Danny Petrasek
MESOPHYSIOLOGY
A poorly represented area of physiological research is that which focuses
on bridging molecular biology and cell biology to the macroscopic organismic
physiology. The importance of this idea is summarized by the question: Given the
complete details of the molecular biology of a single isolated cell, can we then predict the behavior of
a connected group of cells? It seems that the answer to this question is proving to be no!
The nature of the intermediate mechanisms that relate the micro physiology to the
macro defines the mesophysiology.
This "mesophysiology" is vital to those of us who wish to exploit the fruits of the
molecular biological results in order to understand and treat
human pathology. Our paper below is an example of what we consider to be a mesophysiological
mechanism.
XS
XS is a computational tool
to simulate cell networks in endocrine glands. In particular we have focussed
on developing a set of heirarchical models to simulate the dynamic response
of the parathyroid gland to serum calcium ion levels.
We developed a novel approach to simulate the entire
gland as well as networks of cells by employing a Cartesian based mesh
approach combined with a level-set technique to handle complex
geometries.
AJP
AJP
The image that is displayed here is our computational representation of a neoplasm in the
Parathyroid gland inhibiting the diffusive transport of calcium. The blue color
represents a low calcium concentration. A preprint of our AJP article appears below.

Chad's Home page Chad's Page
A list of papers, talks and animated simulations from work in
progress
- Preprint of our AJP article "Glandular regulation of interstitial diffusion: a model and simulation of a novel physiological mechanism."
Click here for .pdf file
- Mathematical appendix for AJP Endocrine and Metabolism
Glandular regulation of Interstitial diffusion.
Click here for .pdf file
- powerpoint for Ravi
Glandular regulation of Interstitial diffusion.
Click here for .ppt file
- Melanoma-I where the anatgonist is deposited in the tumor. The "density dependent" diffusion coefficient slows the drug transport in this case more than the second case since the depot is more concentrated.(Despite the total drug given being the same in both cases).
Click here for .avi file
- Melanoma-II where the anatagonist is infused through the blood and the diluted drug enters the tumor through the cappilaries(Lower boundary)
Click here for .avi file
- Tau-Mu, here is a preliminary movie of a Cyclic-GMP diffusing from a
photon-activated rhodopsin site.
Click here for .avi file
- Ca diffusing from a Calcium channel.
Click here for .avi file
- Tau-Mu: here is Cyclic-GMP diffusing. The acitivated rhodopsin is abruptly
turned on and off. Note the blue center of the Cyclic GMP diffusion process,
representing a lower concentration of Cyclic GMP (consistent with the
expected kinetics).After the initial diffusion I skipped several frames to show the later parts of the simulation, hence the abrupt change in the middle of the movie.
Click here for .avi file
- REVISED MODEL showing Cyclic GMP diffusion. Note the lower concentration of C-GMP near the rhodopsin site on the bottom of the central disc.
Click here for .tif
- avi movie of Gamma-Meinhardt with MGP added after stripes were formed
Click here for .avi file
- a second movie of Gamma-Meinhardt with MGP added after stripes were formed
Click here for .avi file
- New movie(5-11)of Gamma-Meinhardt with MGP added after stripes were formed
Click here for .avi file
- New movie(5-24)of POM with mode doubling. The dark stripes are high density of cells
Click here for .avi file
- New movie(6-5-02)of DGP density plot with Z axis = density.
The dark stripes are high density
Click here for .avi file
- New movie(6-6-02)of DGP density plot with Z axis = density.
The dark stripes are high density. The companion XY projection is below.
Note that since I have "painted" black all densities above a certain threshold,
the map doesnt distinguish shades above a certain altitude.
Click here for .avi file
- Companion movie(6-6-02) to densityplot4 projetced on XY plane
The dark stripes are high density
Click here for .avi file
- mpeg movie Pattern Formation (gray-scott)
Click here for .mpeg file
- Kondo model 3000 time steps
Click here for .avi file
- NEW MOVIE 9-11-02 MODE_SPLITTING
Click here for .avi file
- 2nd NEW MOVIE 9-11-02 MODE_SPLITTING
Click here for .avi file
- 2nd LATEST MOVIE 11-05-02 MODE_SPLITTING
Click here for .avi file
- XS MGP(INHIBITOR) SHOWING STRIPES-SPOTS simulation 04-29-03 ADDING XS MGP
Click here for .avi file
- Photo-Transduction movie
Click here for .avi file
- powerpoint presentation at Cedars-Sinai research seminar.
Click here for .ppt file
- MATHEMATICAL SUMMARY to the PATTERN FORMATION PAPER under review.
Click here for .ppt file
- For Ravi
Click here for .pdf file
- Petrasek- Thesis Rough Draft
Click here for .pdf file
Biosketch
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Biosketch
Click here for word file
Collaborators
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Professor Donald S. Cohen (Applied and Compuational
Math, Caltech)
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Professor Scott E. Fraser (Biology, Caltech)
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Professor Ravi Samtaney (Caltech, UCLA, Princeton, Lawrence Berkeley Lab, Rutgers)
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Professor Alan Garfinkel (UCLA School of Medicine)
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Professor Wayne L. Hubbell (UCLA School of Medicine)
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Professor Karoly Holczer (Dept. of Physics, UCLA)
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Professor Bill Goodman (UCLA School of Medicine)
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Professor Isidro Salusky (UCLA School of Medicine)