Searching for transition paths in multidimensional space with a fixed repulsive bias potential

Trushin, Oleg; Salo, Petri; Ala-Nissilä, Tapio; Ying, S. C.

doi:10.1103/physrevb.69.033405

Cited by 11 publications

(14 citation statements)

References 31 publications

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“…For example, with the drag method we were able to achieve speed-up of atleast an order of magnitude in the cpu time for the calculation of the energy barriers, as compared to one in which we applied the spherical repulsion methode [27] to obtain the final states for a given initial state followed by application of NEB method for the calculation of the activation energies.…”

Section: B Examination Of the Collected Databasementioning

confidence: 99%

Self-learning kinetic Monte Carlo method: Application to Cu(111)

Trushin¹,

et al. 2005

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We present a novel way of performing kinetic Monte Carlo simulations which does not require an a priori list of diffusion processes and their associated energetics and reaction rates. Rather, at any time during the simulation, energetics for all possible (single or multi-atom) processes, within a specific interaction range, are either computed accurately using a saddle point search procedure, or retrieved from a database in which previously encountered processes are stored. This self-learning procedure enhances the speed of the simulations along with a substantial gain in reliability because of the inclusion of many-particle processes. Accompanying results from the application of the method to the case of two-dimensional Cu adatom-cluster diffusion and coalescence on Cu (111) with detailed statistics of involved atomistic processes and contributing diffusion coefficients attest to the suitability of the method for the purpose.

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Section: B Examination Of the Collected Databasementioning

confidence: 99%

Self-learning kinetic Monte Carlo method: Application to Cu(111)

Trushin¹,

et al. 2005

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“…23 On the activation stage we also apply MDC but now the system is under the influence of the repulsive bias potential ͑RBP͒. 24,25 In some cases, before turning on the RBP, we increase the chance of getting certain kind of defects by perturbing some selected atoms slightly to a direction which is likely to initiate a nucleation process. After switching off the RBP we further relax the final state with MDC.…”

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confidence: 99%

“…We perform the energy minimizations with the Molecular Dynamics Cooling (MDC) technique 23 . On the activation stage we also apply MDC but now the system is under the influence of the repulsive bias potential (RBP) 24,25 . In some cases, before turning on the RBP, we increase the chance of getting certain kind of defects by perturbing some selected atoms slightly to a direction which is likely to initiate a nucleation process.…”

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confidence: 99%

Stress release mechanisms for Cu on Pd(111) in the submonolayer and monolayer regimes

et al. 2010

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We study the strain relaxation mechanisms of Cu on Pd͑111͒ up to the monolayer regime using two different computational methodologies, basin-hopping global optimization and energy minimization with a repulsive bias potential. Our numerical results are consistent with experimentally observed layer-by-layer growth mode. However, we find that the structure of the Cu layer is not fully pseudomorphic even at low coverages. Instead, the Cu adsorbates forms fcc and hcp stacking domains, separated by partial misfit dislocations. We also estimate the minimum energy path and energy barriers for transitions from the ideal epitaxial state to the fcc-hcp domain pattern. Introduction. Metallic surfaces and nanostructures are essential systems for heterogeneous catalysis. Combination of two metals can lead to significant improvements in the variability and frequency of the reactions catalyzed. To prepare controlled nanostructures, it is crucial to understand the growth and stability of heteroepitaxial metal systems, in particular for close-packed surfaces. On fcc͑111͒ it has been found that to release the stress, the overlayer can adopt several alternative strategies which lead to a structure of domains separated by partial misfit dislocations.1-7 The domains correspond to the two favorable sites, fcc and hcp. This behavior is expected to be ubiquitous and should not depend strongly on the interaction potentials or the overlayer-substrate mismatch.

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“…We have recently introduced [10] a particularly simple but efficient method called the repulsive bias potential (RBP) method for transition path searching. In the RBP method, the system is placed in a fixed external repulsive bias potential which makes the initial state unstable but keeps the other nearby minima unaffected:…”

Section: Methods For Generating Transition Paths To Isolated Dislocationsmentioning

confidence: 99%

Atomistic studies of strain relaxation in heteroepitaxial systems

Trushin¹,

Jalkanen²,

Granato³

et al. 2009

J. Phys.: Condens. Matter

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We present a review of recent theoretical studies of different atomistic mechanisms of strain relaxation in heteroepitaxial systems. We explore these systems in two and three dimensions using different semi-empirical interatomic potentials of Lennard-Jones and many-body embedded atom model type. In all cases we use a universal molecular static method for generating minimum energy paths for transitions from the coherent epitaxial (defect free) state to the state containing an isolated defect (localized or extended). This is followed by a systematic search for the minimum energy configuration as well as self-organization in the case of a periodic array of islands. In this way we are able to understand many general features of the atomic mechanisms and energetics of strain relaxation in these systems. Finally, for the special case of Pd/Cu(100) and Cu/Pd(100) heteroepitaxy we also use conventional molecular dynamics simulation techniques to compare the compressively and tensilely strained cases. The results for this case are in good agreement with the existing experimental data.

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Searching for transition paths in multidimensional space with a fixed repulsive bias potential

Cited by 11 publications

References 31 publications

Self-learning kinetic Monte Carlo method: Application to Cu(111)

Self-learning kinetic Monte Carlo method: Application to Cu(111)

Stress release mechanisms for Cu on Pd(111) in the submonolayer and monolayer regimes

Atomistic studies of strain relaxation in heteroepitaxial systems

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