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How to Demo Biophotonic Reaction in Viability PCR dyes

In biophotonics, sometimes, we would like to show how light/power is absorbed, or demo the biophotonic reaction in an PCR tube, this article will show you how to create intricate PCR dye models of the voxels in a Detector Volume.

Viability PCR dyes like PMA are membrane-impermeant, which makes them dead cell specific. Once inside of a dead cell, they bind to DNA. Exposure to intense visible blue light renders the dyes reactive, and causes them to covalently attach to the DNA. In this biophotonic reaction, this DNA modification prevents amplification in subsequent PCR reactions.

In this example, we will show absorbed energy/light/flux in the tube, to find and check if the light absorbed by the Viability PCR tube is uniform, or, there is any hotspot in the PCR tube, to check the biophotonic reaction.

In this biophotonic demo, we will use Volume detector, unlike the Detector Rectangle object, which records light as it passes through square pixels arranged on a flat rectangle, the Detector Volume object records light as it passes through cubic volume-pixels, or voxels, arranged in a rectangular solid. This detector object is very powerful.

The setting of the tubes and light source is as below, There is 3 Led light source to illuminate the PCR tube, and you could download the film at the end of this article.

Note that we will use this Detector Volume to show absorbed flux in the biophotonic reaction; we will only generate data in regions which are inside an object that has some finite absorption.

This window shows us the absorbed flux as a function of position inside the detector volume. At the bottom of the window, we see that this graph represents “Z Plane 8 of 10” , And while this window is up, we can press the left and right arrow keys to scroll through all the various Z Planes, and it seems very tedious. And anytime we find that things are getting tedious, we know it’s time to write a ZPL macro! “Voxel Maker.ZPL” macro is also attached in in the articles.

To simplify the example, we only keep one tube in the array. You can clearly see where the ‘hot’ voxels are inside the glass cylinder, which will represent the biophotonic reaction, in other words, which is the reaction of blue light with PMA dyes. Keep in mind that this simple example had just 50 pixels in each of the x-, y-, and z-directions; there are 75000 voxels in the detector volume. A detector volume with finer pixels will have far more voxels.

The attached macro is designed to handle such large voxel numbers with ease. Of course, the resulting CAD object files will be quite large, and the production of these files will take some time. But the results can be truly illuminating. How to create an annotation, How To Demonstrate The Optical Illumination System In An Animation, please refer to our previous article.

Here is another example for your reference.


The design file used in this particle is attached, please download it here.  As Biophotonic searcher, How to demo absorbed flux by 3D in Viability PCR dyes

Reference  Source:

  2. Zemax Optical Design Program User’s Guide, Zemax Development Corporation


    The material used in this knowledge sharing, is only for research, academic, non-profit educational or personal use, the blog owner has strived to credit the original sources, but cannot warrant the accuracy of copyrights or completeness of the information sources.

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