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Visualization of Nanostructures

Nanostructure modeling is the computation of the positions and orbitals of atoms in arbitrary nanostructures.

Accurate atomic-scale quantum theory of nanostructures and nanosystems fabricated from nanostructures enables precision metrology of these nanosystems and provides the predictive, precision modeling tools needed for engineering these systems for applications including advanced semiconductor lasers and detectors, single photon sources and detectors, biosensors, and nanoarchitectures for quantum coherent technologies such as quantum computing. The tight-binding model based upon the Linear Combination of Atomic Orbitals (LCAO) method provides an accurate atomistic theory for nanostructures.

The visualizations are studied interactively in the NIST immersive environment. This provides a detailed view of the structures and the atomic scale variation of the calculated nanostructure properties.

The parallel code outputs the positions of the atoms and the orbitals. Then the NanoVis tool uses multiple processes and shaders to keep the graphics at interactive frame rates, giving the researcher constant feedback, encouraging data exploration. Specifically, this tool utilizes the following two programs:

  1. Visprep: a preprocessing program, reads atomic positions and associated orbital data, performs error checking and data analysis, and creates binary data files which can be quickly read by orbitalVisualization, the visualization program. This step needs to be performed only once per data set.
  2. OrbitalVisualzation: reads the binary files into memory and starts two asynchronous background process: one that calculates which orbitals should be displayed based on the parameters of a selected geometric shape, and one that modifies the position and geometry of the selected shape. OrbitalVisualzation also creates several GUIs that control which orbitals are to be displayed and how they will be presented. Orbitals are of two types; P orbitals, which are axis aligned dumbbell shapes, and S orbitals, which are spherical. OrbitalVisualzation uses a set of graphic shader programs to create S and P orbital shapes and to dynamically determine which objects should be drawn; this allows a greater number of orbitals to be displayed than by using traditional graphics techniques. Using shaders, OrbitalVisualzation can represent an S orbital by a point, a P orbital by two points, and the orbital selection by a texture map, which drastically reduces the amount of data to pass to the graphics card.

(bullet) Papers/Presentations
(bullet) G. Bryant, M. Zielinski, N. Malkova, J. Sims, W. Jaskolski and J. Aizpurua, Effect of Mechanical Strain on the Optical Properties of Quantum Dots: Controlling Exciton Shape, Orientation, and Phase with a Mechan ical Strain, Physical Review Letters, 105 (6) , 2010. ID: 067404.
Note: Pages 067404-1 to 067404-1=4 DOI: 10.1103/PhysRevLett.105.067404
(bullet) G. Bryant, N. Malkova, J. Sims, M. Zielinski, W. Jaskolski and J. Aizpurua, Re-engineering the optics of quantum dots with mechanical strain in Optics of Excitons in Confined Systems (OECS11), Madrid, Spain, September 7-11, 2009.
(bullet) G. Bryant, N. Malkova, J. Sims, M. Zielinski, W. Jaskolski and J. Aizpurua, Re-engineering the optics of quantum dots with mechanical strain in Electronic Materials Conference, University Park, PA, June 24-26, 2009.
(bullet) James S. Sims, W. L. George , Terrence J. Griffin , John G. Hagedorn, Howard K. Hung, John T. Kelso, Marc Olano, Adele P. Peskin, Steven G. Satterfield, Judith E. Terrill, Garnett W. Bryant and Jose G. Diaz, Accelerating Scientific Discovery Through Computation and Visualization III. Tight-Binding Wave Functions for Quantum Dots, NIST Journal of Research, 113 (3) , May-June, 2008, pp. 131-142.
Links:  pdf and pdf.
(bullet) James S. Sims, William L. George, Steven G. Satterfield, Howard K. Hung, John G. Hagedorn, Peter M. Ketcham, Terence J. Griffin, Stanley A. Hagstrom, Julien C. Franiatte, Garnett W. Bryant, W. Jaskolski, Nicos S. Martys, Charles E. Bouldin, Vernon Simmons, Olivier P. Nicolas, James A. Warren, Barbara A. am Ende, John E. Koontz, B. James Filla, Vital G. Pourprix, Stefanie R. Copley, Robert B. Bohn, Adele P. Peskin, Yolanda M. Parker and Judith E. Devaney, Accelerating Scientific Discovery Through Computation and Visualization II, NIST Journal of Research, 107 (3) , May-June, 2002, pp. 223-245.
Links:  postscript and pdf.
(bullet) Julien C. Franiatte, Steven G. Satterfield, Garnett W. Bryant and Judith E. Devaney, Parallelization and Visualization of Computational Nanotechnology LCAO Method delivered at Nanotechnology at the Interface of Information Technology, New Orleans, LA, February 7-9, 2002.
Links:  pdf and pdf.
(bullet) Garnett W. Bryant, J. Aizpurua, Rui-Hui Xie, Julien C. Franiatte, Judith E. Devaney, W. Jaskolski, M. Zielinski, S. Lee, J. Kim, L. Jonsson and J. W. Wilkins, Designing the Nanoworld: Atomic Scale Simulations of Nanostructures and Nanodevices delivered at NIST Nanotechnology Open House, Gaithersburg, MD, June 20, 2002.
(bullet) Julien C. Franiatte, Judith E. Devaney, Garnett W. Bryant, Steven G. Satterfield and William L. George, Building Nanostructures Interactively in an Immersive Visualization Environment delivered at NIST Nanotechnology Open House, Gaithersburg, MD, June 20, 2002.


Modeling Quantum Dots: The optics of self-assembled quantum dots, also known as artificial atoms, has been studied using our parallelization. Such systems contain up to a million atoms and can only be studied using the parallel implementation. We show how nanomech anical strain can be used to dynamically reengineer the optics of these quantum dots, giving a tool to manipulate mechanoexciton shape, fine-s tructure splitting and optical transitions, transfer carriers between dots and interact qubits for quantum processing. Most importantly, nanomechanical strain pro vides both phase and energy control to modify the inner workings of excitons. These are all capabilities needed to use QDs in nanophotonics, quantum information processing, and in optically active de vices, such as optomechanical cavities and semiconductor nanotubes.

  1. Atoms (left) with Orbitals (right).
    Atoms (left) with Orbitals (right).
  2. Concentric spheres.
    Concentric spheres.
  3. Pyramid.
  4. Movie exploring structure of atoms with orbitals.
    Movie exploring structure of atoms with orbitals.
  5. P orbital created with shaders.
    P orbital created with shaders.
  6. NanoVis tool.
    NanoVis tool.

(bullet) Parallel Algorithms and Implementation: James S. Sims , Howard Hung, Julien Franiatte
(bullet) Collaborating Scientist: Garnett Bryant
(bullet) Visualization: John Kelso , Howard Hung, Julien Franiatte
(bullet) Group Leader: Judith E. Terrill

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Date created: 2002-02-19, Last updated: 2011-01-12.