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Number Cited by Other Article(s)
1
Schwerdtfeger P, Wales DJ. 100 Years of the Lennard-Jones Potential. J Chem Theory Comput 2024;20:3379-3405. [PMID: 38669689 DOI: 10.1021/acs.jctc.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
2
Woods EJ, Wales DJ. Analysis and interpretation of first passage time distributions featuring rare events. Phys Chem Chem Phys 2024;26:1640-1657. [PMID: 38059562 DOI: 10.1039/d3cp04199a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2023]
3
Roth M, Toker Y, Major DT. Monte Carlo-Simulated Annealing and Machine Learning-Based Funneled Approach for Finding the Global Minimum Structure of Molecular Clusters. ACS OMEGA 2024;9:1298-1309. [PMID: 38222530 PMCID: PMC10785639 DOI: 10.1021/acsomega.3c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2023] [Revised: 11/09/2023] [Accepted: 11/15/2023] [Indexed: 01/16/2024]
4
Liu YR, Jiang Y. Growth mechanism prediction for nanoparticles via structure matching polymerization. Phys Chem Chem Phys 2024;26:1267-1273. [PMID: 38105690 DOI: 10.1039/d3cp04702d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
5
Smith NB, Jowett T, Yu D, Pahl E, Garden AL. Comparison of Taboo Search Methods for Atomic Cluster Global Optimization with a Basin-Hopping Algorithm. J Chem Inf Model 2023;63:5784-5793. [PMID: 37665618 DOI: 10.1021/acs.jcim.3c00526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
6
Kanayama K, Seko A, Toyoura K. Structure search method for atomic clusters based on the dividing rectangles algorithm. Phys Rev E 2023;108:035303. [PMID: 37849110 DOI: 10.1103/physreve.108.035303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 08/11/2023] [Indexed: 10/19/2023]
7
Wang Y, Lv J, Gao P, Ma Y. Crystal Structure Prediction via Efficient Sampling of the Potential Energy Surface. Acc Chem Res 2022;55:2068-2076. [DOI: 10.1021/acs.accounts.2c00243] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
8
Cox S, White AD. Symmetric Molecular Dynamics. J Chem Theory Comput 2022;18:4077-4081. [PMID: 35699649 PMCID: PMC9281392 DOI: 10.1021/acs.jctc.2c00401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
9
Bauer MN, Probert MIJ, Panosetti C. Systematic Comparison of Genetic Algorithm and Basin Hopping Approaches to the Global Optimization of Si(111) Surface Reconstructions. J Phys Chem A 2022;126:3043-3056. [PMID: 35522778 PMCID: PMC9126620 DOI: 10.1021/acs.jpca.2c00647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
10
Weal GR, McIntyre SM, Garden AL. Development of a Structural Comparison Method to Promote Exploration of the Potential Energy Surface in the Global Optimization of Nanoclusters. J Chem Inf Model 2021;61:1732-1744. [PMID: 33844537 DOI: 10.1021/acs.jcim.0c01128] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
11
Srivastava R. Application of Optimization Algorithms in Clusters. Front Chem 2021;9:637286. [PMID: 33777900 PMCID: PMC7994592 DOI: 10.3389/fchem.2021.637286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/21/2021] [Indexed: 12/23/2022]  Open
12
Swinburne TD, Kannan D, Sharpe DJ, Wales DJ. Rare events and first passage time statistics from the energy landscape. J Chem Phys 2020;153:134115. [PMID: 33032418 DOI: 10.1063/5.0016244] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
13
Olson MA, Bhatia S, Larson P, Militzer B. Prediction of chlorine and fluorine crystal structures at high pressure using symmetry driven structure search with geometric constraints. J Chem Phys 2020;153:094111. [PMID: 32891084 DOI: 10.1063/5.0018402] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
14
Hernández-Rojas J, Calvo F. The Structure of Adamantane Clusters: Atomistic vs. Coarse-Grained Predictions From Global Optimization. Front Chem 2019;7:573. [PMID: 31475136 PMCID: PMC6707085 DOI: 10.3389/fchem.2019.00573] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 07/29/2019] [Indexed: 11/24/2022]  Open
15
Li X, Tang Y, Li S, Gui Y. Spectroscopic properties and activated mechanism of NO on isolated cationic tantalum clusters: A first-principles study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019;216:335-341. [PMID: 30909090 DOI: 10.1016/j.saa.2019.03.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 02/18/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
16
Röder K, Joseph JA, Husic BE, Wales DJ. Energy Landscapes for Proteins: From Single Funnels to Multifunctional Systems. ADVANCED THEORY AND SIMULATIONS 2019. [DOI: 10.1002/adts.201800175] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
17
Grajciar L, Heard CJ, Bondarenko AA, Polynski MV, Meeprasert J, Pidko EA, Nachtigall P. Towards operando computational modeling in heterogeneous catalysis. Chem Soc Rev 2018;47:8307-8348. [PMID: 30204184 PMCID: PMC6240816 DOI: 10.1039/c8cs00398j] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Indexed: 12/19/2022]
18
Aguado A, Vega A, Lebon A, von Issendorff B. Are zinc clusters really amorphous? A detailed protocol for locating global minimum structures of clusters. NANOSCALE 2018;10:19162-19181. [PMID: 30302480 DOI: 10.1039/c8nr05517c] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
19
Li X, Li S, Wang Z, Yang X, Yan Z. A Frank-Kasper polyhedral structure of 17-atom vanadium clusters. Chem Phys Lett 2018. [DOI: 10.1016/j.cplett.2018.08.024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
20
Elenewski JE, Velizhanin KA, Zwolak M. A spin-1 representation for dual-funnel energy landscapes. J Chem Phys 2018;149:035101. [PMID: 30037251 PMCID: PMC7723752 DOI: 10.1063/1.5036677] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
21
Wales DJ. Exploring Energy Landscapes. Annu Rev Phys Chem 2018;69:401-425. [PMID: 29677468 DOI: 10.1146/annurev-physchem-050317-021219] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
22
Ballard AJ, Das R, Martiniani S, Mehta D, Sagun L, Stevenson JD, Wales DJ. Energy landscapes for machine learning. Phys Chem Chem Phys 2018;19:12585-12603. [PMID: 28367548 DOI: 10.1039/c7cp01108c] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
23
Conquering the hard cases of Lennard-Jones clusters with simple recipes. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2016.09.032] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
24
Lazauskas T, Sokol AA, Woodley SM. An efficient genetic algorithm for structure prediction at the nanoscale. NANOSCALE 2017;9:3850-3864. [PMID: 28252128 DOI: 10.1039/c6nr09072a] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
25
Zhao J, Shi R, Sai L, Huang X, Su Y. Comprehensive genetic algorithm forab initioglobal optimisation of clusters. MOLECULAR SIMULATION 2016. [DOI: 10.1080/08927022.2015.1121386] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
26
Ballard AJ, Stevenson JD, Das R, Wales DJ. Energy landscapes for a machine learning application to series data. J Chem Phys 2016;144:124119. [DOI: 10.1063/1.4944672] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
27
Symmetry in Sphere-Based Assembly Configuration Spaces. Symmetry (Basel) 2016. [DOI: 10.3390/sym8010005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
28
Calvo F, Schebarchov D, Wales DJ. Grand and Semigrand Canonical Basin-Hopping. J Chem Theory Comput 2016;12:902-9. [PMID: 26669731 PMCID: PMC4750084 DOI: 10.1021/acs.jctc.5b00962] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
29
Zhang J, Dolg M. Global optimization of clusters of rigid molecules using the artificial bee colony algorithm. Phys Chem Chem Phys 2016;18:3003-10. [DOI: 10.1039/c5cp06313b] [Citation(s) in RCA: 195] [Impact Index Per Article: 24.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
30
Three-Dimensional Assignment of the Structures of Atomic Clusters: an Example of Au8M (M=Si, Ge, Sn) Anion Clusters. Sci Rep 2015;5:17738. [PMID: 26631620 PMCID: PMC4668548 DOI: 10.1038/srep17738] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2015] [Accepted: 10/30/2015] [Indexed: 11/29/2022]  Open
31
Neogi SG, Chaudhury P. Structure, electronic properties and vibrational spectra of (MgF2)nclusters through a combination of genetic algorithm and DFT-based approach. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1059508] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
32
Schebarchov D, Wales DJ. Quasi-combinatorial energy landscapes for nanoalloy structure optimisation. Phys Chem Chem Phys 2015;17:28331-8. [PMID: 25970479 DOI: 10.1039/c5cp01198a] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
33
Wales DJ. Perspective: Insight into reaction coordinates and dynamics from the potential energy landscape. J Chem Phys 2015;142:130901. [DOI: 10.1063/1.4916307] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
34
Free energy basin-hopping. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.02.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
35
Guo Y, Bo M, Wang Y, Liu Y, Huang Y, Sun CQ. Atomistic bond relaxation, energy entrapment, and electron polarization of the RbN and CsN clusters (N ≤ 58). Phys Chem Chem Phys 2015;17:30389-97. [DOI: 10.1039/c5cp05729a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
36
Zhang J, Dolg M. ABCluster: the artificial bee colony algorithm for cluster global optimization. Phys Chem Chem Phys 2015;17:24173-81. [DOI: 10.1039/c5cp04060d] [Citation(s) in RCA: 271] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
37
Ballard AJ, Wales DJ. Superposition-Enhanced Estimation of Optimal Temperature Spacings for Parallel Tempering Simulations. J Chem Theory Comput 2014;10:5599-5605. [PMID: 25512744 PMCID: PMC4262936 DOI: 10.1021/ct500797a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Indexed: 01/31/2023]
38
Chill ST, Stevenson J, Ruehle V, Shang C, Xiao P, Farrell JD, Wales DJ, Henkelman G. Benchmarks for Characterization of Minima, Transition States, and Pathways in Atomic, Molecular, and Condensed Matter Systems. J Chem Theory Comput 2014;10:5476-82. [DOI: 10.1021/ct5008718] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
39
Barcaro G, Sementa L, Fortunelli A. A grouping approach to homotop global optimization in alloy nanoparticles. Phys Chem Chem Phys 2014;16:24256-65. [DOI: 10.1039/c4cp03745f] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
40
Truong NX, Savoca M, Harding DJ, Fielicke A, Dopfer O. Vibrational spectra and structures of neutral Si6X clusters (X = Be, B, C, N, O). Phys Chem Chem Phys 2014;16:22364-72. [DOI: 10.1039/c4cp03414g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
41
Hédin F, Plattner N, Doll JD, Meuwly M. Spatial Averaging: Sampling Enhancement for Exploring Configurational Space of Atomic Clusters and Biomolecules. J Chem Theory Comput 2014;10:4284-96. [DOI: 10.1021/ct500529w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
42
Wu X, Wu G. An adaptive immune optimization algorithm with dynamic lattice searching operation for fast optimization of atomic clusters. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.06.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
43
Wu X. Theoretical Study of Structural Symmetry in Ternary Clusters. J CLUST SCI 2014. [DOI: 10.1007/s10876-014-0760-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
44
Gould AL, Heard CJ, Logsdail AJ, Catlow CRA. Segregation effects on the properties of (AuAg)147. Phys Chem Chem Phys 2014;16:21049-61. [DOI: 10.1039/c4cp00753k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
45
Liu YR, Wen H, Huang T, Lin XX, Gai YB, Hu CJ, Zhang WJ, Huang W. Structural Exploration of Water, Nitrate/Water, and Oxalate/Water Clusters with Basin-Hopping Method Using a Compressed Sampling Technique. J Phys Chem A 2014;118:508-16. [DOI: 10.1021/jp4109128] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
46
Performance of modified Lennard–Jones potential to seed ab initio calculations of small cadmium clusters. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.07.041] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
47
Rondina GG, Da Silva JLF. Revised Basin-Hopping Monte Carlo Algorithm for Structure Optimization of Clusters and Nanoparticles. J Chem Inf Model 2013;53:2282-98. [DOI: 10.1021/ci400224z] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
48
Rogan J, Varas A, Valdivia JA, Kiwi M. A strategy to find minimal energy nanocluster structures. J Comput Chem 2013;34:2548-56. [PMID: 24037778 DOI: 10.1002/jcc.23419] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Revised: 07/25/2013] [Accepted: 08/04/2013] [Indexed: 12/19/2022]
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