Surface-Exposed Waveguides for Z-Axis Illumination Control
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Solution Overview
Problem
Existing analytical systems lack precise control over illumination volume and area, particularly in the z-axis, leading to excessive illumination of non-relevant regions and auto-fluorescence noise, which affects the accuracy and efficiency of analyses on substrates like DNA arrays.
Innovation Solution
The use of surface-exposed optical waveguides that emit an evanescent field for controlled illumination, eliminating the need for a cladding layer and allowing selective illumination of materials proximal to the substrate surface, reducing auto-fluorescence and improving alignment precision.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If wide area illumination is used to interrogate large numbers of analytical features, then the ability to analyze multiple molecule groups is improved, but control over the volume of material illuminated is reduced
Solution Approach 1:
The illumination system is segmented into multiple independent zero mode waveguides, each capable of being individually addressed and controlled. This allows selective illumination of specific regions while maintaining the ability to interrogate large numbers of analytical features across the array.
Solution Approach 2:
The patent introduces precise control in the z-dimension (vertical axis) through zero mode waveguides with sub-wavelength apertures. This adds a new dimension of control to the traditionally two-dimensional (x-y plane) illumination systems, enabling volumetric confinement of the evanescent field.
2Area of stationary object
If flood illumination is used to illuminate large areas, then coverage of the substrate is improved, but control in the z-axis is lost
Solution Approach 1:
Each zero mode waveguide aperture provides locally confined illumination with an evanescent field that decays exponentially in the z-direction. This creates localized regions of high illumination intensity precisely where needed, while maintaining large overall area coverage through arrays of such waveguides.
3Productivity
If linearized beam illumination is used for wide area coverage, then the number of features interrogated is improved, but alignment precision with analytes is reduced
Solution Approach 1:
The zero mode waveguides are fabricated directly into the substrate at predetermined locations that self-align with the analyte positions. This eliminates the need for separate alignment procedures, as the waveguide positions are inherently registered to the analytical features through the fabrication process.
4Ease of operation
If conventional illumination methods are used, then ease of operation is maintained, but auto-fluorescence noise increases
Solution Approach 1:
The harmful auto-fluorescence signal is extracted from the system by confining illumination to a minimal evanescent field volume. This removes the excitation of out-of-focus and background materials that generate auto-fluorescence noise, while maintaining ease of operation through integrated waveguide structures.
Applied Scientific Principles
This section explains which scientific principles are used to turn an abstract innovation direction into a practical engineering solution.
Function Achieved in This Case
This approach enables efficient, controlled illumination with reduced background interference, enhancing the accuracy and efficiency of analytical operations by minimizing auto-fluorescence and allowing precise alignment of illumination with analytes of interest.
Implementation Method 1
an evanescent field emanating from the waveguide when light is passed through the waveguide, e.g., the light field that decays exponentially as a function of distance from the waveguide surface
Data Source
Figure 1
Figure 2
Figure 3A~3B
AI summary
Substrates, systems and methods for analyzing materials that include waveguide arrays disposed upon or within the substrate such that evanescent fields emanating from the waveguides illuminate materials disposed upon or proximal to the surface of the substrate, permitting analysis of such materials. The substrates, systems and methods are used in a variety of analytical operations, including, inter alia, nucleic acid analysis, including hybridization and sequencing analyses, cellular analyses and other molecular analyses.