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Kinugawa K, Takemoto A. Quantum polyamorphism in compressed distinguishable helium-4. J Chem Phys 2021; 154:224503. [PMID: 34241222 DOI: 10.1063/5.0048539] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We demonstrate that two amorphous solid states can exist in 4He consisting of distinguishable Boltzmann atoms under compressed conditions. The isothermal compression of normal or supercritical fluid 4He was conducted at 3-25 K using the isobaric-isothermal path integral centroid molecular dynamics simulation. The compression of fluid first produced the low-dispersion amorphous (LDA) state possessing modest extension of atomic necklaces. Further isothermal compression up to the order of 10 kbar to 1 Mbar or an isobaric cooling of LDA induced the transition to the high-dispersion amorphous (HDA) state. The HDA was characterized by long quantum wavelengths of atoms extended over several Angstroms and the promotion of atomic residual diffusion. They were related to the quantum tunneling of atoms bestriding the potential saddle points in this glass. The change in pressure or temperature induced the LDA-HDA transition reversibly with hysteresis, while it resembled the coil-globule transition of classical polymers. The HDA had lower kinetic and higher Gibbs free energies than the LDA at close temperature. The HDA was absent at T ≥ 13 K, while the LDA-HDA transition pressure significantly decreased with lowering temperature. The LDA and HDA correspond to the trapped and tunneling regimes proposed by Markland et al. [J. Chem. Phys. 136, 074511 (2012)], respectively. The same reentrant behavior as they found was observed for the expansion factor of the quantum wavelength as well as for atomic diffusivity.
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Affiliation(s)
- Kenichi Kinugawa
- Division of Chemistry, Graduate School of Humanities and Sciences, Nara Women's University, Nara 630-8506, Japan
| | - Ayumi Takemoto
- Division of Chemistry, Graduate School of Humanities and Sciences, Nara Women's University, Nara 630-8506, Japan
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2
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Das S, Shimshi M, Raz K, Nitoker Eliaz N, Mhashal AR, Ansbacher T, Major DT. EnzyDock: Protein–Ligand Docking of Multiple Reactive States along a Reaction Coordinate in Enzymes. J Chem Theory Comput 2019; 15:5116-5134. [DOI: 10.1021/acs.jctc.9b00366] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Susanta Das
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Mor Shimshi
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Keren Raz
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | | | - Anil Ranu Mhashal
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
| | - Tamar Ansbacher
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
- Hadassah Academic College, 7 Hanevi’im Street, Jerusalem 9101001, Israel
| | - Dan T. Major
- Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900, Israel
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Hamid AKM, Salvatore JC, Wang K, Murahari P, Guljas A, Rágyanszki A, Owen M, Jójárt B, Szőri M, Csizmadia IG, Viskolcz B, Fiser B. Oxidatively-mediated in silico epimerization of a highly amyloidogenic segment in the human calcitonin hormone (hCT15-19). Comput Biol Chem 2019; 80:259-269. [DOI: 10.1016/j.compbiolchem.2019.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 04/01/2019] [Accepted: 04/06/2019] [Indexed: 10/27/2022]
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Quhe R, Nava M, Tiwary P, Parrinello M. Path Integral Metadynamics. J Chem Theory Comput 2015; 11:1383-8. [DOI: 10.1021/ct501002a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Ruge Quhe
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
- State
Key Laboratory of Mesoscopic Physics, Department of Physics and Academy
for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, P. R. China
| | - Marco Nava
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
| | - Pratyush Tiwary
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
| | - Michele Parrinello
- Department
of Chemistry and Applied Biosciences, ETH Zurich, and Facoltà
di Informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, Via G. Buffi 13, 6900 Lugano, Switzerland
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Soley M, Markmann A, Batista VS. Steered quantum dynamics for energy minimization. J Phys Chem B 2015; 119:715-27. [PMID: 25122515 DOI: 10.1021/jp5046723] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We introduce a quantum optimal control algorithm for energy minimization that combines the diffeomorphic modulation under observable response preserving homotopy (D-MORPH) gradient and the Broyden Fletcher Goldfarb Shanno (BFGS) iterative scheme for nonlinear optimization. An extended set of controls defining the time-dependent mass, dipole moment, and external perturbational field are optimized to find an effective Hamiltonian that steers the dynamics of the system into the global minimum without getting trapped into local minima. The algorithm is illustrated as applied to energy minimization on rugged surfaces and golf potentials comparable to those previously explored for testing quantum annealing methodologies.
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Affiliation(s)
- Micheline Soley
- Department of Chemistry, Yale University , P.O. Box 208107, New Haven, Connecticut 06520-8107, United States
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Peng Y, Cao Z, Zhou R, Voth GA. Path Integral Coarse-Graining Replica Exchange Method for Enhanced Sampling. J Chem Theory Comput 2014; 10:3634-40. [DOI: 10.1021/ct500447r] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yuxing Peng
- Department
of Chemistry, James Franck Institute, and Computation Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Zhen Cao
- Department
of Chemistry, James Franck Institute, and Computation Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
| | - Ruhong Zhou
- Computational
Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Gregory A. Voth
- Department
of Chemistry, James Franck Institute, and Computation Institute, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States
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Wang LC, Xie DQ. Simulated Annealing Study on Structures and Energetics of CO2 in Argon Clusters. CHINESE J CHEM PHYS 2011. [DOI: 10.1088/1674-0068/24/05/620-624] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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8
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Kim SY. An off-lattice frustrated model protein with a six-stranded β-barrel structure. J Chem Phys 2010; 133:135102. [DOI: 10.1063/1.3494038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Stella L, Santoro GE. Quantum annealing of an Ising spin-glass by Green's function Monte Carlo. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2007; 75:036703. [PMID: 17500822 DOI: 10.1103/physreve.75.036703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2006] [Revised: 12/08/2006] [Indexed: 05/15/2023]
Abstract
We present an implementation of quantum annealing (QA) via lattice Green's function Monte Carlo (GFMC), focusing on its application to the Ising spin glass in transverse field. In particular, we study whether or not such a method is more effective than the path-integral Monte Carlo- (PIMC) based QA, as well as classical simulated annealing (CA), previously tested on the same optimization problem. We identify the issue of importance sampling, i.e., the necessity of possessing reasonably good (variational) trial wave functions, as the key point of the algorithm. We performed GFMC-QA runs using such a Boltzmann-type trial wave function, finding results for the residual energies that are qualitatively similar to those of CA (but at a much larger computational cost), and definitely worse than PIMC-QA. We conclude that, at present, without a serious effort in constructing reliable importance sampling variational wave functions for a quantum glass, GFMC-QA is not a true competitor of PIMC-QA.
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Affiliation(s)
- Lorenzo Stella
- International School for Advanced Studies (SISSA) and INFM Democritos National Simulation Center, Via Beirut 2-4, I-34014 Trieste, Italy
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Santoro GE, Tosatti E. Optimization using quantum mechanics: quantum annealing through adiabatic evolution. ACTA ACUST UNITED AC 2006. [DOI: 10.1088/0305-4470/39/36/r01] [Citation(s) in RCA: 225] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Martonák R, Santoro GE, Tosatti E. Quantum annealing of the traveling-salesman problem. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2004; 70:057701. [PMID: 15600807 DOI: 10.1103/physreve.70.057701] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2004] [Indexed: 05/24/2023]
Abstract
We propose a path-integral Monte Carlo quantum annealing scheme for the symmetric traveling-salesman problem, based on a highly constrained Ising-like representation, and we compare its performance against standard thermal simulated annealing. The Monte Carlo moves implemented are standard, and consist in restructuring a tour by exchanging two links (two-opt moves). The quantum annealing scheme, even with a drastically simple form of kinetic energy, appears definitely superior to the classical one, when tested on a 1002-city instance of the standard TSPLIB.
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Affiliation(s)
- Roman Martonák
- Computational Science, Department of Chemistry and Applied Biosciences, ETH Zürich, USI Campus, Via Giuseppe Buffi 13, CH-6900 Lugano, Switzerland
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Kim SY, Lee SJ, Lee J. Conformational space annealing and an off-lattice frustrated model protein. J Chem Phys 2003. [DOI: 10.1063/1.1616917] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Liu P, Berne BJ. Quantum path minimization: An efficient method for global optimization. J Chem Phys 2003. [DOI: 10.1063/1.1527919] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Santoro GE, Martonák R, Tosatti E, Car R. Theory of quantum annealing of an Ising spin glass. Science 2002; 295:2427-30. [PMID: 11923532 DOI: 10.1126/science.1068774] [Citation(s) in RCA: 438] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Probing the lowest energy configuration of a complex system by quantum annealing was recently found to be more effective than its classical, thermal counterpart. By comparing classical and quantum Monte Carlo annealing protocols on the two-dimensional random Ising model (a prototype spin glass), we confirm the superiority of quantum annealing relative to classical annealing. We also propose a theory of quantum annealing based on a cascade of Landau-Zener tunneling events. For both classical and quantum annealing, the residual energy after annealing is inversely proportional to a power of the logarithm of the annealing time, but the quantum case has a larger power that makes it faster.
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Affiliation(s)
- Giuseppe E Santoro
- Scuola Internazionale Superiore di Studi Avanzati (SISSA) and Istituto Nazionale per la Fisica della Materia (INFM) (Unità di Ricerca SISSA), I-34014 Trieste, Italy
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Miller TF, Clary DC. Torsional path integral Monte Carlo method for the quantum simulation of large molecules. J Chem Phys 2002. [DOI: 10.1063/1.1467342] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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