Sampling a rare protein transition with a hybrid classical-quantum computing algorithm
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arXiv
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| Auteurs principaux: | , , |
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| Format: | Preprint |
| Publié: |
2023
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| _version_ | 1866917350523011072 |
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| author | Ghamari, Danial Covino, Roberto Faccioli, Pietro |
| author_facet | Ghamari, Danial Covino, Roberto Faccioli, Pietro |
| contents | Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time intervals up to tens of $μ$s, while many key events occur on exponentially longer time scales. Transition path sampling techniques have the advantage of focusing the computational power on barrier-crossing trajectories, but generating uncorrelated transition paths that explore diverse conformational regions remains an unsolved problem. We employ a path-sampling paradigm combining machine learning (ML) with quantum computing (QC) to address this issue. We use ML on a classical computer to perform a preliminary uncharted exploration of the conformational space. The data set generated in this exploration is then post-processed to obtain a network representation of the reactive kinetics.
Quantum annealing machines can exploit quantum superposition to encode all the transition pathways in this network in the initial quantum state and ensure the generation of completely uncorrelated transition paths. In particular, we resort to the DWAVE quantum computer to perform an all-atom simulation of a protein conformational transition that occurs on the ms timescale. Our results match those of a special purpose supercomputer designed to perform MD simulations. These results highlight the role of biomolecular simulation as a ground for applying, testing, and advancing quantum technologies. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2311_15891 |
| institution | arXiv |
| publishDate | 2023 |
| record_format | arxiv |
| spellingShingle | Sampling a rare protein transition with a hybrid classical-quantum computing algorithm Ghamari, Danial Covino, Roberto Faccioli, Pietro Biological Physics Statistical Mechanics Quantum Physics Simulating spontaneous structural rearrangements in macromolecules with classical Molecular Dynamics (MD) is an outstanding challenge. Conventional supercomputers can access time intervals up to tens of $μ$s, while many key events occur on exponentially longer time scales. Transition path sampling techniques have the advantage of focusing the computational power on barrier-crossing trajectories, but generating uncorrelated transition paths that explore diverse conformational regions remains an unsolved problem. We employ a path-sampling paradigm combining machine learning (ML) with quantum computing (QC) to address this issue. We use ML on a classical computer to perform a preliminary uncharted exploration of the conformational space. The data set generated in this exploration is then post-processed to obtain a network representation of the reactive kinetics. Quantum annealing machines can exploit quantum superposition to encode all the transition pathways in this network in the initial quantum state and ensure the generation of completely uncorrelated transition paths. In particular, we resort to the DWAVE quantum computer to perform an all-atom simulation of a protein conformational transition that occurs on the ms timescale. Our results match those of a special purpose supercomputer designed to perform MD simulations. These results highlight the role of biomolecular simulation as a ground for applying, testing, and advancing quantum technologies. |
| title | Sampling a rare protein transition with a hybrid classical-quantum computing algorithm |
| topic | Biological Physics Statistical Mechanics Quantum Physics |
| url | https://arxiv.org/abs/2311.15891 |