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CCS Art Show 2008

 

Art and Descriptions 

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Chia-Yu Hsu
Post-doctoral researcher

3D simulation of a lamprey swimming with external hydrodynamics under sinusoidal wave propagation along the body.

This is a CCS collaboration with the University of Maryland, Cal State Fullerton and Princeton University. 

 

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John Chrispell
Post-doctoral researcher

Stretched immersed boundary (fiber or bubble) moving toward its rest position in Newtonian fluid as time progresses.

This is a CCS collaboration with NYU, UCLA and Washington State University.

 

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Ricardo Cortez
Faculty

Surface plot of the distribution of CO2 released by a group of roosting birds.  The birds perform a two-dimensional random walk as they release CO2.  The concentration is then advected by a slight wind velocity and diffused to its surroundings.  The peaks of the landscape are areas of high concentration based on the positions and random motion of the birds.  The colors represent levels of concentration. 

This is a CCS collaboration with the Epidemiology department at Tulane. 

 

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Hideki Fujioka
Computational Scientist

Surfactant desorption into a liquid plug propagating through a tube
A liquid plug propagates through a circular tube whose inner surface is coated by a thin liquid film. The liquid contains a soluble surfactant which can exist on the air-liquid interface or in the bulk fluid. The Finite-Volume Method was used to compute the flow, interface shape and the surfactant transport. The boundary fitted mesh was used. The plot shows the surfactant concentration in the bulk fluid. As the plug propagates, the interfacial surfactant on the front film accumulates on the front meniscus surface and desorbs into the plug core. A recirculation mixes the surfactant in the plug core. 

 

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Hoa Nguyen
Post-doctoral researcher

A tessellation is a tiling of a given domain with regions such that among them, there are no overlaps and no gaps. A centroidal Voronoi tessellation is a Voronoi tessellation of a given set such that the associated generating points are centroids (centers of mass with respect to a given density function) of the corresponding Voronoi regions. These tessellations arise in many natural phenomena such as the honeycomb structure, cellular biology, and the territorial behavior of animals. They are also useful in many other contexts such as optimal distribution of resources and finite element methods.

The pictures are part of my dissertation work at Florida State University. Project collaborators were at the University of South Carolina and Virginia Tech. 

 

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Hoa Nguyen
Post-doctoral researcher

Pfiesteria piscicida is a group of dinoflagellates which can produce toxins strong enough to kill large fish and damage the human nervous system. We are building this model for the dinoflagellate and solving Stokes equations to understand their motion. Background photo courtesy of Delaware Biotechnology Institute.

This is a CCS collaboration with the University of Maine and George Washington University.  

 

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Katharine Hamlington
Ph.D candidate

A Microfluidic Mixing Chamber Model

The boundary element method was implemented in parallel to determine the flow field due to a pressure drop placed across the inlet on the left and outlet on the right in a microfluidic mixing chamber with 18 C-shaped obstructions. The boundaries were discretized into 3603 nodes, and the computation was completed in 171 seconds, after which internal velocity values were computed. Shown is the magnitude of the velocity within the chamber.

This is a CCS collaboration with Louisiana Tech University and Louisiana State University. 

 

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Sarah Lukens
Ph.D Candidate

FTLE plot of equally spaced cilia beating in phase integrated forward in time.  The pink represents higher contours, which show regions of maximum particle displacement that represent repelling fluid-fluid boundaries.

This is a collaboration between CCS and Mississippi State University. 

 

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Ricardo Ortiz
Post-doctoral researcher


Stuck bacteria and flow fields created by rotating flagella bundle near infinite wall. Velocity field near bacteria. 

 

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Ricardo Ortiz
Post-doctoral researcher


Stuck bacteria and flow fields created by rotating flagella bundle near infinite wall. Swirls created by beating flagella and stuck body.



This is a CCS collaboration with University of Arizona and University of Glasgow 

 

 

 

 

 

 

 

 

 

 

 

 

 

 


 

CCS Art Show 2

 

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Ricardo Ortiz
Post-doctoral researcher

Stuck bacteria and flow fields created by rotating flagella bundle near infinite wall. Streamlines for velocity field.

This is a CCS collaboration with University of Arizona and University of Glasgow. 


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Sergei Ponomarev
Post-doctoral researcher

Jigsaw-rendered yeast nucleosome (pdbid:1id3): DNA strands are shown in pink and white, histone protein subunits in red, green, blue, grey, yellow, orange, black and white.
Colored spheres represent ions, white grids correspond to protein density, cyan springs and colored cylinders denote alpha-helixes. 

High throughput -- high performance simulation workflows are being developed in collaboration with LONI Institute researchers at Louisiana State University's Center for Computation & Technology. 

 

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Priya Shilpa Boindala
Ph.D Candidate

The emergence of wakes in the fluid regions surrounding two equal spheres translating along their line of centers, with uniform velocity in Stokes flows is demonstrated here. The two spheres are represented by a regularized stokeslet and dipole at their center. In isolation, this representation would result in streamlines (in any plane) that stretch to and from infinity along the surface of the sphere, with the stagnation points situated at the ends of the diameter. As the center-center distance is reduced and the two spheres are in contact, wakes that form coalesce and the two spheres are surrounded by a region of fluid that consists of innumerable ring vortices.

Here the two spheres translate with unit velocity along the x-axis. The relative fluid velocity vectors far away from the spheres are in the negative x-direction. 


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Priya Shilpa Boindala
Ph.D Candidate

Cilia are hair like structures that project from cells. They are of two kinds, motile and non-motile. Motile cilia usually come in large numbers and beat in a coordinated fashion. In humans, motile cilia are found in the trachea, where they help to move the mucus and dirt outside the lungs. They are also found in the fallopian tubes, where the beating cilia help to move the ovum from the ovary to the uterus.
Non-motile cilium on the other hand is found as one cilium per cell, and in recent studies has shown to aid in cell signaling and development.
Depicted here is a single cilium (red-filament), attached at one end to a wall and the flow during its power stroke and recovery stroke. The forces responsible and the fluid velocity were computed using the Method of Images for Regularized Stokeslets. The fluid velocity is shown in the x-y plane, as a vector field with streamlines.
[Ref: The Method of images for regularized Stokeslets, J.Comp Phys.,227 (2008)] 

 

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Thomas Bishop
Faculty

Richard Stolz
Graduate student, Math and Public Health

Structure of the Mouse Mammary Tumor Virus Promoter

The MMTV is a naturally occurring sequence of DNA whose primary function is to control gene expression. It is a genetic switch. When steroids are present the gene is expressed. Without steroids the gene is silent. Left: Structure of the MMTV with six nucleosomes (blue spheres) bound to DNA (yellow beads). Nucleosome B contains binding sites for four steroid receptors (red), two octamer binding proteins (orange), nuclear factor I (blue) and a TATAbox binding protein (green). Right: Five tandem repeats of the MMTV fully populated with nucleosomes shifts the positioning of nucleosome B and produces bent chromatin.

This work is part of a collaboration with researchers at Tulane-Xavier Center for Bioenvironmental Research.   

 

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Thomas Bishop
Faculty

The Other Helix

Helices are a common geometric shape. They can form a left-handed spiral (left half of each image) or a right-handed spiral (right half of each image). Bottom: For common materials a helix can be made from a circular object by twisting the material. Twisting the material one way makes a right-handed helix, twisting the other way makes a left-handed helix. Top: Shear rather than torsion can also be used to make a helix, but not for common engineering materials. We have demonstrated that nucleosomal DNA has both Torsion Helix and Shear Helix properties.

This work is featured in the math biology component of the Flexible and Extendable Scientific Undergraduate Experience (FEScUE) program at Colorado State University. 

 

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Yuen-Yick Kwan
Post-doctoral researcher

A spectral-element mesh for the ring
{(x,y): 0.5^2 < x^2+y^2 < 1} 

 

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Yuri V. Sereda
Post-doctoral researcher

Folding of the entire sequence of yeast chromosome 1 from free DNA without nucleosomes (left) to a maximally compacted structure (top). An intermediate structure of extended chromatin with 100 nucleosomes (bottom). DNA is blue, nucleosomes are red.

This work is featured in the math biology component of the Flexible and Extendable Scientific Undergraduate Experience (FEScUE) program at Colorado State University. 

 

 

 

 

 

 

 

Center for Computational Science, Stanley Thomas Hall 402, New Orleans, LA 70118 ccs@tulane.edu