Abstract This paper presents the implementation of a quantum sequence alignment (QSA) algorithm on biological data in environments simulating noisy intermediate-scale quantum (NISQ) computers. The approach to quantum bioinformatics adapts the original QSA algorithm proposed in 2000 to current capabilities and limitations of NISQ-era quantum computers and uses a genetic algorithm for state preparation (GASP) to create encoding circuits to load both database and target sequences into the quantum data registers. The implementation is tested in a simulated quantum computer environment to validate the approach and refine the GASP data-loading circuit designs. The results demonstrate the practicalities of deploying the QSA algorithm and exemplify the potential of GASP for data encoding in the realm of quantum circuit design, particularly for complex algorithms in quantum bioinformatics and other data-rich problems.
Abstract This paper presents the implementation of a quantum sequence alignment (QSA) algorithm on biological data in environments simulating noisy intermediate-scale quantum (NISQ) computers. The approach to quantum bioinformatics adapts the original QSA algorithm proposed in 2000 to current capabilities and limitations of NISQ-era quantum computers and uses a genetic algorithm for state preparation (GASP) to create encoding circuits to load both database and target sequences into the quantum data registers. The implementation is tested in a simulated quantum computer environment to validate the approach and refine the GASP data-loading circuit designs. The results demonstrate the practicalities of deploying the QSA algorithm and exemplify the potential of GASP for data encoding in the realm of quantum circuit design, particularly for complex algorithms in quantum bioinformatics and other data-rich problems.
The efficient preparation of quantum states is an important step in the execution of many quantum algorithms. In the noisy intermediate-scale quantum (NISQ) computing era, this is a significant challenge given quantum resources are scarce and typically only low-depth quantum circuits can be implemented on physical devices. We present a genetic algorithm for state preparation (GASP) which generates relatively low-depth quantum circuits for initialising a quantum computer in a specified quantum state. The method uses a basis set of [Formula: see text], [Formula: see text], [Formula: see text], and CNOT gates and a genetic algorithm to systematically generate circuits to synthesize the target state to the required fidelity. GASP can produce more efficient circuits of a given accuracy with lower depth and gate counts than other methods. This variability of the required accuracy facilitates overall higher accuracy on implementation, as error accumulation in high-depth circuits can be avoided. We directly compare the method to the state initialisation technique based on an exact synthesis technique by implemented in IBM Qiskit simulated with noise and implemented on physical IBM Quantum devices. Results achieved by GASP outperform Qiskit's exact general circuit synthesis method on a variety of states such as Gaussian states and W-states, and consistently show the method reduces the number of gates required for the quantum circuits to generate these quantum states to the required accuracy.
The efficient preparation of quantum states is an important step in the execution of many quantum algorithms. In the noisy intermediate-scale quantum (NISQ) computing era, this is a significant challenge given quantum resources are scarce and typically only low-depth quantum circuits can be implemented on physical devices. We present a genetic algorithm for state preparation (GASP) which generates relatively low-depth quantum circuits for initialising a quantum computer in a specified quantum state. The method uses a basis set of R_x, R_y, R_z, and CNOT gates and a genetic algorithm to systematically generate circuits to synthesize the target state to the required fidelity. GASP can produce more efficient circuits of a given accuracy with lower depth and gate counts than other methods. This variability of the required accuracy facilitates overall higher accuracy on implementation, as error accumulation in high-depth circuits can be avoided. We directly compare the method to the state initialisation technique based on an exact synthesis technique by implemented in IBM Qiskit simulated with noise and implemented on physical IBM Quantum devices. Results achieved by GASP outperform Qiskit's exact general circuit synthesis method on a variety of states such as Gaussian states and W-states, and consistently show the method reduces the number of gates required for the quantum circuits to generate these quantum states to the required accuracy.
This paper explores the application of principles from quantum biology to design novel bioinformatics algorithms. Traditional bioinformatics relies heavily on classical computational models, often neglecting the potential influence of quantum effects observed within biological systems. This research proposes a framework that leverages these quantum phenomena, specifically focusing on quantum tunneling, superposition, and entanglement, to address complex challenges in biological data analysis. The core mechanism involves simulating quantum effects during processes like protein folding and DNA sequence recognition, and utilizing quantum algorithms – such as Grover's algorithm and quantum annealing – to optimize sequence data analysis. We present a conceptual approach to formulating biological problems as quantum computing problems, offering a fundamentally new perspective for bioinformatics. The potential impact of this approach lies in developing more efficient and accurate algorithms for tasks including genomic sequence alignment, protein structure prediction, and drug discovery. This work aims to bridge the gap between quantum mechanics and biology, paving the way for a new era of bioinformatics driven by quantum principles. ---
Quantum computing holds immense potential for transforming financial analysis and decision-making. Realising this potential necessitates the efficient encoding and processing of financial data on quantum computers. In this study, we propose using the GASP (Genetic Algorithm for State Preparation) framework to optimise the encoding of stock price data into quantum states and show it can enhance both the fidelity and efficiency of the encoding process. We demonstrate the efficacy of our approach by encoding stock price data onto both a simulated and real quantum computer to calculate the Singular Value Decomposition (SVD) entropy. Our results show improvements in fidelity and the potential for more precise financial analysis. This research provides insights into the applicability of GASP for the efficient encoding of real-world data, specifically stock price data, which is crucial for quantum advantage on noisy intermediate-scale quantum (NISQ) era quantum computers.
This paper explores the emerging field of quantum bioinformatics, proposing a novel approach to tackling complex challenges within biological information analysis. Traditional biological data processing often encounters limitations due to the exponential growth of datasets and the computational intensity of tasks like sequence alignment, gene prediction, and protein structure prediction. We posit that quantum computing, leveraging phenomena like superposition and entanglement, offers a paradigm shift capable of dramatically accelerating these calculations. This document details the core concept of representing biological sequences as quantum states and utilizing quantum algorithms – specifically tailored for bioinformatics applications – to perform these computations. The theoretical framework incorporates key quantum principles to enhance efficiency and potentially unlock new insights in biological systems. We present a foundational model for quantum sequence alignment, quantum gene prediction, and quantum protein structure prediction, outlining the mathematical formulations and algorithmic approaches. The potential impact of this work is significant, suggesting a future where quantum bioinformatics becomes a cornerstone of biological research. ---
Quantum computing is emerging as a transformative approach in bioinformatics and quantum chemistry, addressing fundamental computational limitations of classical methods in molecular science. Many biological and chemical systems are inherently governed by quantum mechanics, making accurate simulation with classical algorithms computationally expensive or infeasible. This review examines how quantum computing, particularly in the Noisy Intermediate-Scale Quantum (NISQ) era, is advancing molecular modeling, reaction dynamics, and bioinformatics applications. Key quantum algorithms, including the Variational Quantum Eigensolver (VQE) and Quantum Phase Estimation (QPE), demonstrate increasing capability in approximating molecular energies and simulating quantum systems. In parallel, applications in bioinformatics—such as protein folding, genomic search, and combinatorial optimization—highlight the potential of quantum computing to address complex biological problems. Quantum machine learning further extends these capabilities by integrating quantum algorithms with data-driven modeling. However, current progress is constrained by NISQ-era limitations, including noise, limited qubit counts, and scalability challenges. These constraints highlight the need for hybrid quantum–classical approaches and improved error mitigation strategies. Overall, quantum computing represents a complementary computational paradigm that can enhance classical methods in bioinformatics and chemistry. Continued advances in quantum algorithms, hardware, and hybrid modeling frameworks are expected to expand its role in molecular science and computational biology.