Bioinfo Chem
System biology and Infochemistry | Online ISSN 3071-4826
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Quantum Computing in Molecular Science: Quantum Chemistry, Bioinformatics, and Machine Learning in the NISQ Era
Priya Vij 1, Sushree Sasmita Dash 1, Akanksha Mishra 1
Bioinfo Chem 4 (1) 1-12 https://doi.org/10.25163/bioinformatics.4110727
Submitted: 21 August 2022 Revised: 13 October 2022 Accepted: 23 October 2022 Published: 25 October 2022
Abstract
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.
Keywords: Quantum computing; Bioinformatics; Quantum chemistry; NISQ era; Quantum machine learning
References
Abdesslem, L., Meshoul, S., & Batouche, M. (2006). Multiple sequence alignment by quantum genetic algorithm. Proceedings 20th IEEE International Parallel and Distributed Processing Symposium.
Abrams, D. S., & Lloyd, S. (1997). Simulation of many-body Fermi systems on a universal quantum computer. Physical Review Letters, 79(13), 2586–2589. https://doi.org/10.1103/PhysRevLett.79.2586
Abrams, D. S., & Lloyd, S. (1999). Quantum algorithm providing exponential speed increase for finding eigenvalues and eigenvectors. Physical Review Letters, 83(24), 5162–5165. https://doi.org/10.1103/PhysRevLett.83.5162
Aspuru-Guzik, A., Dutoi, A. D., Love, P. J., & Head-Gordon, M. (2005). Simulated quantum computation of molecular energies. Science, 309(5741), 1704–1707. https://doi.org/10.1126/science.1113479
Benenti, G., & Strini, G. (2008). Quantum simulation of the single-particle Schrödinger equation. American Journal of Physics, 76(7), 657–662. https://doi.org/10.1119/1.2894532
Biamonte, J., Wittek, P., Pancotti, N., Rebentrost, P., Wiebe, N., & Lloyd, S. (2017). Quantum machine learning. Nature, 549(7671), 195–202. https://doi.org/10.1038/nature23474
Boixo, S., Rønnow, T. F., Isakov, S. V., Wang, Z., Wecker, D., Lidar, D. A., ... & Troyer, M. (2014). Evidence for quantum annealing with more than one hundred qubits. Nature Physics, 10(3), 218–224. https://doi.org/10.1038/nphys2900
Cao, Y., Romero, J., & Aspuru-Guzik, A. (2018). Potential of quantum computing for drug discovery. IBM Journal of Research and Development, 62(6), 6:1–6:20. https://doi.org/10.1147/JRD.2018.2888987
Farhi, E., Goldstone, J., & Gutmann, S. (2014). A quantum approximate optimization algorithm. arXiv preprint arXiv:1411.4028.
Feynman, R. P. (1982). Simulating physics with computers. International Journal of Theoretical Physics, 21(6/7), 467–488. https://doi.org/10.1007/BF02650179
Fingerhuth, M., Babej, T., & Ing, C. (2018). A quantum alternating operator ansatz with hard and soft constraints for lattice protein folding. arXiv preprint arXiv:1810.13411.
Fowler, A. G., Mariantoni, M., Martinis, J. M., & Cleland, A. N. (2012). Surface codes: Towards practical large-scale quantum computation. Physical Review A, 86(3), 032324. https://doi.org/10.1103/PhysRevA.86.032324
Grover, L. K. (1996). A fast quantum mechanical algorithm for database search. Proceedings of the Twenty-Eighth Annual ACM Symposium on Theory of Computing. https://doi.org/10.1145/237814.237866
Harrow, A. W., Hassidim, A., & Lloyd, S. (2009). Quantum algorithm for linear systems of equations. Physical Review Letters, 103(15), 150502. https://doi.org/10.1103/PhysRevLett.103.150502
Hart, W. E., & Istrail, S. (1997). Robust proofs of NP-hardness for protein folding: General lattices and energy potentials. Journal of Computational Biology, 4(1), 1–22. https://doi.org/10.1089/cmb.1997.4.1
Hollenberg, L. C. (2000). Fast quantum search algorithms in protein sequence comparisons: Quantum bioinformatics. Physical Review E, 62(5), 7532–7535. https://doi.org/10.1103/PhysRevE.62.7532
Kassal, I., Jordan, S. P., Love, P. J., Mohseni, M., & Aspuru-Guzik, A. (2008). Polynomial-time quantum algorithm for the simulation of chemical dynamics. Proceedings of the National Academy of Sciences, 105(48), 18681–18686. https://doi.org/10.1073/pnas.0808245105
Kassal, I., Whitfield, J. D., Perdomo-Ortiz, A., Yung, M. H., & Aspuru-Guzik, A. (2011). Simulating chemistry using quantum computers. Annual Review of Physical Chemistry, 62, 185–207. https://doi.org/10.1146/annurev-physchem-032210-103512
Lidar, D. A., & Wang, H. (1999). Calculating the thermal rate constant with exponential speedup on a quantum computer. Physical Review E, 59(2), 2429–2438. https://doi.org/10.1103/PhysRevE.59.2429
Lloyd, S. (1996). Universal quantum simulators. Science, 273(5278), 1073–1078. https://doi.org/10.1126/science.273.5278.1073
Lloyd, S., Mohseni, M., & Rebentrost, P. (2014). Quantum principal component analysis. Nature Physics, 10(9), 631–633. https://doi.org/10.1038/nphys3029
Manin, Y. (1980). Vychislimoe i nevychislimoe (Computable and uncomputable). Moscow: Sovetskoye Radio.
McClean, J. R., Romero, J., Babbush, R., & Aspuru-Guzik, A. (2016). The theory of variational hybrid quantum-classical algorithms. New Journal of Physics, 18(2), 023023. https://doi.org/10.1088/1367-2630/18/2/023023
Nielsen, M. A., & Chuang, I. L. (2011). Quantum computation and quantum information: 10th anniversary edition. Cambridge University Press. https://doi.org/10.1017/CBO9780511976667
O'Malley, P. J., Babbush, R., Kivlichan, I. D., Romero, J., McClean, J. R., Barends, R., ... & Martinis, J. M. (2016). Scalable quantum simulation of molecular energies. Physical Review X, 6(3), 031007. https://doi.org/10.1103/PhysRevX.6.031007
Perdomo-Ortiz, A., Dickson, N., Drew-Brook, M., Rose, G., & Aspuru-Guzik, A. (2012). Finding low-energy conformations of lattice protein models by quantum annealing. Scientific Reports, 2, 571. https://doi.org/10.1038/srep00571
Peruzzo, A., McClean, J., Shadbolt, P., Yung, M. H., Zhou, X. Q., Love, P. J., ... & O'Brien, J. L. (2014). A variational eigenvalue solver on a photonic quantum processor. Nature Communications, 5(1), 4213. https://doi.org/10.1038/ncomms5213
Preskill, J. (2018). Quantum computing in the NISQ era and beyond. Quantum, 2, 79. https://doi.org/10.22331/q-2018-08-06-79
Rebentrost, P., Mohseni, M., & Lloyd, S. (2014). Quantum support vector machine for big data classification. Physical Review Letters, 113(13), 130503. https://doi.org/10.1103/PhysRevLett.113.130503
Reiher, M., Wiebe, N., Svore, K. M., Wecker, D., & Troyer, M. (2017). Elucidating reaction mechanisms on quantum computers. Proceedings of the National Academy of Sciences, 114(29), 7555–7560. https://doi.org/10.1073/pnas.1619152114
Schaller, R. R. (1997). Moore's law: Past, present and future. IEEE Spectrum, 34(6), 52–59. https://doi.org/10.1109/6.591665
Schuld, M., Sinayskiy, I., & Petruccione, F. (2016). Prediction by linear regression on a quantum computer. Physical Review A, 94(2), 022342. https://doi.org/10.1103/PhysRevA.94.022342
Senn, H. M., & Thiel, W. (2009). QM/MM methods for biomolecular systems. Angewandte Chemie International Edition, 48(7), 1198–1229. https://doi.org/10.1002/anie.200802019
Szabo, A., & Ostlund, N. S. (2012). Modern quantum chemistry: Introduction to advanced electronic structure theory. Dover Publications.
Torlai, G., Mazzola, G., Carrasquilla, J., Troyer, M., Melko, R., & Carleo, G. (2018). Neural-network quantum state tomography. Nature Physics, 14, 447–450. https://doi.org/10.1038/s41567-018-0048-5
Wang, B. X., Tao, M. J., Ai, Q., Xin, T., Lambert, N., Ruan, D., ... & Long, G. L. (2018). Efficient quantum simulation of photosynthetic light harvesting. npj Quantum Information, 4(1), 52. https://doi.org/10.1038/s41534-018-0102-2
Wiebe, N., Kapoor, A., & Svore, K. M. (2014). Quantum deep learning. arXiv preprint arXiv:1412.3489.
Zhang, L., Wang, H., & E, W. (2018). Reinforced dynamics for enhanced sampling in large atomic and molecular systems. The Journal of Chemical Physics, 148(12), 124113. https://doi.org/10.1063/1.5019675
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