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Chen Y, Huang JH, Sun Y, Zhang Y, Li Y, Xu X. Haplotype-resolved assembly of diploid and polyploid genomes using quantum computing. CELL REPORTS METHODS 2024; 4:100754. [PMID: 38614089 PMCID: PMC11133727 DOI: 10.1016/j.crmeth.2024.100754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Revised: 01/03/2024] [Accepted: 03/20/2024] [Indexed: 04/15/2024]
Abstract
Precision medicine's emphasis on individual genetic variants highlights the importance of haplotype-resolved assembly, a computational challenge in bioinformatics given its combinatorial nature. While classical algorithms have made strides in addressing this issue, the potential of quantum computing remains largely untapped. Here, we present the vehicle routing problem (VRP) assembler: an approach that transforms this task into a vehicle routing problem, an optimization formulation solvable on a quantum computer. We demonstrate its potential and feasibility through a proof of concept on short synthetic diploid and triploid genomes using a D-Wave quantum annealer. To tackle larger-scale assembly problems, we integrate the VRP assembler with Google's OR-Tools, achieving a haplotype-resolved local assembly across the human major histocompatibility complex (MHC) region. Our results show encouraging performance compared to Hifiasm with phasing accuracy approaching the theoretical limit, underscoring the promising future of quantum computing in bioinformatics.
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Affiliation(s)
- Yibo Chen
- BGI Research, Shenzhen 518083, China
| | | | - Yuhui Sun
- BGI Research, Shenzhen 518083, China
| | - Yong Zhang
- BGI Research, Wuhan 430047, China; Guangdong Bigdata Engineering Technology Research Center for Life Sciences, BGI Research, Shenzhen 518083, China.
| | - Yuxiang Li
- BGI Research, Wuhan 430047, China; Guangdong Bigdata Engineering Technology Research Center for Life Sciences, BGI Research, Shenzhen 518083, China.
| | - Xun Xu
- BGI Research, Shenzhen 518083, China; BGI Research, Wuhan 430047, China.
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2
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He K, Yuan M, Wong Y, Chakram S, Seif A, Jiang L, Schuster DI. Efficient multimode Wigner tomography. Nat Commun 2024; 15:4138. [PMID: 38755182 PMCID: PMC11099137 DOI: 10.1038/s41467-024-48573-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 05/07/2024] [Indexed: 05/18/2024] Open
Abstract
Advancements in quantum system lifetimes and control have enabled the creation of increasingly complex quantum states, such as those on multiple bosonic cavity modes. When characterizing these states, traditional tomography scales exponentially with the number of modes in both computational and experimental measurement requirement, which becomes prohibitive as the system size increases. Here, we implement a state reconstruction method whose sampling requirement instead scales polynomially with system size, and thus mode number, for states that can be represented within such a polynomial subspace. We demonstrate this improved scaling with Wigner tomography of multimode entangled W states of up to 4 modes on a 3D circuit quantum electrodynamics (cQED) system. This approach performs similarly in efficiency to existing matrix inversion methods for 2 modes, and demonstrates a noticeable improvement for 3 and 4 modes, with even greater theoretical gains at higher mode numbers.
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Affiliation(s)
- Kevin He
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA.
- Department of Physics, University of Chicago, Chicago, IL, 60637, USA.
| | - Ming Yuan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Yat Wong
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Srivatsan Chakram
- Department of Physics and Astronomy, Rutgers University, Piscataway, NJ, 08854, USA
| | - Alireza Seif
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - Liang Jiang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
| | - David I Schuster
- James Franck Institute, University of Chicago, Chicago, IL, 60637, USA
- Department of Physics, University of Chicago, Chicago, IL, 60637, USA
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, 60637, USA
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3
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Chen L, Wu B, Lu L, Wang K, Lu Y, Zhu S, Ma XS. Observation of quantum nonlocality in Greenberger-Horne-Zeilinger entanglement on a silicon chip. OPTICS EXPRESS 2024; 32:14904-14913. [PMID: 38859154 DOI: 10.1364/oe.515070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 03/23/2024] [Indexed: 06/12/2024]
Abstract
Nonlocality is the defining feature of quantum entanglement. Entangled states with multiple particles are of crucial importance in fundamental tests of quantum physics as well as in many quantum information tasks. One of the archetypal multipartite quantum states, Greenberger-Horne-Zeilinger (GHZ) state, allows one to observe the striking conflict of quantum physics to local realism in the so-called all-versus-nothing way. This is profoundly different from Bell's theorem for two particles, which relies on statistical predictions. Here, we demonstrate an integrated photonic chip capable of generating and manipulating the four-photon GHZ state. We perform a complete characterization of the four-photon GHZ state using quantum state tomography and obtain a state fidelity of 0.729±0.006. We further use the all-versus-nothing test and the Mermin inequalities to witness the quantum nonlocality of GHZ entanglement. Our work paves the way to perform fundamental tests of quantum physics with complex integrated quantum devices.
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4
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Huang J, Li X, Chen X, Zhai C, Zheng Y, Chi Y, Li Y, He Q, Gong Q, Wang J. Demonstration of hypergraph-state quantum information processing. Nat Commun 2024; 15:2601. [PMID: 38521765 PMCID: PMC10960808 DOI: 10.1038/s41467-024-46830-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Accepted: 03/12/2024] [Indexed: 03/25/2024] Open
Abstract
Complex entangled states are the key resources for measurement-based quantum computations, which is realised by performing a sequence of measurements on initially entangled qubits. Executable quantum algorithms in the graph-state quantum computing model are determined by the entanglement structure and the connectivity of entangled qubits. By generalisation from graph-type entanglement in which only the nearest qubits interact to a new type of hypergraph entanglement in which any subset of qubits can be arbitrarily entangled via hyperedges, hypergraph states represent more general resource states that allow arbitrary quantum computation with Pauli universality. Here we report experimental preparation, certification and processing of complete categories of four-qubit hypergraph states under the principle of local unitary equivalence, on a fully reprogrammable silicon-photonic quantum chip. Genuine multipartite entanglement for hypergraph states is certificated by the characterisation of entanglement witness, and the observation of violations of Mermin inequalities without any closure of distance or detection loopholes. A basic measurement-based protocol and an efficient resource state verification by color-encoding stabilizers are implemented with local Pauli measurement to benchmark the building blocks for hypergraph-state quantum computation. Our work prototypes hypergraph entanglement as a general resource for quantum information processing.
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Affiliation(s)
- Jieshan Huang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
| | - Xudong Li
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Xiaojiong Chen
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
| | - Chonghao Zhai
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
| | - Yun Zheng
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
| | - Yulin Chi
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
| | - Yan Li
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
- Frontiers Science Center for Nano-optoelectronics and Collaborative Innovation Center of Quantum Matter, Peking University, 100871, Beijing, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, 030006, Shanxi, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010, Jiangsu, China
- Hefei National Laboratory, Hefei, 230088, China
| | - Qiongyi He
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
- Frontiers Science Center for Nano-optoelectronics and Collaborative Innovation Center of Quantum Matter, Peking University, 100871, Beijing, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, 030006, Shanxi, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010, Jiangsu, China
- Hefei National Laboratory, Hefei, 230088, China
| | - Qihuang Gong
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China
- Frontiers Science Center for Nano-optoelectronics and Collaborative Innovation Center of Quantum Matter, Peking University, 100871, Beijing, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, 030006, Shanxi, China
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010, Jiangsu, China
- Hefei National Laboratory, Hefei, 230088, China
| | - Jianwei Wang
- State Key Laboratory for Mesoscopic Physics, School of Physics, Peking University, 100871, Beijing, China.
- Frontiers Science Center for Nano-optoelectronics and Collaborative Innovation Center of Quantum Matter, Peking University, 100871, Beijing, China.
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, 030006, Shanxi, China.
- Peking University Yangtze Delta Institute of Optoelectronics, Nantong, 226010, Jiangsu, China.
- Hefei National Laboratory, Hefei, 230088, China.
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Wakizaka M, Gupta S, Wan Q, Takaishi S, Noro H, Sato K, Yamashita M. Spin qubits of Cu(II) doped in Zn(II) metal-organic frameworks above microsecond phase memory time. Chemistry 2024; 30:e202304202. [PMID: 38146235 DOI: 10.1002/chem.202304202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 12/27/2023]
Abstract
With the aim of creating Cu(II) spin qubits in a rigid metal-organic framework (MOF), this work demonstrates a doping of 5 %, 2 %, 1 %, and 0.1 % mol of Cu(II) ions into a perovskite-type MOF [CH6 N3 ][ZnII (HCOO)3 ]. The presence of dopant Cu(II) sites are confirmed with anisotropic g-factors (gx =2.07, gy =2.12, and gz =2.44) in the S=1/2 system by experimentally and theoretically. Magnetic dynamics indicate the occurrence of a slow magnetic relaxation via the direct and Raman processes under an applied field, with a relaxation time (τ) of 3.5 ms (5 % Cu), 9.2 ms (2 % Cu), and 15 ms (1 % Cu) at 1.8 K. Furthermore, pulse-ESR spectroscopy reveals spin qubit properties with a spin-spin relaxation (phase memory) time (T2 ) of 0.21 μs (2 %Cu), 0.39 μs (1 %Cu), and 3.0 μs (0.1 %Cu) at 10 K as well as Rabi oscillation between MS =±1/2 spin sublevels. T2 above microsecond is achieved for the first time in the Cu(II)-doped MOFs. It can be observed at submicrosecond around 50 K. These spin relaxations are very sensitive to the magnetic dipole interactions relating with cross-relaxation between the Cu(II) sites and can be tuned by adjusting the dopant concentration.
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Affiliation(s)
- Masanori Wakizaka
- Department of Applied Chemistry and Bioscience, Faculty of Science and Technology, Chitose Institute of Science and Technology, 758-65 Bibi, Chitose, 066-8655, Japan
| | - Shraddha Gupta
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-Ku, Sendai, 980-8578, Japan
| | - Qingyun Wan
- Department of Chemistry, State Key Laboratory of Synthetic Chemistry, HKU-CAS Joint Laboratory on New Materials, The University of Hong Kong
| | - Shinya Takaishi
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-Ku, Sendai, 980-8578, Japan
| | - Honoka Noro
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Kazunobu Sato
- Department of Chemistry, Graduate School of Science, Osaka Metropolitan University, 3-3-138 Sugimoto, Sumiyoshi-ku, Osaka, 558-8585, Japan
| | - Masahiro Yamashita
- Department of Chemistry, Graduate School of Science, Tohoku University, 6-3 Aramaki-Aza-Aoba, Aoba-Ku, Sendai, 980-8578, Japan
- School of Chemical Science and Engineering, Tongji University, Siping Road 1239, Shanghai, 200092, P. R. China
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Shirizly L, Misguich G, Landa H. Dissipative Dynamics of Graph-State Stabilizers with Superconducting Qubits. PHYSICAL REVIEW LETTERS 2024; 132:010601. [PMID: 38242658 DOI: 10.1103/physrevlett.132.010601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 11/21/2023] [Accepted: 11/29/2023] [Indexed: 01/21/2024]
Abstract
We study experimentally and numerically the noisy evolution of multipartite entangled states, focusing on superconducting qubit devices accessible via the cloud. We find that a valid modeling of the dynamics requires one to properly account for coherent frequency shifts, caused by stochastic charge-parity fluctuations. We introduce an approach modeling the charge-parity splitting using an extended Markovian environment. This approach is numerically scalable to tens of qubits, allowing us to simulate efficiently the dissipative dynamics of some large multiqubit states. Probing the continuous-time dynamics of increasingly larger and more complex initial states with up to 12 coupled qubits in a ring-graph state, we obtain a good agreement of the experiments and simulations. We show that the underlying many-body dynamics generate decays and revivals of stabilizers, which are used extensively in the context of quantum error correction. Furthermore, we demonstrate the mitigation of 2-qubit coherent interactions (crosstalk) using tailored dynamical decoupling sequences. Our noise model and the numerical approach can be valuable to advance the understanding of error correction and mitigation and invite further investigations of their dynamics.
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Affiliation(s)
- Liran Shirizly
- IBM Quantum, IBM Research - Israel, Haifa University Campus, Mount Carmel, Haifa 31905, Israel
| | - Grégoire Misguich
- Université Paris-Saclay, CNRS, CEA, Institut de Physique Théorique, 91191 Gif-sur-Yvette, France
| | - Haggai Landa
- IBM Quantum, IBM Research - Israel, Haifa University Campus, Mount Carmel, Haifa 31905, Israel
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Zhou JY, Zhao SL, Yang Y, Xiao S, He D, Nie W, Hu Y, Lu J, Kuang LM, Liu YX, Deng MT, Zheng DN, Xiang ZC, Zhou L, Peng ZH. Experimental study of modified Tavis-Cummings model with directly-coupled superconducting artificial atoms. OPTICS EXPRESS 2024; 32:179-187. [PMID: 38175047 DOI: 10.1364/oe.509250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 12/02/2023] [Indexed: 01/05/2024]
Abstract
The Tavis-Cummings model is intensively investigated in quantum optics and has important applications in generation of multi-atom entanglement. Here, we employ a superconducting circuit quantum electrodynamic system to study a modified Tavis-Cummings model with directly-coupled atoms. In our device, three superconducting artificial atoms are arranged in a chain with direct coupling through fixed capacitors and strongly coupled to a transmission line resonator. By performing transmission spectrum measurements, we observe different anticrossing structures when one or two qubits are resonantly coupled to the resonator. In the case of the two-qubit Tavis-Cummings model without qubit-qubit interaction, we observe two dips at the resonance point of the anticrossing. The splitting of these dips is determined by Δ λ=2g12+g32, where g1 and g3 are the coupling strengths between Qubit 1 and the resonator, and Qubit 3 and the resonator, respectively. The direct coupling J12 between the two qubits results in three dressed states in the two-qubit Tavis-Cummings model at the frequency resonance point, leading to three dips in the transmission spectrum. In this case, the distance between the two farthest and asymmetrical dips, arising from the energy level splitting, is larger than in the previous case. The frequency interval between these two dips is determined by the difference in eigenvalues (Δ λ=ε 1+-ε 1-), obtained through numerical calculations. What we believe as novel and intriguing experimental results may potentially advance quantum optics experiments, providing valuable insights for future research.
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