Publications by authors named "Risto M Nieminen"

Electronic excitations can be efficiently analyzed in terms of the underlying Kohn-Sham (KS) electron-hole transitions. While such a decomposition is readily available in the linear-response time-dependent density-functional theory (TDDFT) approaches based on the Casida equations, a comparable analysis is less commonly conducted within the real-time-propagation TDDFT (RT-TDDFT). To improve this situation, we present here an implementation of a KS decomposition tool within the local-basis-set RT-TDDFT code in the free GPAW package.

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We propose a computational model for noncontact atomic force microscopy (AFM) in which the atomic force between the cantilever tip and the surface is calculated using a molecular dynamics method, and the macroscopic motion of the cantilever is modeled by an oscillating spring. The movement of atoms in the tip and surface is connected with the oscillating spring using a recently developed coupling method. In this computational model, the oscillation energy is dissipated, as observed in AFM experiments.

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Quantum aspects, such as electron tunneling between closely separated metallic nanoparticles, are crucial for understanding the plasmonic response of nanoscale systems. We explore quantum effects on the response of the conductively coupled metallic nanoparticle dimer. This is realized by stretching a nanorod, which leads to the formation of a narrowing atomic contact between the two nanorod ends.

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We present an approach for generating local numerical basis sets of improving accuracy for first-principles nanoplasmonics simulations within time-dependent density functional theory. The method is demonstrated for copper, silver, and gold nanoparticles that are of experimental interest but computationally demanding due to the semi-core d-electrons that affect their plasmonic response. The basis sets are constructed by augmenting numerical atomic orbital basis sets by truncated Gaussian-type orbitals generated by the completeness-optimization scheme, which is applied to the photoabsorption spectra of homoatomic metal atom dimers.

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The presence of plasmonic material influences the optical properties of nearby molecules in untrivial ways due to the dynamical plasmon-molecule coupling. We combine quantum and classical calculation schemes to study this phenomenon in a hybrid system that consists of a Na(2) molecule located in the gap between two Au/Ag nanoparticles. The molecule is treated quantum-mechanically with time-dependent density-functional theory, and the nanoparticles with quasistatic classical electrodynamics.

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Encapsulation of coronene inside single-walled carbon nanotubes (SWNTs) was studied under various conditions. Under high vacuum, two main types of molecular encapsulation were observed by using transmission electron microscopy: coronene dimers and molecular stacking columns perpendicular or tilted (45-60°) with regard to the axis of the SWNTs. A relatively small number of short nanoribbons or polymerized coronene molecular chains were observed.

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Effective and fast convergence toward an equilibrium state for long-chain polymer melts is realized by a hybrid method coupling molecular dynamics and the elastic continuum. The required simulation time to achieve the equilibrium state is reduced compared with conventional equilibration methods. The polymers move on a wide range phase space due to large-scale fluctuation generated by the elastic continuum.

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A novel material, graphene nanoribbons encapsulated in single-walled carbon nanotubes (GNR@SWNT), was synthesized using confined polymerization and fusion of polycyclic aromatic hydrocarbon (PAH) molecules. Formation of the GNR is possible due to confinement effects provided by the one-dimensional space inside nanotubes, which helps to align coronene or perylene molecules edge to edge to achieve dimerization and oligomerization of the molecules into long nanoribbons. Almost 100% filling of SWNT with GNR is achieved while nanoribbon length is limited only by the length of the encapsulating nanotube.

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Electron-beam-mediated postsynthesis doping of boron-nitride nanostructures with carbon atoms [Nature (London) 464, 571 (2010); J. Am. Chem.

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Reconstructed point defects in graphene are created by electron irradiation and annealing. By applying electron microscopy and density functional theory, it is shown that the strain field around these defects reaches far into the unperturbed hexagonal network and that metal atoms have a high affinity to the nonperfect and strained regions of graphene. Metal atoms are attracted by reconstructed defects and bonded with energies of about 2 eV.

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We present a comparative study of oxygen vacancies in In2O3, SnO2, and ZnO based on the hybrid-functional method within the density-functional theory (DFT). For In2O3 and SnO2, our results provide strong evidence of shallow donor states at oxygen vacancies. In comparison with the (semi)local exchange-correlation approximations in DFT, the hybrid-functional method strongly lowers the formation energy of the positive charge state and keeps that of the neutral state nearly intact.

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The electronic and magnetic structures of the double perovskite oxide Ba 2MnWO6 (BMW) were determined by employing the density functional theory within the generalized gradient approximation (GGA) + U approach. BMW is considered a prototype double perovskite due to its high degree of B-site ordering and is a good case study for making a comparison between computations and experiments. By adjusting the U-parameter, the electronic energy band structure and magnetic properties, which were consistent with the experimental results, were obtained.

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We study the spectral properties of two kinds of derivatives of the carbon fullerene C(60), small fullerenes and Si-heterofullerenes, by ab initio calculations. The principal method of study is the time-dependent density-functional theory in its full time-propagation form. C(20), C(28), C(32), C(36), and C(50), the most stable small fullerenes in the range of C(20)-C(50), are found to have characteristic features in their optical absorption spectra, originating from the geometry of the molecules in question.

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Optical absorption spectra have been calculated for a series of boron nitride fullerenelike cage structures BnNn of sizes n=12-36. The method used is a real-time, real-space implementation of the time-dependent density-functional theory, involving the full time propagation of the time-dependent Kohn-Sham equations. The spectra are found to be a possible tool for distinguishing between different boron nitride fullerene species and isomers.

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We report the results of a Born-Oppenheimer molecular dynamics study on an L-alanine amino acid in neutral aqueous solution. The whole system, the L-alanine zwitterion and 50 water molecules, was treated quantum mechanically. We found that the hydrophobic side chain (R = CH3) defines the trajectory path of the molecule.

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In this study we use ab initio molecular dynamics simulations to analyze the structure and dynamics of the oxygen ligand in models of the oxymyoglobin active site and its cobalt-substituted analog. Our calculations are performed for iron-porphyrin and cobalt-porphyrin complexes with imidazole and oxygen as axial ligands, and we investigate the effect of the distal histidine in the structure and dynamics of the metal-oxygen unit (MeO(2), Me = Fe, Co). We find that the interaction between the distal histidine and the oxygen ligand is stronger for the cobalt complex than for the iron one, consistent with the superoxide ion character of the bound O(2).

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Recent advances in dynamic force microscopy show that it is possible to measure the forces between atomically sharp tips and particular atomic positions on surfaces as a function of distance. However, on most ionic surfaces, the positive and negative ions can so far not be distinguished. In this paper, we use the CaF2(111) surface, where atomic resolution force microscopy has allowed identification of the positions of the Ca2+ and F- ions in the obtained images, to demonstrate that short-range interaction forces can be measured selectively above chemically identified surface sites.

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