Orthogonal Domain DNA Sequence Matching via Wavefunction Interference
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Solution Overview
Problem
Current methods for searching large DNA/RNA sequence databases are inefficient due to exponentially growing complexities and combinatorial explosions, leading to slow processing speeds and inability to handle vast amounts of data effectively, especially in bioinformatics applications.
Innovation Solution
The method involves transforming probe and target sequences into orthogonal domains, applying modulation functions, and interfering these representations to detect matches through inverse transforms, allowing for efficient and accurate sequence matching with high-speed processing.
Engineering Contradictions & Design Principles
Engineering Contradiction Analysis
1Measurement precision
If parallel recognition processes are used for searching DNA/RNA sequences, then search accuracy is improved, but device complexity grows exponentially
Solution Approach 1:
The patent transforms sequence data from a traditional digital representation into a quantum mechanical wavefunction representation. This parameter change enables parallel recognition processes to operate on quantum states, achieving exponential speedup while maintaining accuracy through the mathematical properties of wavefunctions and their interference patterns.
Solution Approach 2:
The patent replaces classical computational mechanisms with quantum mechanical processes. Instead of using traditional digital logic gates and memory cells, the system uses quantum wavefunctions, superposition, and interference to perform sequence matching, thereby reducing the effective complexity of the recognition process.
2Productivity
If traditional associative memory search methods are used, then implementation simplicity is maintained, but processing speed becomes insufficient for large databases
Solution Approach 1:
The patent introduces a quantum mechanical dimension to the associative memory search process. By representing sequences as wavefunctions and utilizing quantum interference, the system achieves parallel processing capability that dramatically increases search speed without proportionally increasing implementation complexity.
Solution Approach 2:
The system performs preliminary quantum mechanical transformations and preparations of wavefunctions before the actual search operation. This preliminary action sets up the quantum states in advance, enabling the search process to proceed at quantum speeds when the query is submitted.
3Quantity of substance
If database size increases to handle more genetic information, then information capacity is improved, but search efficiency deteriorates
Solution Approach 1:
The patent changes the fundamental parameter of data representation from classical bits to quantum wavefunctions. This enables the database to store and process genetic information at a scale that classical systems cannot handle, maintaining search efficiency through quantum parallelism even as database capacity increases.
Solution Approach 2:
The quantum wavefunction representation serves multiple functions simultaneously: it stores sequence information, enables parallel search operations, provides interference patterns for pattern recognition, and maintains scalability. This multi-functionality allows the system to handle large databases efficiently without requiring separate systems for each function.
Data Source
AI summary
A method for searching sequences includes storing a probe sequence and a target sequence expressed in a first orthogonal domain. The target sequence includes potential probe match sequences each characterized by the length of the target sequence. The probe sequence representation and the target sequence are transformed into an orthogonal domain. In the orthogonal domain, the target sequence is encoded with modulation functions to produce a plurality of encoded target sequences, each of the modulation functions having a position index corresponding to one of the potential probe match sequences. The plurality of encoded target sequences is interfered with the probe sequence in the orthogonal domain and an inverse transform result is obtained. If the inverse transform result exceeds a threshold, information is output indicating a match between the probe sequence and a corresponding one of the potential probe match sequences.