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For: Sharapov VA, Mandelshtam VA. Solid−Solid Structural Transformations in Lennard-Jones Clusters:  Accurate Simulations versus the Harmonic Superposition Approximation. J Phys Chem A 2007;111:10284-91. [PMID: 17685597 DOI: 10.1021/jp072929c] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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
Keith AD, Sawyer EB, Choy DCY, Xie Y, Biggs GS, Klein OJ, Brear PD, Wales DJ, Barker PD. Combining experiment and energy landscapes to explore anaerobic heme breakdown in multifunctional hemoproteins. Phys Chem Chem Phys 2024;26:695-712. [PMID: 38053511 DOI: 10.1039/d3cp03897a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
4
Settem M, Roncaglia C, Ferrando R, Giacomello A. Structural transformations in Cu, Ag, and Au metal nanoclusters. J Chem Phys 2023;159:094303. [PMID: 37668252 DOI: 10.1063/5.0159257] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 08/15/2023] [Indexed: 09/06/2023]  Open
5
Finkler JA, Goedecker S. Experimental absence of the non-perovskite ground state phases of MaPbI3 explained by a Funnel Hopping Monte Carlo study based on a neural network potential. MATERIALS ADVANCES 2023;4:184-194. [PMID: 36685989 PMCID: PMC9812259 DOI: 10.1039/d2ma00958g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/11/2022] [Indexed: 06/17/2023]
6
Settem M, Ferrando R, Giacomello A. Tempering of Au nanoclusters: capturing the temperature-dependent competition among structural motifs. NANOSCALE 2022;14:939-952. [PMID: 34988565 DOI: 10.1039/d1nr05078h] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
7
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
8
Finkler JA, Goedecker S. Funnel hopping Monte Carlo: An efficient method to overcome broken ergodicity. J Chem Phys 2020;152:164106. [DOI: 10.1063/5.0004106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]  Open
9
Griffiths M, Wales DJ. Nested Basin-Sampling. J Chem Theory Comput 2019;15:6865-6881. [PMID: 31557432 DOI: 10.1021/acs.jctc.9b00567] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
10
Grigoryan VG, Springborg M. Temperature and isomeric effects in nanoclusters. Phys Chem Chem Phys 2019;21:5646-5654. [PMID: 30793128 DOI: 10.1039/c9cp00123a] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
11
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]
12
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]
13
Wales DJ. Atomic clusters with addressable complexity. J Chem Phys 2018;146:054306. [PMID: 28178805 DOI: 10.1063/1.4974838] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
14
Vishwanathan K, Springborg M. Retracted Article: A highest stable cluster Au58 (C 1) re-optimized via a density-functional tight-binding (DFTB) approach. RSC Adv 2018;8:11357-11366. [PMID: 35542769 PMCID: PMC9079119 DOI: 10.1039/c7ra13171b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 02/26/2018] [Indexed: 11/21/2022]  Open
15
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]
16
Schebarchov D, Baletto F, Wales DJ. Structure, thermodynamics, and rearrangement mechanisms in gold clusters-insights from the energy landscapes framework. NANOSCALE 2018;10:2004-2016. [PMID: 29319705 PMCID: PMC5901115 DOI: 10.1039/c7nr07123j] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Accepted: 12/15/2017] [Indexed: 05/27/2023]
17
Chakraborty D, Wales DJ. Energy Landscape and Pathways for Transitions between Watson-Crick and Hoogsteen Base Pairing in DNA. J Phys Chem Lett 2018;9:229-241. [PMID: 29240425 DOI: 10.1021/acs.jpclett.7b01933] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
18
Wales DJ. Decoding heat capacity features from the energy landscape. Phys Rev E 2017;95:030105. [PMID: 28415307 DOI: 10.1103/physreve.95.030105] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Indexed: 04/28/2023]
19
Cezar HM, Rondina GG, Da Silva JLF. Parallel tempering Monte Carlo combined with clustering Euclidean metric analysis to study the thermodynamic stability of Lennard-Jones nanoclusters. J Chem Phys 2017;146:064114. [DOI: 10.1063/1.4975601] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
20
Husic BE, Schebarchov D, Wales DJ. Impurity effects on solid-solid transitions in atomic clusters. NANOSCALE 2016;8:18326-18340. [PMID: 27775141 DOI: 10.1039/c6nr06299g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
21
Christensen HM, Jake LC, Curotto E. Smart darting diffusion Monte Carlo: Applications to lithium ion-Stockmayer clusters. J Chem Phys 2016;144:174115. [PMID: 27155633 DOI: 10.1063/1.4948562] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
22
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
23
Carr JM, Mazauric D, Cazals F, Wales DJ. Energy landscapes and persistent minima. J Chem Phys 2016;144:054109. [DOI: 10.1063/1.4941052] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
24
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]
25
Chebaro Y, Ballard AJ, Chakraborty D, Wales DJ. Intrinsically disordered energy landscapes. Sci Rep 2015;5:10386. [PMID: 25999294 PMCID: PMC4441119 DOI: 10.1038/srep10386] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 04/10/2015] [Indexed: 12/19/2022]  Open
26
Mehta D, Chen T, Morgan JWR, Wales DJ. Exploring the potential energy landscape of the Thomson problem via Newton homotopies. J Chem Phys 2015;142:194113. [PMID: 26001453 DOI: 10.1063/1.4921163] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
27
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
28
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]
29
Exploiting the potential energy landscape to sample free energy. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2015. [DOI: 10.1002/wcms.1217] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
30
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]
31
Mehta D, Chen T, Hauenstein JD, Wales DJ. Communication: Newton homotopies for sampling stationary points of potential energy landscapes. J Chem Phys 2014;141:121104. [DOI: 10.1063/1.4896657] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
32
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]
33
Mochizuki K, Whittleston CS, Somani S, Kusumaatmaja H, Wales DJ. A conformational factorisation approach for estimating the binding free energies of macromolecules. Phys Chem Chem Phys 2014;16:2842-53. [PMID: 24213246 DOI: 10.1039/c3cp53537a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
34
Stevenson JD, Wales DJ. Communication: Analysing kinetic transition networks for rare events. J Chem Phys 2014;141:041104. [DOI: 10.1063/1.4891356] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
35
Hughes C, Mehta D, Wales DJ. An inversion-relaxation approach for sampling stationary points of spin model Hamiltonians. J Chem Phys 2014;140:194104. [PMID: 24852527 DOI: 10.1063/1.4875697] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
36
Senn F, Wiebke J, Schumann O, Gohr S, Schwerdtfeger P, Pahl E. Melting of “non-magic” argon clusters and extrapolation to the bulk limit. J Chem Phys 2014;140:044325. [DOI: 10.1063/1.4862906] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
37
Wales DJ. Surveying a complex potential energy landscape: Overcoming broken ergodicity using basin-sampling. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.066] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
38
Somani S, Wales DJ. Energy landscapes and global thermodynamics for alanine peptides. J Chem Phys 2013;139:121909. [DOI: 10.1063/1.4813627] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
39
Wallace AF. Replica Exchange Methods in Biomineral Simulations. Methods Enzymol 2013;532:71-93. [DOI: 10.1016/b978-0-12-416617-2.00004-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
40
Georgescu I, Mandelshtam VA. Self-consistent phonons revisited. I. The role of thermal versus quantum fluctuations on structural transitions in large Lennard-Jones clusters. J Chem Phys 2012;137:144106. [DOI: 10.1063/1.4754819] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
41
Aguado A, Jarrold MF. Melting and Freezing of Metal Clusters. Annu Rev Phys Chem 2011;62:151-72. [DOI: 10.1146/annurev-physchem-032210-103454] [Citation(s) in RCA: 100] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
42
Pártay LB, Bartók AP, Csányi G. Efficient Sampling of Atomic Configurational Spaces. J Phys Chem B 2010;114:10502-12. [DOI: 10.1021/jp1012973] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
43
Starace AK, Cao B, Judd OH, Bhattacharyya I, Jarrold MF. Melting of size-selected aluminum nanoclusters with 84–128 atoms. J Chem Phys 2010;132:034302. [DOI: 10.1063/1.3285836] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
44
Schnabel S, Bachmann M, Janke W. Elastic Lennard-Jones polymers meet clusters: differences and similarities. J Chem Phys 2009;131:124904. [PMID: 19791918 DOI: 10.1063/1.3223720] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
45
Cao B, Starace AK, Judd OH, Bhattacharyya I, Jarrold MF. Metal clusters with hidden ground states: Melting and structural transitions in Al115(+), Al116(+), and Al117(+). J Chem Phys 2009;131:124305. [PMID: 19791879 DOI: 10.1063/1.3224124] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
46
Deckman J, Mandelshtam VA. Effects of Quantum Delocalization on Structural Changes in Lennard-Jones Clusters. J Phys Chem A 2009;113:7394-402. [DOI: 10.1021/jp900095f] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
47
Deckman J, Mandelshtam VA. Quantum disordering versus melting in Lennard-Jones clusters. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2009;79:022101. [PMID: 19391788 DOI: 10.1103/physreve.79.022101] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2008] [Indexed: 05/27/2023]
48
Free energy surfaces from an extended harmonic superposition approach and kinetics for alanine dipeptide. Chem Phys Lett 2008. [DOI: 10.1016/j.cplett.2008.10.085] [Citation(s) in RCA: 99] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
49
Calvo F, Wales DJ. Relaxation of caloric curves on complex potential energy surfaces. J Chem Phys 2008;128:154501. [DOI: 10.1063/1.2850322] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
50
Frantsuzov PA, Mandelshtam VA. Equilibrium properties of quantum water clusters by the variational Gaussian wavepacket method. J Chem Phys 2008;128:094304. [DOI: 10.1063/1.2833004] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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