapsulation of biological entities.This technology will probably become an important tool for drug delivery and biosensing, by providing new solutions for state of the art diagnostics and therapeutics.Optofluidics and microfluidics.Optfluidics is an emerging fast growing science resulting from the combination of three fields of science microphotonics, optics and microfluidics.Aim Atoms In Molecules Software Developer' title='Aim Atoms In Molecules Software Developer' />Microphotonics or the micron scale control of light, implicates the ordered transport of photons commonly emanating from a laser.Optics is the study of the behaviour and characteristics of light at large scale including its interactions with other elements and the fabrication of devices that utilize or detect it.Optofluidics merges light and liquids into miniaturized optical devices that take advantage of the properties of fluids to generate high precision and flexibility.Optofluidic applications include lab on chip devices, fluid waveguides, deformable lenses, microdroplets lasers, displays, biosensors, optical switches or molecular imaging tools and energy.Acoustofluidics and microfluidics.Acoustofluidics deal with the use of acoustic fields, mainly ultrasonics onto fluids within microfluidic channels allowing to manipulate cells and particles.It refers to the study and manipulation of acoustic waves on microscale to nanoscale fluidic environments.These mechanical waves are inflicted on the fluid through the excitation of the microchannels walls with an actuator.Acoustics offer promising abilities in the manipulation of both fluids and particles within those fluids on the micro nano meter scale.This has proven to be a method that is gentle to the cells and that can be employed in many applications such as biomedical applications lab on a chip functionalization, moving of particles, separation of cells, acoustic trapping.Electrophoresis and microfluidics.Electrophoresis is a technique used in clinical and research laboratories in order to separate molecules based on their size, electrical charge and shape.Electrophoresis rests on the movement of ions in an electric field.An electric current flows through a medium holding the mixture of molecules.Positively charged ions cations proceed towards a negative electrode whereas negatively charged ions anions proceed towards a positive electrode.Ions have distinctive migration rates and they can be separated.Electrophoresis of positively charged ions is called cataphoresis, while electrophoresis of negatively charged particles is called anaphoresis.This method is used for both DNA and RNA analysis.Avogadro an advanced semantic chemical editor, visualization, and analysis platform.The Avogadro project was started in earnest in 2.So far, it has been cited over 1.From the beginning, the project has strived to make a robust, flexible framework for both building and visualizing molecular structures.Much of the initial focus has been placed on preparing input and analyzing output from quantum calculations.Other applications such as preparing input for MD simulations and visualizing periodic structures will also be presented, demonstrating the flexibility of the Avogadro platform.The development team has also been members of the Blue Obelisk movement, following the three pillars outlined by the group Open Data, Open Standards, and Open Source 4.Software architecture.One area that seems to suffer in many code bases in chemistry is software architecture.This can lead to less maintainable code, poor code reuse, and a much higher barrier to entry.Problems were identified in other projects with a view to minimize their impact when developing Avogadro.Modern software design processes were used in the initial planning stages of Avogadro, along with the choice of modern programming languages and libraries.Avogadro has close ties to several other free, cross platform, open source projects to reuse as much code as is practical.These projects include Qt 5.Open Babel 5. 1 for chemical file inputoutput, geometry optimization, and other chemical perception Eigen 5.Open. GLGLSL for real time, three dimensional rendering and POV Ray for ray traced rendering.Based on the previous experience of the authors and a review of available programs at the time, several fundamental choices were made.The C programming language the Qt graphical toolkit Open.GL for 3. D visualization CMake as the build system and Open Babel as the chemical library.Using this combination of languages and libraries requires the project to be licensed under the GNU GPLv.The core of Avogadro is written in portable C code with platform specific differences abstracted away by Qt, Open. How To Stop Your Bones Cracking Means . GL, and Open Babel.The CMake build system makes the build process relatively simple on all supported platforms.Avogadro has been successfully built and tested on Linux, Apple Mac OS X, and Microsoft Windows in common 3.The Avogadro framework uses the model, view, controller paradigm.The model is comprised of the core data classes such as Molecule, Atom, and Bond, views are made up of the enginedisplay plugins, and controllers are the tools interactive mouse and extensions non interactive, form basedmenu based.Every plugin has full access to the core data model, but view and controller plugins are conceptually different views are responsible for displaying data and controllers are responsible for modifyingchanging data.Plugins rely on Avogadros set of programming interfaces and almost all functionality is implemented in self contained plugins that are loaded at runtime.The majority of plugins distributed with Avogadro are written in C, but the API is also available in the Python scripting language.This allows for a great deal of choice in how plugins are implemented.Each plugin is a singleton class that implements a particular set of functionsdepending on the type of pluginwhich allows for features to be implemented in a very modular way.Over the last few years Avogadro development has started to use nightly builds of the latest version of the code in order to automatically flag issues introduced in new commits.Code review was also introduced in order to add a review step before new code is merged, along with softening the line between someone with commit rights and someone without anyone can propose and upload a patch, but a small group can choose ifwhen the patch will be merged.Some automated testing has been added, but coverage at this point remains relatively low.API documentation is automatically generated from comments in the code using Doxygen.Plugin interface.Avogadro plugins are divided into four different types corresponding to four main classes that derive from this common base class, specializing their interface for specific activities Figure 1.The Avogadro Color base class defines the virtual interface for applying colors to atoms, bonds, and other properties.Avogadro Engine defines the common interface for all display types in Avogadro simple ball and stick, Van der Waals visualizations, surfaces, and force visualizations.The Avogadro Tool base class provides the interface for all interactive tools, focusing principally on mouse and keyboard interaction with Avogadro.Examples of tool plugins include the draw tool used to draw molecules atom by atom, and the navigation tool used to pan, rotate, and scale the view of the molecule.There are also several specialized tools such as the alignment tool.Figure 1. General code architecture of Avogadro.General code architecture of Avogadro, indicating major plugin interfaces for colors, display engines, tools, and extensions.Red boxes indicate code dependencies of Avogadro, blue boxes indicate plugin API classes, and green boxes inidicate examples of each plugin type.Finally there is the Avogadro Extension class, which defines the interface for dialog based plugins.These extensions can interact with the molecule, and are used for a variety of purposes from molecule properties dialogs to input file generation dialogs for many quantum codes including NWChem, Gaussian, GAMESS, and others.This class of plugin is also applied to file import, and network aware extensions querying web databases for structures given their common name for example.At start up, several standard directories, which may be customized, are searched for plugins.The Qt plugin framework is used to check that the plugins have a recent enough version to be loaded, and the plugin type can be deduced once loaded.The user interface is then populated with appropriate entries tools are added to the main toolbar using their embedded icons, display types are added to the display type list, and menu entries are added for all loaded extensions.The tool and display type plugins can both optionally provide a dialog for configuring the plugin.Dialogs are specific to each plugin and integrated into the user interface.Display types. Display plugins are referred to as engines internally.Their primary focus is rendering graphics to the screen.As is the case with most molecular graphics, a large portion of the geometric primitives are spheres and cylinders, typically used to represent atoms and bonds.There are many other properties that can be rendered using the display type plugins, for example, some of the engines also convey information about the underlying data the geometric primitives represent to allow for the molecule to be edited.Table 1 shows a summary of the display plugins distributed with Avogadro.Table 1. List of default display type engine plugins.Engines are performance critical as the render functions are called each time a frame is requested for display.Efficient rendering is also critical since multiple display types can be combined to form a composite display.For example, ball and stick display overlaid with a transparent Van der Waals space filling display and ring rendering to highlight all rings in the structure.Figure 2 d and f show two such combinations of multiple display types.Figure 2. Standard molecular structure representations.Several molecular representations of thiophene, a wireframe, b sticklicorice, c ball and stick, d ball and stick with ring, e Van der WaalsCPK and f transparent Van der Waals with stick.Tools. The tools are responsible for virtually all mouse and keyboard interaction with the molecule.A list of all tools is given in Table 2.Table 2. List of default mouse tool plugins.The navigation tool provides basic scene navigation, implementing rotation,panning, tilting, and zooming support.The initial point of interaction where the click occurs changes the anchor point for navigation navigation takes place about the center of molecule when clicking in empty space or about the center of any clicked atom.During interaction, the navigation tool provides visual cues to show what type of navigation is taking place.The navigation tool is also used as the default tool if the currently active tool does not handle the mouse event passed to it.
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