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Kim, S. H.; Lee, K. W.; Jang, Jin; Lee, Cheol Eui; Choi, Jae Young; Lee, K.-S.; Kim, J.

doi:10.1103/physrevb.72.214107

Cited by 19 publications

(27 citation statements)

References 26 publications

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“…We note that the degrees of freedom of the system S n in three dimensions increases as 2n which corresponds to the number of backbone angles of a protein with n residues. Table 1 shows the results of the lowest energy of model1 in two dimensions, along with the values reported in the literature by nPERMis, 4 ACMC, 5 our previous work, 6 and STMD 7 for comparison. All methods except nPERMis report identical results for S 13 , S 21 , and S 34 .…”

Section: Resultsmentioning

confidence: 99%

“…Although putative groundstate conformations have been reported, they are continually being updated, [4][5][6][7][8][9] and thus it is not clear if they correspond to true ground-state conformations.…”

Section: Introductionmentioning

confidence: 99%

“…6, a global optimization method called conformational space annealing (CSA) [10][11][12] is applied to find ground-state conformations of protein AB models. At that time, optimization by CSA was terminated when a new structure was obtained with lower energy than reported in the literature.…”

Section: Introductionmentioning

confidence: 99%

“…A distinguished point from ref. 6 is that a "shift operator" is introduced to accelerate the convergence. It effectively reduces the search space, and new low energy conformations are reported for four separate cases.…”

Section: Introductionmentioning

confidence: 99%

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Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing

et al. 2008

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Abstract:The global structural optimization is carried out for off-lattice protein AB models in two and three dimensions by conformational space annealing. The models consist of hydrophobic and hydrophilic monomers in Fibonacci sequences. To accelerate the convergence, we have introduced a shift operator in the internal coordinate system, and effectively reduced the search space by forming a quotient space. With this, we significantly improve our previous results on AB models, and provide new low energy conformations. This work provides insights on exploring complicated energy landscapes by exploiting the advantages and limitations of CSA.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing

et al. 2008

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“…Relevant work has been published by Kim and coworkers, who investigated the proton ion beam irradiation effects on monoclinic TlH 2 PO 4 (crystal structure similar to gadolinite) [45]. The polycrystalline sample was irradiated by a 1 MeV proton ion beam to a dose of 10 15 ions/cm 2 .…”

Section: Discussionmentioning

confidence: 99%

Electrical properties of annealed, fully metamict REE2Fe2+Be2Si2O10

Malczewski

Molak

2011

Journal of Nuclear Materials

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Size‐guided multi‐seed heuristic method for geometry optimization of clusters: Application to benzene clusters

Takeuchi

2018

J Comput Chem

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Since searching for the global minimum on the potential energy surface of a cluster is very difficult, many geometry optimization methods have been proposed, in which initial geometries are randomly generated and subsequently improved with different algorithms. In this study, a size-guided multi-seed heuristic method is developed and applied to benzene clusters. It produces initial configurations of the cluster with n molecules from the lowest-energy configurations of the cluster with n - 1 molecules (seeds). The initial geometries are further optimized with the geometrical perturbations previously used for molecular clusters. These steps are repeated until the size n satisfies a predefined one. The method locates putative global minima of benzene clusters with up to 65 molecules. The performance of the method is discussed using the computational cost, rates to locate the global minima, and energies of initial geometries. © 2018 Wiley Periodicals, Inc.

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Proton-beam irradiation effect inTlH2PO4

Cited by 19 publications

References 26 publications

Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing

Re‐examination of structure optimization of off‐lattice protein AB models by conformational space annealing

Electrical properties of annealed, fully metamict REE2Fe2+Be2Si2O10

Size‐guided multi‐seed heuristic method for geometry optimization of clusters: Application to benzene clusters

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