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Tags: visualization

Simulators can produce all sorts of numbers, but the numbers themselves aren't terribly meaningful until they are put into context by visualization techniques. For example, the coordinates of the various atoms in a molecule don't readily convey the shape of the molecule. But once those coordinates are loaded into VMD, the the resulting picture conveys not only the shape of the molecule, but other important properties as well.

Learn more about visualization techniques from the resources on this site, listed below.

Resources

Tools

Online Presentations

  • 10.0 Ranking Leary: Engineering Nanomedical Systems

    Engineering Nanomedical Systems

    Type Online Presentations
    Contributor(s) James Leary
    Date 14 Mar. 2006
    Avg. Rating 5.0 out of 5 stars  (3)
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    This tutorial will cover general problems and approaches to the design of engineered nanomedical systems. An example to be covered is the engineering design of programmable multilayered nanoparticles (PMNP) to control a multi-sequence process of targeting to rare cells in-vivo, re-targeting ...

  • 10.0 Ranking Ebert: Is Seeing Believing? How to Think ...

    Is Seeing Believing? How to Think Visually and Analyze with Both Your Eyes and Brain

    Type Online Presentations
    Contributor(s) David Ebert
    Date 26 Mar. 2007
    Avg. Rating 5.0 out of 5 stars  (1)
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    In this talk, I will cover the basic techniques for visualization, some of the tools available, and how to NOT miscommunicate information from your visualizations.

  • 9.9 Ranking Stach: Electron and Ion Microscopies as ...

    Electron and Ion Microscopies as Characterization Tools for Nanoscience and Nanotechnology

    Type Online Presentations
    Contributor(s) Eric Stach
    Date 17 Mar. 2006
    Avg. Rating 5.0 out of 5 stars  (1)
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    Electron and ion microscopy techniques allow one to obtain high spatial resolution images and spectroscopic information of both the surface and internal structure of nanostructured materials. In this tutorial, I will present a broad overview of the basic physical principles that underly the ...

  • 9.8 Ranking Stach: What Can the TEM Tell You About ...

    What Can the TEM Tell You About Your Nanomaterial?

    Type Online Presentations
    Contributor(s) Eric Stach
    Date 26 Feb. 2007
    Avg. Rating 5.0 out of 5 stars  (1)
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    In this tutorial, I will present a brief overview of the ways that transmission electron microscopy can be used to characterize nanoscale materials. This tutorial will emphasize what TEM does well, as well where difficulties arise. In particular, I will discuss in an overview manner how ...

  • 9.8 Ranking Strachan: First Principles-based Atomistic ...

    First Principles-based Atomistic and Mesoscale Modeling of Materials

    Type Online Presentations
    Contributor(s) Alejandro Strachan
    Date 16 Nov. 2005
    Avg. Rating 5.0 out of 5 stars  (6)
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    The quantitativelly accurate prediction of materials behavior from first principles requires the chracterization of a wide range of phenomena with disparate temporal and spatial scales form electrons and atoms to devices. No single theory of computational model can capture all these phenomena ...

  • 9.7 Ranking Klimeck: Quantum Dots

    Quantum Dots

    Type Online Presentations
    Contributor(s) Gerhard Klimeck
    Date 26 Sep. 2005
    Avg. Rating 5.0 out of 5 stars  (4)
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    Quantum Dots are man-made artificial atoms that confine electrons to a small space. As such they have atomic-like behavior and enable the study of quantum mechanical effects on a length scale that is around 100 times larger than the pure atomic scale. Quantum dots offer application opportunities ...

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Learning Modules

  • 7.6 Ranking McLennan: Add Rappture to Your Software ...

    Add Rappture to Your Software Development

    Type Learning Modules
    Contributor(s) Michael McLennan
    Date 01 Nov. 2005
    Avg. Rating 4.5 out of 5 stars  (6)
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    Rappture is the Rapid APPlication infrastrucTURE, a toolkit that you can use to accelerate the development of scientific simulation tools. Scientists developing a code are often led astray by all of the elements surrounding their code. They end up developing their own command language for input, ...

Teaching Materials

  • 10.0 Ranking Grossman: Computational Nanoscience, Lecture ...

    Computational Nanoscience, Lecture 4: Geometry Optimization and Seeing What You're Doing

    Type Teaching Materials
    Contributor(s) Jeffrey C Grossman, Elif Ertekin
    Date 13 Feb. 2008
    Avg. Rating 5.0 out of 5 stars  (1)
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    In this lecture, we discuss various methods for finding the ground state structure of a given system by minimizing its energy. Derivative and non-derivative methods are discussed, as well as the importance of the starting guess and how to find or generate good initial structures. We also briefly ...

Downloads

  • 10.0 Ranking Xie: Molecular Workbench: An Interface ...

    Molecular Workbench: An Interface to the Molecular World

    Type Downloads
    Contributor(s) Charles Xie
    Date 31 Aug. 2006
    Avg. Rating 5.0 out of 5 stars  (2)
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    The Molecular Workbench software is a free, open-source modeling and authoring program specifically designed for use in science education. Powered by a set of real-time molecular simulation engines that compute and visualize the motion of particles interacting through force fields, in both 2D and ...

  • 5.5 Ranking Suenaga: Facio

    Facio

    Type Downloads
    Contributor(s) Masahiko Suenaga
    Date 27 May. 2008
    Avg. Rating 0.0 out of 5 stars  (0)
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    Facio is a 3D-graphics program for molecular modeling and visualization of quantum chemical calculations(GAMESS and Gaussian). It is a GUI for FMO (Fragment MO) calculation. Selected features include: (1) From a PDB file, create GAMESS/FMO input with 4 mouse clicks. (2) Manual fragmentation for ...

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