Structured substrates for improving detection of light emissions and methods relating to the same
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Solution Overview
Problem
Current sequencing systems face challenges in detecting light emissions from small and densely packed reaction sites with high accuracy and efficiency, particularly due to reduced light intensity and increased difficulty in distinguishing between sites, which affects sequencing performance and error rates.
Innovation Solution
The use of structured substrates with ensemble amplifiers, comprising nanostructures such as plasmonic nanostructures, to enhance light emissions by amplifying electromagnetic energy at reaction sites, thereby increasing signal intensity and directionality for improved detection.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Productivity
If reaction sites are made smaller and more densely packed to increase throughput, then productivity increases, but light emission intensity decreases and detection precision deteriorates
Solution Approach 1:
The patent introduces optical amplifiers (such as microlenses, photonic crystals, or plasmonic structures) as intermediary elements between the reaction sites and detectors. These amplifiers collect and concentrate the weak light emissions from densely packed reaction sites, thereby maintaining detection precision even when reaction sites are miniaturized and densely arranged to increase throughput
Solution Approach 2:
The patent employs three-dimensional optical structures (such as stacked microlens arrays, photonic crystal layers, or vertically arranged optical amplifiers) to enhance light collection from planar reaction sites. By adding vertical dimensionality to the optical path, the system can distinguish and detect light emissions from densely packed lateral reaction sites, resolving the contradiction between high density and detection precision
2Productivity
If scan time is decreased to increase productivity, then throughput increases, but the number of detected photons decreases and measurement precision deteriorates
Solution Approach 1:
Optical amplifiers are positioned between the reaction sites and detectors to actively enhance and concentrate light emissions during brief scan intervals. This mediation allows sufficient photons to be collected and amplified even when the scan time is reduced, maintaining measurement precision while enabling faster throughput
Solution Approach 2:
The optical amplifiers are pre-positioned and configured to maximize light collection efficiency before the actual sequencing scan begins. This preliminary optimization of the optical path ensures that during the rapid scan, the maximum possible photons are captured and amplified within the shortened time window, preserving accuracy despite increased speed
3Productivity
If reaction site density is increased to improve productivity, then throughput increases, but the ability to distinguish between adjacent sites deteriorates
Solution Approach 1:
The patent divides the optical detection system into spatially segmented optical amplifiers, with each amplifier or small group of amplifiers assigned to specific reaction sites or site clusters. This segmentation allows independent optimization of light collection for each site, enabling clear distinction between adjacent reaction sites even when densely packed
Solution Approach 2:
The patent uses vertically stacked optical amplifier layers or three-dimensional optical structures to provide depth resolution in addition to lateral positioning. This additional dimensional information allows the system to distinguish light emissions from adjacent reaction sites that are densely packed in the lateral plane, preventing signal cross-contamination and maintaining site-specific detection accuracy
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
The structured substrates enhance light emission intensity, reduce error rates, and enable faster scan speeds by increasing the number of photons captured, leading to more reliable and cost-effective sequencing results.
Implementation Method 1
The plurality of nanostructures form an ensemble amplifier of the corresponding reaction cavity that is configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity
Data Source
AI summary
A structured substrate includes a substrate body having an active side. The substrate body includes reaction cavities that open along the active side and interstitial regions that separate the reaction cavities. The structured substrate includes an ensemble amplifier positioned within each of the reaction cavities. The ensemble amplifier includes a plurality of nanostructures configured to at least one of amplify electromagnetic energy that propagates into the corresponding reaction cavity or amplify electromagnetic energy that is generated within the corresponding reaction cavity.