Finding low-energy conformations of lattice protein models by quantum annealing

Perdomo-Ortiz, Alejandro, Dickson, Neil, Drew-Brook, Marshall, Rose, Geordie, Aspuru-Guzik, Alán·2012·Scientific Reports

Cited by (372)

Items 201–300 of 372

  1. Modernizing quantum annealing II: genetic algorithms with the inference primitive formalism
    Nicholas Chancellor · 2022 · Natural Computing
  2. A Paired-Ion Framework Composed of Vanadyl Porphyrin Molecular Qubits Extends Spin Coherence Times
    Casandra M. Moisanu, Hannah J. Eckvahl, Charlotte L. Stern, Michael R. Wasielewski, William R. Dichtel · 2024 · Journal of the American Chemical Society
  3. Cyclic quantum annealing: searching for deep low-energy states in 5000-qubit spin glass
    Hao Zhang, Kelly Boothby, Alex Kamenev · 2024 · Scientific Reports
  4. The Convergence of Distributed Computing and Quantum Computing: A Paradigm Shift in Computational Power
    Prudhvi Naayini, Chiranjeevi Bura, Anil Kumar Jonnalagadda · 2025 · International Journal Of Scientific Advances
  5. Fluctuation-guided search in quantum annealing
    Nicholas Chancellor · 2020 · Physical Review A
  6. On the Viability of Quantum Annealers to Solve Fluid Flows
    Navamita Ray, Tirtha Banerjee, Balu T. Nadiga, Satish Karra · 2022 · Frontiers in Mechanical Engineering
  7. Quantum-inspired optimization for wavelength assignment
    Aleksey S. Boev, Sergey R. Usmanov, Alexander M. Semenov, Maria M. Ushakova, Gleb V. Salahov, Alena S. Mastiukova, Evgeniy O. Kiktenko, Aleksey K. Fedorov · 2023 · Frontiers in Physics
  8. Diversifying Investments and Maximizing Sharpe Ratio: A Novel Quadratic Unconstrained Binary Optimization Formulation
    Mirko Mattesi, Luca Asproni, Christian Mattia, Simone Tufano, Giacomo Ranieri, Davide Caputo, Davide Corbelletto · 2024 · Quantum Reports
  9. Exact methods for lattice protein models
    Martin Mann, Rolf Backofen · 2014 · Bio-Algorithms and Med-Systems
  10. Dynamics of order parameters of nonstoquastic Hamiltonians in the adaptive quantum Monte Carlo method
    Shunta Arai, Masayuki Ohzeki, Kazuyuki Tanaka · 2019 · Physical review. E
  11. Protein Design by Integrating Machine Learning and Quantum-Encoded Optimization
    Panizza, Veronica, Hauke, Philipp, Micheletti, Cristian, Faccioli, Pietro · 2024 · PRX Life
  12. Low-temperature environments for quantum computation and quantum simulation*
    Hailong Fu, Pengjie Wang, Zhenhai Hu, Yifan Li, Xi Lin · 2020 · Chinese Physics B
  13. Quantum optimization within lattice gauge theory model on a quantum simulator
    Zheng Yan, Zheng Zhou, Yan-Hua Zhou, Yan-Cheng Wang, Xingze Qiu, Zi Yang Meng, Xue‐Feng Zhang · 2023 · npj Quantum Information
  14. Quantum annealing for microstructure equilibration with long-range elastic interactions
    Roland Sandt, Yann Le Bouar, Robert Spatschek · 2023 · Scientific Reports
  15. How Small-World Interactions Can Lead to Improved Quantum Annealer Designs
    Helmut G. Katzgraber, M. A. Novotny · 2018 · Physical Review Applied
  16. Application of quantum artificial intelligence in healthcare
    Sachinkumar Anandpal Goswami, Saurabh Dave, Kashyap Chaitanya Kumar Patel, Miteshkumar Narmadbhai Raval · 2025 · Elsevier eBooks
  17. A quantum annealing approach to ionic diffusion in solids
    Keishu Utimula, Tom Ichibha, Genki I. Prayogo, Kenta Hongo, Kousuke Nakano, Ryo Maezono · 2021 · Scientific Reports
  18. Solving systems of Boolean multivariate equations with quantum annealing
    Sergi Ramos-Calderer, Carlos Bravo-Prieto, Ruge Lin, Emanuele Bellini, Marc Manzano, Najwa Aaraj, José Ignacio Latorre · 2022 · Physical Review Research
  19. Applications of Quantum Annealing to Music Theory
    Ashish Arya, Ludmila Botelho, Fabiola Cañete, Dhruvi Kapadia, Özlem Salehi · 2022 · Springer eBooks
  20. FoldingZero: Protein Folding from Scratch in Hydrophobic-Polar Model
    Yanjun Li, Hengtong Kang, Ye, Ketian, Shuyu Yin, Xiaolin Li · 2018 · arXiv (Cornell University)
  21. Quantum Computing Systems: A Brief Overview
    Waranont Anukool, Jongseok Lim, Yunheung Song, Jaewook Ahn · 2018 · Journal of the Korean Physical Society
  22. Lossy compression of statistical data using quantum annealer
    Boram Yoon, Nga T. T. Nguyen, Chia Cheng Chang, Ermal Rrapaj · 2022 · Scientific Reports
  23. Hybrid Optimization Method Using Simulated-Annealing-Based Ising Machine and Quantum Annealer
    Shuta Kikuchi, Nozomu Togawa, Shu Tanaka · 2023 · Journal of the Physical Society of Japan
  24. A comparative insight into peptide folding with quantum CVaR-VQE algorithm, MD simulations and structural alphabet analysis
    Akshay Uttarkar, Vidya Niranjan · 2024 · Quantum Information Processing
  25. Efficient quantum algorithm for lattice protein folding
    Youle Wang, Xiangzhen Zhou · 2024 · Quantum Science and Technology
  26. Preserving privacy in a smart grid scenario using quantum mechanics
    Fábio Borges, Raqueline A. M. Santos, Franklin de Lima Marquezino · 2014 · Security and Communication Networks
  27. A Quantum-inspired optimization Heuristic for the Multiple Sequence Alignment Problem in Bio-computing
    Konstantinos Giannakis, Christos Papalitsas, Georgia Theocharopoulou, Sofia Fanarioti, Theodore Andronikos · 2019 · International Conference on Information, Intelligence, Systems & Applications (IISA)
  28. Experimental Demonstrations of Native Implementation of Boolean Logic Hamiltonian in a Superconducting Quantum Annealer
    Daisuke Saida, Yuki Yamanashi, Mutsuo Hidaka, Fuminori Hirayama, Kentaro Imafuku, Shuichi Nagasawa, Shiro Kawabata · 2021 · IEEE Transactions on Quantum Engineering
  29. Multiple network alignment on quantum computers
    Ammar Daskin, Ananth Grama, Sabre Kais · 2014 · Quantum Information Processing
  30. Quantum and quantum-inspired optimization for solving the minimum bin packing problem
    A. A. Bozhedarov, Sergey R. Usmanov, G V Salakhov, Aleksey S. Boev, Evgeniy O. Kiktenko, Aleksey K. Fedorov · 2024 · Journal of Physics Conference Series
  31. Quantum-assisted finite-element design optimization
    Dyon van Vreumingen, Florian Neukart, David Von Dollen, Carsten Othmer, Hartmann, Michael, Voigt, Arne-Christian, Thomas Bäck · 2019 · arXiv (Cornell University)
  32. Coherent Ising machine based on polarization symmetry breaking in a driven Kerr resonator
    Liam Quinn, Yiqing Xu, Julien Fatome, Gian‐Luca Oppo, Stuart G. Murdoch, Miro J. Erkintalo, Stéphane Coen · 2026 · Nature Communications
  33. Computational Design of Peptide-Based Binders to Therapeutic Targets
    Vikram Khipple Mulligan, Parisa Hosseinzadeh · 2022 · ACS symposium series
  34. QiCells: A Modular RFSoC-based Approach to Interface Superconducting Quantum Bits
    Richard Gebauer, Nick Karcher, Mehmed Güler, Oliver Sander · 2022 · ACM Transactions on Reconfigurable Technology and Systems
  35. Hybrid Quantum Annealing with Innovative Trend Ratio Model for Portfolio Optimization
    Yao–Hsin Chou, Ching-Hsuan Wu, Pei-Shin Huang, Shu–Yu Kuo, Yu-Chi Jiang, Sy‐Yen Kuo, Ching‐Ray Chang · 2024 · IEEE Congress on Evolutionary Computation (CEC)
  36. AYRIK YAPAY ARI KOLONİSİ ALGORİTMASI İLE PROTEİN YAPISI TAHMİNİ
    Turgay Batbat, Celal Öztürk · 2016 · Bilişim Teknolojileri Dergisi
  37. QUBO formulation for the contact map overlap problem
    Nicolas M. de Oliveira, Ricardo Martins de Abreu Silva, Wilson Rosa de Oliveira · 2018 · International Journal of Quantum Information
  38. Factorization by quantum annealing using superconducting flux qubits implementing a multiplier Hamiltonian
    Daisuke Saida, Mutsuo Hidaka, Kentaro Imafuku, Yuki Yamanashi · 2022 · Scientific Reports
  39. Dynamical Process of a Bit-Width Reduced Ising Model With Simulated Annealing
    Shuta Kikuchi, Nozomu Togawa, Shu Tanaka · 2023 · IEEE Access
  40. Message-passing Algorithm of Quantum Annealing with Nonstoquastic Hamiltonian
    Masayuki Ohzeki · 2019 · Journal of the Physical Society of Japan
  41. Fabrication of atomic junctions with experimental parameters optimized using ground-state searches of Ising spin computing
    Shotaro Sakai, Yosuke Hirata, Mitsuki Ito, Jun‐ichi Shirakashi · 2019 · Scientific Reports
  42. A modular RFSoC-based approach to interface superconducting quantum bits
    Richard Gebauer, Nick Karcher, Oliver Sander · 2021 · International Conference on Field-Programmable Technology (FPT)
  43. Quantum Annealing
    Sei Suzuki, Jun‐ichi Inoue, Bikas K. Chakrabarti · 2012 · Lecture notes in physics
  44. Accelerating Simulated Quantum Annealing with GPU and Tensor Cores
    Yi-Hua Chung, Cheng-Jhih Shih, Shih‐Hao Hung · 2022 · Lecture notes in computer science
  45. Simulation: Quantum leaps
    Geoff Brumfiel · 2012 · Nature
  46. Computational complexity of three-dimensional Ising spin glass: Lessons from D-wave annealer
    Hao Zhang, Alex Kamenev · 2025 · Physical Review Research
  47. Superconducting quantum circuit of NOR in quantum annealing
    Daisuke Saida, Mutsuo Hidaka, Kouhei Miyake, Kentaro Imafuku, Yuki Yamanashi · 2022 · Scientific Reports
  48. Computational Properties of Ising Spin Model on Spin Connection Parameters
    Tsukasa Miki, Mitsuki Ito, Y. Hirata, Yuki Kushitani, M. Shimada, Jun‐ichi Shirakashi · 2019 · IEEE International Conference on Nanotechnology (IEEE-NANO)
  49. Characterization of energy potential in tunable rf-SQUIDs with the classical regime toward precise design of superconducting flux qubit
    Daisuke Saida, Narii Watase, Yuki Yamanashi · 2021 · Japanese Journal of Applied Physics
  50. Investigating the potential for a limited quantum speedup on protein lattice problems
    Carlos Outeiral, Garrett M. Morris, Jiye Shi, Martin Strahm, Simon C. Benjamin, Charlotte Mary Deane · 2021 · New Journal of Physics
  51. Quantum-based optimization methods for the linear redundancy allocation problem: A comparative analysis
    Isis Didier Lins, Lavìnia Maria Mendes Araújo, Caio Bezerra Souto Maior, Erico S. Teixeira, Pâmela Thays Lins Bezerra, Márcio José das Chagas Moura, Enrique López Droguett · 2025 · Reliability Engineering & System Safety
  52. Quantum algorithm for protein-ligand docking sites identification in the interaction space
    Ioannis Liliopoulos, Georgios D. Varsamis, Theodora Karamanidou, Christos Papalitsas, Grigorios Koulouras, Vassilios Pantazopoulos, Thanos G. Stavropoulos, Ioannis G. Karafyllidis · 2025 · Journal of Computer-Aided Molecular Design
  53. Exploring the topological sector optimization on quantum computers
    Yi-Ming Ding, Yan-Cheng Wang, Shi‐Xin Zhang, Yan Qing Zheng · 2024 · Physical Review Applied
  54. Emerging generalization advantage of quantum-inspired machine learning in the diagnosis of hepatocellular carcinoma
    Domenico Pomarico, Alfonso Monaco, Nicola Amoroso, Loredana Bellantuono, Antonio Lacalamita, Marianna La Rocca, T. Maggipinto, Ester Pantaleo, Sabina Tangaro, Sebastiano Stramaglia et al. · 2025 · Discover Applied Sciences
  55. Performance Models for Split-Execution Computing Systems
    T. Humble, A. McCaskey, Jonathan Schrock, H. Seddiqi, Keith A. Britt, N. Imam · 2016 · IEEE International Symposium on Parallel & Distributed Processing, Workshops and Phd Forum
  56. Hybridization of Spin Decision Logics for Ising Machine with Logic Circuits
    Tsukasa Miki, Ai Yoshida, M. Shimada, Jun‐ichi Shirakashi · 2021 · IEEE International Conference on Nanotechnology (IEEE-NANO)
  57. Nonlinear Systems for Unconventional Computing
    Kirill P. Kalinin, Natalia G. Berloff · 2020 · Nonlinear systems and complexity
  58. Leveraging Artificial Intelligence to Advance Problem-Solving with Quantum Annealers
    Ramin Ayanzadeh · 2020 · Maryland Shared Open Access Repository (USMAI Consortium)
  59. Quantum Annealing and Computation: A Brief Documentary Note
    Asim Kumar Ghosh, Sudip Mukherjee · 2013 · arXiv (Cornell University)
  60. Simulating charging characteristics of lithium iron phosphate by electro-ionic optimization on a quantum annealer
    Tobias Binninger, Yin‐Ying Ting, Konstantin Köster, Nils Bruch, Payam Kaghazchi, Piotr M. Kowalski, Michael Hermann Eikerling · 2025 · Physical review. B./Physical review. B
  61. The Intractable and the Undecidable - Computation and Anticipatory Processes
    Mihai Nadin · 2013 · International Journal of Applied Research on Information Technology and Computing
  62. Spin Connection Topology and Multi-Bit Spin Interaction Coefficients of Ising Spin Model with Digital Logic Gates
    Tsukasa Miki, M. Shimada, Jun‐ichi Shirakashi · 2020 · IEEE International Conference on Design & Test of Integrated Micro & Nano-Systems (DTS)
  63. Quantum annealing with pairs of 2Σ molecules as qubits
    Kasra Asnaashari, Roman V. Krems · 2022 · Physical Review A
  64. Computational Methods for Peptide Macrocycle Drug Design
    Vikram Khipple Mulligan · 2022 · AAPS advances in the pharmaceutical sciences series
  65. Estimating the number of states of a quantum system via the rodeo algorithm for quantum computation
    J. C. S. Rocha, Raphael Fortes Infante Gomes, W. A. T. Nogueira, R. A. Dias · 2024 · Quantum Information Processing
  66. Degeneracy engineering for classical and quantum annealing: A case study of sparse linear regression in collider physics
    Eric R. Anschuetz, Lena Funcke, Patrick Komiske, Serhii Kryhin, Jesse Thaler · 2022 · Physical review. D/Physical review. D.
  67. Limits of Short-Time Evolution of Local Hamiltonians
    Ali Hamed Moosavian, Seyed Sajad Kahani, Salman Beigi · 2022 · Quantum
  68. Decoding quantum error correction with Ising model hardware
    Joschka Roffe, Stefan Zohren, Dominic C. Horsman, Nicholas Chancellor · 2019 · arXiv (Cornell University)
  69. Enhancing Combinatorial Optimization with Quantum Generative Models
    Javier A. Alcazar, Alejandro Perdomo‐Ortiz · 2021 · arXiv (Cornell University)
  70. RinQ: Towards predicting central sites in proteins on current quantum computers
    Shah Ishmam Mohtashim · 2025 · Materials Today Quantum
  71. Interrogating the performance of quantum annealing for the solution of steady-state subsurface flow
    Jessie M. Henderson, Daniel O’Malley, Hari Viswanathan · 2021 · IEEE High Performance Extreme Computing Conference
  72. Exploring Quantum Annealing for Enhanced International Financial Stock Portfolio Management
    Yao–Hsin Chou, Ching-Hsuan Wu, Pei-Shin Huang, Jyun–Yi Shen, Shu–Yu Kuo, Sy‐Yen Kuo, Ching‐Ray Chang · 2024 · IEEE International Conference on Quantum Computing and Engineering (QCE)
  73. Quadratic constrained mixed discrete optimization with an adiabatic quantum optimizer
    Rishabh Chandra, N. Tobias Jacobson, Jonathan E. Moussa, Steven H. Frankel, Sabre Kais · 2014 · Physical Review A
  74. Protein Tertiary Structure Prediction with Hybrid Clonal Selection and Differential Evolution Algorithms
    Iryna Fefelova, Andrey Fefelov, Volodymyr I. Lytvynenko, Róża Dzierżak, Iryna Lurie, Nataliia B. Savina, Mariia A. Voronenko, Svitlana Vyshemyrska · 2019 · Advances in intelligent systems and computing
  75. Frustration and inhomogeneous environments in relaxation of open chains with Ising-type interactions
    D. Valente, T. Werlang · 2020 · Physical review. E
  76. Quantum walk in a reinforced free-energy landscape: Quantum annealing with reinforcement
    Abolfazl Ramezanpour · 2022 · Physical Review A
  77. Quantum computing in drug discovery
    Ruby Srivastava · 2023 · Information System and Smart City
  78. A Quantum Approach to Diagnosis of Multiple Faults in Electrical Power Systems
    Alejandro Perdomo‐Ortiz, Joseph Flueguemann, Sriram Narasimhan, Vadim Smelyanskiy, Rupak Biswas · 2014 · IEEE International Conference on Space Mission Challenges for Information Technology
  79. Quasi-Adiabatic Quantum Computing Treated with c-Numbers Using the Local-Field Response
    Tatsuya Tomaru · 2016 · Journal of the Physical Society of Japan
  80. Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional
    Unidad Zacatenco · 2013
  81. Development of research network on Quantum Annealing Computation and Information using Google Scholar data
    Antika Sinha · 2022 · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences
  82. Quantum computing enhanced machine learning for physico-chemical applications
    Manas Sajjan, Junxu Li, Raja Selvarajan, Shree Hari Sureshbabu, Sumit Suresh Kale, Rishabh Gupta, Sabre Kais · 2021 · arXiv (Cornell University)
  83. QuPepFold: A python package for hybrid quantum-classical protein folding simulations with CVaR-optimized VQE
    Akshay Uttarkar, Vidya Niranjan, Amit Saxena, Vinay Kumar · 2026 · PLoS ONE
  84. Computing canonical averages with quantum and classical optimizers: Thermodynamic reweighting for QUBO models of physical systems
    Francesco Slongo, Cristian Micheletti · 2025 · Physical Review Research
  85. Quadratic unconstrained binary optimization and constraint programming approaches for lattice-based cyclic peptide docking
    John Kyle Brubaker, Kyle E. C. Booth, Akihiko Arakawa, Fabian Furrer, Jayeeta Ghosh, Tsutomu Sato, Helmut G. Katzgraber · 2025 · Scientific Reports
  86. Folding lattice proteins confined on minimal grids using a quantum-inspired encoding
    Anders Irbäck, Lucas Knuthson, Sandipan Mohanty · 2025 · Physical review. E
  87. Learning-Driven Annealing with Adaptive Hamiltonian Modification for Solving Large-Scale Problems on Quantum Devices
    Sebastian Schulz, Dennis Willsch, Kristel F. L. Michielsen · 2025 · Quantum
  88. Quantum annealing for remote sensing data processing: A review of optimization based applications
    Indranil Misra, S. Manthira Moorthi, Debajyoti Dhar · 2026 · Remote Sensing Applications Society and Environment
  89. Online Taxi Dispatching Algorithm Based on Quantum Annealing
    Chao Wang, Tongyu Ji, Suming Wang · 2022 · Lecture notes in computer science
  90. Genetic Algorithm for Automated Parameterization of Network Hamiltonian Models of Amyloid Fibril Formation
    Gianmarc Grazioli, Andy Tao, Inika Bhatia, Patrick Regan · 2024 · The Journal of Physical Chemistry B
  91. A Reposition Algorithm for E-Hailing Based on Quantum Annealing and Intuitive Reasoning
    Chao Wang, Yiyun Shi, Sumin Wang · 2024 · Intelligent and Converged Networks
  92. Statistical Mechanics of Heteropolymers from Lattice Gauge Theory
    Veronica Panizza, Alessandro Roggero, Philipp Hauke, Pietro Faccioli · 2025 · Physical Review Letters
  93. Lattice Folding Simulation of Peptide by Quantum Computation
    Rui SAITO, Koji Okuwaki, Yuji Mochizuki, Ryutaro Nagai, Takumi Kato, Kenji Sugisaki, Yuichiro Minato · 2023 · Journal of Computer Chemistry Japan -International Edition
  94. Microstructure equilibration with consideration of elastic and interfacial interactions via quantum annealing with application to the solid electrolyte LLZO
    Roland Sandt, Yann Le Bouar, Robert Spatschek · 2024 · Physical Review Research
  95. Noise effects on diabatic quantum annealing protocols
    Giulia Salatino, Maximilian Matzler, Annarita Scocco, Procolo Lucignano, Gianluca Passarelli · 2025 · Physical Review A
  96. Exploring quantum annealing for coarse-grained protein folding
    Timon Scheiber, Matthias Heller, Andreas Giebel · 2026 · Scientific Reports
  97. Fast Embedding of Constrained Satisfaction Problem to Quantum Annealer with Minimizing Chain Length
    Juexiao Su, Lei He · 2017 · ACM/IEEE Design Automation Conference (DAC)
  98. Quantum Computing-Applications in Bioinformatics
    Divya Baiskhiyar, Ravi Kumar · 2019 · International Journal of Computer Applications
  99. Forging Connections Between AI and Quantum Computing in Decentralized Networks
    Haresh Damjibhai Khachariya, R. Augustian Isaac, R. Sasikala, M. Gokilavani · 2024 · Advances in computational intelligence and robotics book series
  100. Comparison of quantum annealing and simulated annealing
    Hidetoshi Nishimori · 2015 · The European Physical Journal Special Topics