VizWorld.com

InformationAesthetics brings us a great talk from TEDx on Molecular Animation.  Chemistry was one of the earliest forms of visualization, classic ball and stick visualizations that brought particles tinier than the eye can see to life.  Today, many molecular visualizations are the same but new technologies are coming along to show new effects in bonds and structures with amazing detail and opening the world to whole new types of computational chemistry.

Next to a movie that originates back from around 2003 that focuses on the replication of DNA, he also shows a newer version that has been accomplished through “updated science, updated technology”, revealing how DNA mitosis through a nifty process of some quite ‘mechanical’ signal broadcasting system. At the end, he highlights the processes behind a malaria infection of a human child via a mosquito bite, through invasion of cellular tissues including the liver and blood. malaria spreads in your blood.

via TEDx Talk on Molecular Animation: Combining Cinema and Biology – information aesthetics.

Science chemistry, molecular, ted

With SC11 on the horizon, you can expect many more such announcements, but today China and NVidia are excited about the use of 2,200 Nvidia Tesla cards to run the first ever computer simulation of a complete H1N1 flu virus at atomic levels.

The CAS-IPE researchers made the simulation breakthrough by developing a molecular dynamics simulation application that takes advantage of GPU acceleration2. It was run on the Mole-8.5 GPU supercomputer, which is comprised of 288 server nodes. The system was able to simulate 770 picoseconds per day with an integration time step of 1 femtosecond for 300 million atoms or radicals1.

via Chinese Researchers Tap GPU Supercomputer for World’s First Simulation of Complete H1N1 Virus – NVIDIA Newsroom.

Hardware, Science hpc, molecular, nvidia

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A new case study from NVidia covers the creation of an impressive 3D Display wall 25 JVC monitors driven by 13 NVidia Quadroplex systems.  The result is an amazing synchronized display driven by a handful of workstations, offering up 52 million pixels of scientific data in a beautiful stereoscopic interactive display.

“Most of what people see on the display is the output of an interactive application. It’s not pre-rendered but rather interactively drawn on the screen,” he explained. “For a protein crystal structure, for example, it’s just a PDB file converted into a mesh, and this software knows how to render it. For volumetric data like an MRI [magnetic resonance imaging], it’s a Z-stack of images.  What this means is that instead of a clinician having to cycle through a series of single grayscale images one at a time, if we write the right tools, people can visualize the MRI in stereo 3D as a continuous surface and see things like lesions more clearly.”

I’ve seen similar displays built on a smaller scale, but this is quite possibly the largest and highest resolution 3D display built to date.   Now that it’s up and running, more and more schools are coming to them to try it out.

“It’s really one of those things where the sky’s the limit,” said McCrory.  “We have astronomers doing incredible work with simulating the evolution of star systems. The Business School has shown an interest in visualizing economic data to show trends.  We have requests coming from every school.”

Get the full case study after the break.

Read more…

Hardware, Science 3d, interactive, molecular, nvidia, stereoscopic

The New York Times has a great article about the growing field of biomedical animation, specifically Molecular animation.  They talk to some of the big names in the field like Rober Lue, Janet Iwasa, and Drew Berry to learn how they do it and what the benefits of molecular animation are to researchers.

“All that we had before — microscopy, X-ray crystallography — were all snapshots,” said Tomas Kirchhausen, a professor in cell biology at Harvard Medical School and a frequent collaborator with Dr. Iwasa. “For me, the animations are a way to glue all this information together in some logical way. By doing animation I can see what makes sense, what doesn’t make sense. They force us to confront whether what we are doing is realistic or not.” For example, Dr. Kirchhausen studies the process by which cells engulf proteins and other molecules. He says animations help him picture how a particular three-legged protein called clathrin functions within the cell.

via Molecular Animation – Where Cinema and Biology Meet – NYTimes.com.

Graphics, Science animation, biomed, molecular, nytimes

Robert Kosara has a new blog-post online about the important advances created by Jane Richardson in visualizing proteins.  Finding a clever way of representing the thousands of atoms and molecular bonds in simple, yet beautiful, strands and ribbons easily earns her a metnion as part of “Ada Lovelace Day”.

Scientists only figured out how to determine the three-dimensional structure of proteins in the 1970s. When Jane Richardson was writing a review article about the proteins whose structure was known in 1980, she needed a consistent way of showing them. It was clearly not very practical (or useful for understanding) to draw thousands of atoms that were part of a complex, three-dimensional structure.

via A Visual Language for Proteins: Jane Richardson | EagerEyes.org.

Science molecular, protein

Theodore Gray, of Mathematica fame, has created a periodic table using pictures to actually show the elements. As you roll over the elements with your mouse, a picture of the element is shown along with details about the element, such as its atomic weight, density, melting point, boiling point, and uses. Some of the uses are quite funny. For example, for Einsteinium:

The most famous scientist of all time, Albert Einstein, obviously deserves to have an element named after him. Unfortunately his has a half-life of 472 days and no known applications. Better luck next time?

Want another laugh, try element 107, Bohrium. Want to buy it as a poster, card deck or place mat? You can buy it in their store. The one I want is the 3-D lenticular version.

Via PeriodicTable.com

Science infographic, molecular

The periodic table has been imprinted in the minds of so many people that it’s universally known in it’s shape and use, but researchers at Microsoft believe that they’ve found a new design for the classic infographic that conveys more data such as atom size.

So why change it? According to Mohd Abubakr from Microsoft Research in Hyderabad, the table can be improved by arranging it in circular form. He says this gives a sense of the relative size of atoms–the closer to the centre, the smaller they are–something that is missing from the current form of the table. It preserves the periods and groups that make Mendeleev’s table so useful. And by placing hydrogen and helium near the centre, Abubakr says this solves the problem of whether to put hydrogen with the halogens or alkali metals and of whther to put helium in the 2nd group or with the inert gases.

via Technology Review: Blogs: arXiv blog: A New Graphical Representation of the Periodic Table.

Science infographic, molecular

The Theoretical and Computational Biophysics Group of University of Illinois at Urbana-Champaign has just released VMD 1.8.7, a new version of their amazing molecular simulation package.   The big feature in this new version is support for NVidia’s CUDA, with amazing performance boosts.

One of the key advancements included in VMD 1.8.7 is support for GPU accelerated visualization and analysis, based on NVIDIA CUDA. As reported in several publications, the massively parallel architecture of GPUs makes them ideal devices to accelerate many of the computationally demanding calculations in VMD. The range of acceleration provided by GPUs depends on the capabilities of the specific GPU devices installed, and the details of the calculation. Typical acceleration factors for the algorithms in VMD are: electrostatics 22x to 44x, implicit ligand sampling 20x to 30x, molecular orbital calculation 100x to 120x. Details on making best use of the GPU acceleration capabilities in VMD are provided here.

via VMD 1.8.7.

Science biomed, cuda, molecular, nvidia, simulation, vmd

Cryo-electron microscopy (cryoEM) is an important tool in biological research for its ability to visualize nanometer-scale structures in 3-dimensions.  Researchers have now developed an algorithm to allow even higher-resolution images and models to be constructed from cryoEM images.

A Japanese-UK research team has now demonstrated that cryoEM image analysis may be exploited to obtain structural information of sufficient resolution to reveal the absolute three-dimensional (3D) configuration of a designed DNA nanostructure. With their technique they have obtained structural information at sufficient resolution to visualize the DNA helix and reveal the absolute stereochemistry of a self-assembled DNA tetrahedron.

via Visualizing the DNA helix with cryoEM.

Science algorithm, biomed, molecular

A new system called “BioBrowser” from a German Research Foundation project at Fraunhofer Austria in Gras aims to allow researchers to interactively analyze and manipulate the molecular stucture of massive proteins containing 50,000 and more atoms.

Based on research data of molecular biologists, the software automatically calculates and displays 3D models of complex proteins – at the push of a button, in high quality, and interactively. Researchers can turn the molecule and look at it from every angle, enlarge it at will and select specific areas; the image is always razor sharp and users can switch between the most important variants.

via Super-sized Tiny Proteins: Software Helps Biologists Visualize Molecules.

Science biomed, fraunhofer, molecular, protein