1
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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]
Abstract
The Dividing Rectangles (DIRECT) algorithm is a deterministic optimization method to explore optimal solutions by repeatedly dividing a given hyperrectangle search space into subhyperrectangles. Herein, we propose a structure search method for atomic clusters based on the DIRECT algorithm in combination with a gradient-based local optimizer to enable an efficient structure search in high-dimensional search spaces. We use the Z-matrix representation for defining the hyperrectangle search space, in which the bond lengths, bond angles, and dihedral angles specify a cluster structure. To evaluate its performance, we applied the proposed method to the Lennard-Jones clusters and two kinds of real atomic clusters with many metastable structures, i.e., phosphorus and sulfur clusters, and compared the results with those of conventional methods. The proposed method exhibits a higher efficiency than random search and a comparable efficiency to basin hopping.
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Affiliation(s)
- Kansei Kanayama
- Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501, Japan
| | - Atsuto Seko
- Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501, Japan
| | - Kazuaki Toyoura
- Department of Materials Science and Engineering, Kyoto University, Kyoto 606-8501, Japan
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2
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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]
Abstract
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We present a systematic
study of two widely used material structure
prediction methods, the Genetic Algorithm and Basin Hopping approaches
to global optimization, in a search for the 3 × 3, 5 × 5,
and 7 × 7 reconstructions of the Si(111) surface. The Si(111)
7 × 7 reconstruction is the largest and most complex surface
reconstruction known, and finding it is a very exacting test for global
optimization methods. In this paper, we introduce a modification to
previous Genetic Algorithm work on structure search for periodic systems,
to allow the efficient search for surface reconstructions, and present
a rigorous study of the effect of the different parameters of the
algorithm. We also perform a detailed comparison with the recently
improved Basin Hopping algorithm using Delocalized Internal Coordinates.
Both algorithms succeeded in either resolving the 3 × 3, 5 ×
5, and 7 × 7 DAS surface reconstructions or getting “sufficiently
close”, i.e., identifying structures that only differ for the
positions of a few atoms as well as thermally accessible structures
within kBT/unit area
of the global minimum, with T = 300 K. Overall, the
Genetic Algorithm is more robust with respect to parameter choice
and in success rate, while the Basin Hopping method occasionally exhibits
some advantages in speed of convergence. In line with previous studies,
the results confirm that robustness, success, and speed of convergence
of either approach are strongly influenced by how much the trial moves
tend to preserve favorable bonding patterns once these appear.
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Affiliation(s)
- Maximilian N Bauer
- Department of Physics, University of York, York YO10 5DD, United Kingdom.,Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany
| | - Matt I J Probert
- Department of Physics, University of York, York YO10 5DD, United Kingdom
| | - Chiara Panosetti
- Technical University of Munich, Lichtenbergstraße 4, 85748 Garching, Germany.,Fritz Haber Institute of the Max Planck Society, Faradayweg 4, 14195 Berlin, Germany
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3
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Paleico ML, Behler J. A flexible and adaptive grid algorithm for global optimization utilizing basin hopping Monte Carlo. J Chem Phys 2020; 152:094109. [DOI: 10.1063/1.5142363] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Martín Leandro Paleico
- Institut für Physikalische Chemie, Theoretische Chemie, Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
| | - Jörg Behler
- Institut für Physikalische Chemie, Theoretische Chemie, Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
- International Center for Advanced Studies of Energy Conversion (ICASEC), Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany
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4
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Yu K, Wang X, Chen L, Wang L. Unbiased fuzzy global optimization of Lennard-Jones clusters for N ≤ 1000. J Chem Phys 2019; 151:214105. [DOI: 10.1063/1.5127913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Affiliation(s)
- Kailiang Yu
- Center for Chemistry of Novel & High-Performance Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Xubo Wang
- Center for Chemistry of Novel & High-Performance Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
| | - Liping Chen
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, China
| | - Linjun Wang
- Center for Chemistry of Novel & High-Performance Materials, Department of Chemistry, Zhejiang University, Hangzhou 310027, China
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5
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Analysis of Spatial and Temporal Variability in Libya-4 with Landsat 8 and Sentinel-2 Data for Optimized Ground Target Location. REMOTE SENSING 2019. [DOI: 10.3390/rs11242909] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Pseudo-Invariant Calibration Sites (PICS) have been widely used by the remote sensing community in recent decades for post-launch absolute calibration, cross-calibration, and the monitoring of radiometric stability. The Committee on Earth Observation Satellites (CEOS) has established several official PICS for these purposes. Of these, Libya-4 is the most commonly used, due to its high uniformity and stability. The site was chosen as a large-area site for medium resolution sensors, and with high-resolution sensors now common, smaller sites are being identified. This work has identified an improved area of interest (AOI) within Libya-4 by using combined Landsat 8 and Sentinel 2 data. The Optimized Ground Target (OGT) was determined by calculating the coefficient of variation along with the use of a quasi-Newton optimization algorithm combined with the Basin–Hopping global optimization technique to constrain a search area small enough to perform a final brute-force refinement. The Coefficient of Variation CV of the proposed OGT is significantly lower than that in the original CEOS area, with differences between the CV of both zones in the order of 1% in the visible near-infrared (VNIR) bands. This new AOI has the potential to improve the cross-calibration between high-resolution sensors using the PICS methodology through an OGT with more homogeneous and stable characteristics.
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6
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Bowal K, Grančič P, Martin JW, Kraft M. Sphere Encapsulated Monte Carlo: Obtaining Minimum Energy Configurations of Large Aromatic Systems. J Phys Chem A 2019; 123:7303-7313. [PMID: 31339720 DOI: 10.1021/acs.jpca.9b04821] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a simple global optimization approach that is able to find minimum energy configurations of clusters containing aromatic molecules. The translational and rotational perturbations required in Monte Carlo-based methods often lead to unrealistic configurations within which two or more molecular rings intersect, causing many of the computational steps to be rejected and the optimization process to be inefficient. Here we develop a modification of the basin-hopping global optimization procedure tailored to tackle problems with intersecting molecular rings. Termed the Sphere Encapsulated Monte Carlo (SEMC) method, this method introduces sphere-based rearrangement and minimization steps at each iteration, and its performance is shown through the exploration of potential energy landscapes of polycyclic aromatic hydrocarbon (PAH) clusters, systems of interest in combustion and astrophysics research. The SEMC method provides clusters that are accurate to 5% mean difference of the minimum energy at a 10-fold speed up compared to previous work using advanced molecular dynamics simulations. Importantly, the SEMC method captures key structural characteristics and molecular size partitioning trends as measured by the molecular radial distances and coordination numbers. The advantages of the SEMC method are further highlighted in its application to previously unstudied heterogeneous PAH clusters.
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Affiliation(s)
- Kimberly Bowal
- Department of Chemical Engineering and Biotechnology , University of Cambridge , Cambridge CB3 0AS , U.K
| | - Peter Grančič
- Institute of Soil Research , University of Natural Resources and Life Sciences , Vienna A-1190 , Austria
| | - Jacob W Martin
- Department of Chemical Engineering and Biotechnology , University of Cambridge , Cambridge CB3 0AS , U.K.,Cambridge Centre for Advanced Research and Education in Singapore (CARES) , Singapore 138602 , Singapore
| | - Markus Kraft
- Department of Chemical Engineering and Biotechnology , University of Cambridge , Cambridge CB3 0AS , U.K.,Cambridge Centre for Advanced Research and Education in Singapore (CARES) , Singapore 138602 , Singapore.,School of Chemical and Biomedical Engineering , Nanyang Technological University , Singapore 637459 , Singapore
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7
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Neelamraju S, Oligschleger C, Schön JC. The threshold algorithm: Description of the methodology and new developments. J Chem Phys 2017; 147:152713. [DOI: 10.1063/1.4985912] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Sridhar Neelamraju
- National Centre for Biological Sciences, Tata Institute of Fundamental Research, GKVK Campus, Bengaluru 560065, India
| | - Christina Oligschleger
- University of Applied Sciences Bonn-Rhein-Sieg, Von-Liebig-Str. 20, D-53359 Rheinbach, Germany
| | - J. Christian Schön
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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8
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Abe Y, Suzudo T, Jitsukawa S, Tsuru T, Tsukada T. Effects of Carbon Impurity on Microstructural Evolution in Irradiated α-Iron. FUSION SCIENCE AND TECHNOLOGY 2017. [DOI: 10.13182/fst12-a14126] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yosuke Abe
- Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-Mura, Ibaraki 319-1106, Japan
| | - Tomoaki Suzudo
- Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-Mura, Ibaraki 319-1106, Japan
| | - Shiro Jitsukawa
- Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-Mura, Ibaraki 319-1106, Japan
| | - Tomohito Tsuru
- Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-Mura, Ibaraki 319-1106, Japan
| | - Takashi Tsukada
- Japan Atomic Energy Agency, 2-4 Shirakatashirane, Tokai-Mura, Ibaraki 319-1106, Japan
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9
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Abstract
Understanding protein-inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein-surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein-surface interactions and discuss the successes and limitations of current approaches.
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10
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Lin KH, Ju SP, Li JY, Chen HT. The CO oxidation mechanism on the W(111) surface and the W helical nanowire investigated by the density functional theory calculation. Phys Chem Chem Phys 2016; 18:3322-30. [PMID: 26750423 DOI: 10.1039/c5cp05681k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Two CO oxidation reactions (CO + O2 → CO2 + O and CO + O → CO2) were considered in the Eley-Rideal (ER) reaction mechanism. These oxidation processes on the W(111) surface and the W helical nanowire were investigated by the density functional theory (DFT) calculation. The stable adsorption sites of O2 and O as well as their adsorption energies were obtained first. In order to understand the catalytic properties of the W helical nanowire, the Fukui function and local density of state (LDOS) profiles were determined. The nudged elastic band (NEB) method was applied to locate transition states and minimum energy pathways (MEPs) of CO oxidation processes on the W helical nanowire and on the W(111) surface. In this study, we have demonstrated that the catalytic ability of the W helical nanowire is superior to that of the W(111) surface for CO oxidation.
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Affiliation(s)
- Ken-Huang Lin
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Shin-Pon Ju
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan. and Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung 807, Taiwan
| | - Jia-Yun Li
- Department of Mechanical and Electro-Mechanical Engineering, National Sun Yat-Sen University, Kaohsiung 804, Taiwan.
| | - Hsin-Tsung Chen
- Department of Chemistry, Chung Yuan Christian University, Chungli District, Taoyuan City 32023, Taiwan
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11
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Liu C, Pei Y, Sun H, Ma J. The Nucleation and Growth Mechanism of Thiolate-Protected Au Nanoclusters. J Am Chem Soc 2015; 137:15809-16. [DOI: 10.1021/jacs.5b09466] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Affiliation(s)
- Chunyan Liu
- Key
Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and
Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu Province 210093, People’s Republic of China
| | - Yong Pei
- Department
of Chemistry, Key Laboratory of Environmentally Friendly Chemistry
and Applications of MOE, Xiangtan University, Xiangtan, Hunan Province 411105, People’s Republic of China
| | - Hui Sun
- Key
Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and
Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu Province 210093, People’s Republic of China
| | - Jing Ma
- Key
Laboratory of Mesoscopic Chemistry of MOE, School of Chemistry and
Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing, Jiangsu Province 210093, People’s Republic of China
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12
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13
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Hanson-Heine MW, Besley NA. Spectroscopic and structural analysis of mixed carbon dioxide and fluorinated methane clusters. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.08.056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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14
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Shehu A. A Review of Evolutionary Algorithms for Computing Functional Conformations of Protein Molecules. METHODS IN PHARMACOLOGY AND TOXICOLOGY 2015. [DOI: 10.1007/7653_2015_47] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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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]
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16
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Qin Z, Cong R, Liu Z, Xie H, Tang Z, Fan H. An investigation into low-lying electronic states of HCS2 via threshold photoelectron imaging. J Chem Phys 2014; 140:214318. [DOI: 10.1063/1.4879808] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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17
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Kim Y, Choi S, Kim WY. Efficient Basin-Hopping Sampling of Reaction Intermediates through Molecular Fragmentation and Graph Theory. J Chem Theory Comput 2014; 10:2419-26. [DOI: 10.1021/ct500136x] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Yeonjoon Kim
- Department
of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | - Sunghwan Choi
- Department
of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
| | - Woo Youn Kim
- Department
of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
- KAIST
Institute for NanoCentury, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-701, Korea
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18
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19
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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]
Affiliation(s)
- Yi-Rong Liu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Hui Wen
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Teng Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Xiao-Xiao Lin
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Yan-Bo Gai
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Chang-Jin Hu
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
| | - Wei-Jun Zhang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
| | - Wei Huang
- Laboratory of Atmospheric Physico-Chemistry, Anhui Institute of Optics & Fine Mechanics, Chinese Academy of Sciences, 350 Shushan Lake Road, Hefei, Anhui 230031, China
- School of Environmental Science & Optoelectronic Technology, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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20
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Lin KH, Li JY, Lin JS, Ju SP, Lu JM, Hsieh JY. Mechanical properties and thermal stability of ultrathin tungsten nanowires. RSC Adv 2014. [DOI: 10.1039/c3ra46215c] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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21
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Yan LL, Liu YR, Huang T, Jiang S, Wen H, Gai YB, Zhang WJ, Huang W. Structure, stability, and electronic property of carbon-doped gold clusters AunC− (n = 1–10): A density functional theory study. J Chem Phys 2013; 139:244312. [DOI: 10.1063/1.4852179] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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22
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Olson BS, Shehu A. Rapid sampling of local minima in protein energy surface and effective reduction through a multi-objective filter. Proteome Sci 2013; 11:S12. [PMID: 24564970 PMCID: PMC3908317 DOI: 10.1186/1477-5956-11-s1-s12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Many problems in protein modeling require obtaining a discrete representation of the protein conformational space as an ensemble of conformations. In ab-initio structure prediction, in particular, where the goal is to predict the native structure of a protein chain given its amino-acid sequence, the ensemble needs to satisfy energetic constraints. Given the thermodynamic hypothesis, an effective ensemble contains low-energy conformations which are similar to the native structure. The high-dimensionality of the conformational space and the ruggedness of the underlying energy surface currently make it very difficult to obtain such an ensemble. Recent studies have proposed that Basin Hopping is a promising probabilistic search framework to obtain a discrete representation of the protein energy surface in terms of local minima. Basin Hopping performs a series of structural perturbations followed by energy minimizations with the goal of hopping between nearby energy minima. This approach has been shown to be effective in obtaining conformations near the native structure for small systems. Recent work by us has extended this framework to larger systems through employment of the molecular fragment replacement technique, resulting in rapid sampling of large ensembles. METHODS This paper investigates the algorithmic components in Basin Hopping to both understand and control their effect on the sampling of near-native minima. Realizing that such an ensemble is reduced before further refinement in full ab-initio protocols, we take an additional step and analyze the quality of the ensemble retained by ensemble reduction techniques. We propose a novel multi-objective technique based on the Pareto front to filter the ensemble of sampled local minima. RESULTS AND CONCLUSIONS We show that controlling the magnitude of the perturbation allows directly controlling the distance between consecutively-sampled local minima and, in turn, steering the exploration towards conformations near the native structure. For the minimization step, we show that the addition of Metropolis Monte Carlo-based minimization is no more effective than a simple greedy search. Finally, we show that the size of the ensemble of sampled local minima can be effectively and efficiently reduced by a multi-objective filter to obtain a simpler representation of the probed energy surface.
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Affiliation(s)
- Brian S Olson
- Department of Computer Science, George Mason University, 4400 University Dr., Fairfax, VA, 22030, USA
| | - Amarda Shehu
- Department of Computer Science, George Mason University, 4400 University Dr., Fairfax, VA, 22030, USA
- Department of Bioengineering, George Mason University, 4400 University Dr., Fairfax, VA, 22030, USA
- School of Systems Biology, George Mason University, 10900 University Blvd., Manassas, VA, 20110, USA
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23
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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]
Affiliation(s)
- Gustavo G. Rondina
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, 13560-970, São
Carlos, SP, Brazil
| | - Juarez L. F. Da Silva
- Instituto de Química de São Carlos, Universidade de São Paulo, Caixa Postal 780, 13560-970, São
Carlos, SP, Brazil
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24
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Affiliation(s)
- Hainam Do
- School of Chemistry, University of Nottingham, University Park, Nottingham,
NG7 2RD, U.K
| | - Nicholas A. Besley
- School of Chemistry, University of Nottingham, University Park, Nottingham,
NG7 2RD, U.K
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25
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Oakley MT, Johnston RL, Wales DJ. Symmetrisation schemes for global optimisation of atomic clusters. Phys Chem Chem Phys 2013; 15:3965-76. [DOI: 10.1039/c3cp44332a] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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26
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Do H, Besley NA. Proton transfer or hemibonding? The structure and stability of radical cation clusters. Phys Chem Chem Phys 2013; 15:16214-9. [DOI: 10.1039/c3cp52922c] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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27
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Basin Hopping as a General and Versatile Optimization Framework for the Characterization of Biological Macromolecules. ACTA ACUST UNITED AC 2012. [DOI: 10.1155/2012/674832] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Since its introduction, the basin hopping (BH) framework has proven useful for hard nonlinear optimization problems with multiple variables and modalities. Applications span a wide range, from packing problems in geometry to characterization of molecular states in statistical physics. BH is seeing a reemergence in computational structural biology due to its ability to obtain a coarse-grained representation of
the protein energy surface in terms of local minima. In this paper, we show that the BH framework is general and versatile, allowing to address problems related to the characterization of protein structure, assembly, and motion due to its fundamental ability to sample minima in a high-dimensional variable space. We show how specific implementations of the main components in BH yield algorithmic realizations that attain state-of-the-art results in the context of ab initio protein structure prediction and rigid protein-protein docking. We also show that BH can map intermediate minima related with motions connecting diverse stable functionally relevant states in a protein molecule,
thus serving as a first step towards the characterization of transition trajectories connecting these states.
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28
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Do H, Besley NA. Structural optimization of molecular clusters with density functional theory combined with basin hopping. J Chem Phys 2012; 137:134106. [DOI: 10.1063/1.4755994] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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29
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Jansen M, Doll K, Schön JC. Addressing chemical diversity by employing the energy landscape concept. Acta Crystallogr A 2010; 66:518-34. [DOI: 10.1107/s0108767310026371] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2009] [Accepted: 07/04/2010] [Indexed: 11/11/2022] Open
Affiliation(s)
- Martin Jansen
- Max Planck Institute for Solid State Research, Heisenbergstrasse 1, D-70569 Stuttgart, Germany
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Pentin IV, Schön JC, Jansen M. Ab initio prediction of low-temperature phase diagrams in the Al–Ga–In–As system, MAs–M′As (M, M′ = Al, Ga or In) and AlAs–GaAs–InAs, via the global study of energy landscapes. Phys Chem Chem Phys 2010; 12:8491-9. [DOI: 10.1039/c004040c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Cheng L, Feng Y, Yang J, Yang J. Funnel hopping: Searching the cluster potential energy surface over the funnels. J Chem Phys 2009; 130:214112. [DOI: 10.1063/1.3152121] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rossi G, Ferrando R. Searching for low-energy structures of nanoparticles: a comparison of different methods and algorithms. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2009; 21:084208. [PMID: 21817360 DOI: 10.1088/0953-8984/21/8/084208] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Nanoparticles can have unusual, low symmetry or non-crystalline shapes. Since structure determines nanoparticle physical and chemical properties, many efforts have been devoted to predict what are the most stable structural motifs depending on cluster size and composition. The global optimization of the 3N-dimensional potential energy surface of a nanocluster is nevertheless a very difficult computational problem. Here we depict the scenery of the global optimization strategies applied to the study of nanoclusters, focusing on genetic and Basin-hopping approaches. Moreover, several strategies to improve Basin-hopping efficiency are discussed and compared through the optimization of test-systems with different size and composition.
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Affiliation(s)
- G Rossi
- Dipartimento di Fisica, Università di Genova and CNR/INFM, Via Dodecaneso, 33, 16146 Genova, Italy
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