3D Biophotonic Modeling of PCR Dye Absorption

In biophotonics, it is often necessary to visualize how light, power, or energy is absorbed within biological samples, or to demonstrate light-driven biochemical reactions inside a PCR tube. This article explains how to model and visualize biophotonic reactions in viability PCR dyes by creating voxel-based detector volume models that reveal absorbed light distribution in three dimensions.

Background: Viability PCR Dyes and Biophotonic Reactions

Viability PCR dyes, such as PMA (propidium monoazide), are membrane-impermeant, making them specific to dead cells. Once inside a dead cell, PMA binds to DNA. Upon exposure to intense visible blue light, the dye becomes reactive and covalently attaches to DNA. This modification prevents DNA amplification in subsequent PCR reactions.

In practical terms, the uniformity of light absorption inside the PCR tube directly affects the effectiveness of the biophotonic reaction. Non-uniform illumination or localized hotspots may lead to incomplete or inconsistent PCR inhibition.

Objective of the Simulation

In this example, we demonstrate how to:

• Visualize absorbed energy, light, or flux inside a PCR tube
• Evaluate whether illumination is uniform or hotspot-prone
• Assess the effectiveness of the biophotonic reaction inside the viability PCR sample

Using a Detector Volume for Biophotonic Modeling

Instead of a standard Detector Rectangle, which records light on a flat 2D pixel grid, this simulation uses a Detector Volume object. The reasons why a detector volume is used are as follows:

• Records absorbed flux within 3D cubic pixels (voxels)
• Enables true volumetric analysis of light–matter interaction
• Ideal for modeling absorption-based biophotonic processes

This makes the Detector Volume a powerful tool for studying light absorption inside biological or chemical volumes.

System Configuration

• A single PCR tube is modeled as an absorbing volumetric object
• Three LED light sources illuminate the tube from different directions
• Only regions inside objects with finite absorption generate detector data

The design file and animation are attached at the end of this article for reference.

Visualizing Absorbed Flux in the Detector Volume

The Detector Volume display shows absorbed flux as a function of position within the tube. Each slice corresponds to a Z-plane of the voxel grid.

• The display indicates, for example, “Z Plane 8 of 10”
• Left and right arrow keys allow scrolling through Z-planes

However, manually inspecting dozens (or hundreds) of Z-planes quickly becomes inefficient.

Automating Voxel Visualization with a ZPL Macro

When analysis becomes tedious, automation is the solution. To simplify this process, a ZPL macro named Voxel Maker.ZPL is provided. This macro:

• Automatically processes large voxel datasets
• Converts absorbed-flux data into CAD-style 3D objects
• Makes hotspots and absorption patterns immediately visible

Even in this simplified example:

• Voxel grid: 50 × 50 × 50
• Total voxels: 75,000

Higher-resolution detector volumes may contain hundreds of thousands or millions of voxels, which the macro is designed to handle efficiently.

Results and Interpretation

With only a single tube in the system, the absorbed-flux distribution becomes clear:

• “Hot” voxels appear inside the cylindrical tube
• These regions represent active biophotonic reactions between blue light and PMA dyes
• Non-uniformities highlight potential issues in illumination design

This 3D visualization provides direct insight into reaction uniformity, which is difficult to achieve using 2D detectors alone.

Practical Applications

This modeling approach is useful for:

• Viability PCR system design
• Biophotonic reaction validation
• Illumination uniformity analysis
• Optical system optimization for life-science applications

For animation, annotation, and illumination visualization techniques, please refer to our article on How To Demonstrate The Optical Illumination System In An Animation.

Reference Sources

1. Zemax Optical Design Program – User’s Guide
2. Wikipedia – Biophotonics and fluorescence
3. The design file and ZPL macro used in this article are attached. Please download them to explore or adapt the model.  As Biophotonic searcher, How to demo absorbed flux by 3D in Viability PCR dyes