Biomedical subjects

R M Nieminen

Publications and source records attributed to R M Nieminen.

15 recordsLinked to original sources

PubMed2005

Reactions and clustering of water with silica surface.

The interaction between silica surface and water is an important topic in geophysics and materials science, yet little is known about the reaction process. In this study we use first-principles molecular dynamics to simulate the hydrolysis process of silica surface using large cluster models. We find that a single water molecule is stable near the surface but can easily dissociate at three-coordinated silicon atom defect sites in the presence of other water molecules. These extra molecules provide a mechanism for hydrogen transfer from the original water molecule, hence catalyzing the reaction. The two-coordinated silicon atom is inert to the water molecule, and water clusters up to pentamer could be stably adsorbed at this site at room temperature.

Catalysis↗

PubMed2005

Density-functional study of oxygen adsorption on Mo(112).

Atomic oxygen adsorption on the Mo(112) surface has been investigated by means of first-principles total energy calculations. Among the variety of possible adsorption sites it was found that the bridge sites between two Mo atoms of the topmost row are favored for O adsorption at low and medium coverages. At about one monolayer coverage oxygen atoms prefer to adsorb in a quasithreefold hollow sites coordinated by two first-layer Mo atoms and one second layer atom. The stability of a structural model for an oxygen-induced p(2 x 3) reconstruction of the missing-row type is examined.

Journal Article↗

PubMed2004

Adsorption of acetic and trifluoroacetic acid on the TiO2(110) surface.

We use the first-principles static and dynamic simulations to study the adsorption of acetic (CH(3)COOH) and trifluoroacetic (CF(3)COOH) acid on the TiO(2)(110) surface. The most favorable adsorption for both molecules is a dissociative process, which results in the two oxygens of the carboxylate ion bonding to in-plane titanium atoms in the surface. The remaining proton then bonds to a bridging oxygen site, forming a hydroxyl group. We further show that, by comparing the calculated dipoles of the molecules on the surface, it is possible to understand the difference in contrast over the acetate and trifluoroacetate molecules in the atomically resolved noncontact atomic force microscopy images.

Journal Article↗

PubMed2004

Irradiation-induced magnetism in graphite: a density functional study.

Recent experiments indicate that proton irradiation triggers ferromagnetism in originally nonmagnetic graphite samples while He ion bombardment has a much smaller effect. To understand the origin of irradiation-induced magnetism, we have performed spin-polarized density functional theory calculations of the magnetic properties of the defects which are most likely to appear under irradiation vacancies and vacancy-hydrogen complexes. Both defects are magnetic, but as for the latter we find that H adsorption on one of the vacancy dangling bonds gives rise to a magnetic moment double that of the naked vacancy. We show that for small irradiation doses vacancy-hydrogen complexes result in a macroscopic magnetic signal which agrees well with the experimental values.

Journal Article↗

PubMed2004

Vortex clusters in quantum dots.

We study electronic structures of two-dimensional quantum dots in strong magnetic fields using mean-field density-functional theory and exact diagonalization. Our numerically accurate mean-field solutions show a reconstruction of the uniform-density electron droplet when the magnetic field flux quanta enter one by one the dot in stronger fields. These quanta correspond to repelling vortices forming polygonal clusters inside the dot. We find similar structures in the exact treatment of the problem by constructing a conditional operator for the analysis. We discuss important differences and limitations of the methods used.

Journal Article↗

PubMed2004

Interaction of silicon dangling bonds with insulating surfaces.

We use first principles density functional theory calculations to study the interaction of a model dangling bond silicon tip with the surfaces of CaF2, Al2O3, TiO2, and MgO. In each case the strongest interaction is with the highest anions in the surface. We show that this is due to the onset of chemical bonding with the surface anions, which can be controlled by an electric field across the system. Combining our results and previous studies on semiconductor surfaces suggests that using dangling bond Si tips can provide immediate identification of surface species in atomically resolved noncontact atomic force microscopy and facilitate selective measurements of short-range interactions with surface sites.

Journal Article↗

PubMed2003

Role of interactions in the far-infrared spectrum of a lateral quantum-dot molecule.

We study the effects of electron-electron correlations and confinement potential on the far-infrared spectrum of a lateral two-electron quantum-dot molecule by exact diagonalization. The calculated spectra directly reflect the lowered symmetry of the external confinement potential. Surprisingly, we find interactions to drive the spectrum towards that of a high-symmetry parabolic quantum-dot. We conclude that far-infrared spectroscopy is suitable for probing effective confinement of the electrons in a quantum-dot system, even if interaction effects cannot be resolved in a direct fashion.

Journal Article↗

PubMed2003

Relation between macroscopic and microscopic activation energies in nonequilibrium surface processing.

Realistic Monte Carlo simulations show that the apparent macroscopic activation energy is only partially explained by the expected expression for the average over the microscopic activation energies for surface processing. An additional term accounting for the existence of fluctuations in the fractions of particles has to be taken into account. In all cases considered, the additional term can be accurately estimated by a posteriori analysis of the temperature dependence of the surface densities. In addition, we demonstrate that the relative contribution of the different competing microscopic processes to the macroscopic activation energy can be accurately obtained during the simulations, allowing for the unambiguous identification of the particular surface species which effectively control the process. As an example of the nonequilibrium open interfaces to which the results apply, the case of wet chemical etching of crystalline silicon is considered. The results can be directly applied to surface growth.

Journal Article↗

PubMed2003

Magnetic properties and diffusion of adatoms on a graphene sheet.

We use ab initio methods to calculate the properties of adatom defects on a graphite surface. By applying a full spin-polarized description to the system we demonstrate that these defects have a magnetic moment of about 0.5micro(B) and also calculate its role in diffusion over the surface. The magnetic nature of these intrinsic carbon defects suggests that it is important to understand their role in the recently observed magnetism in pure carbon systems.

Journal Article↗

PubMed2002

Mechanism of interstitial oxygen diffusion in hafnia.

We have performed density functional calculations of oxygen incorporation and diffusion in monoclinic hafnia (HfO2) for a range of oxygen charge states. The calculations demonstrate that oxygen favors atomic incorporation and that O2- is the most stable species. We find that oxygen interstitials diffuse via exchange with lattice oxygen sites in hafnia, and that O- species have the smallest diffusion barrier.

Journal Article↗

PubMed2002

Two-electron quantum dot molecule: composite particles and the spin phase diagram.

We study a two-electron quantum dot molecule in a magnetic field by the direct diagonalization of the Hamiltonian matrix. The ground states of the molecule with the total spin S = 0 and S = 1 provide a possible realization for a qubit of a quantum computer. Switching between the states is best achieved by changing the magnetic field. Based on an analysis of the wave function, we show that the system consists of composite particles formed by an electron and flux quanta attached to it. This picture can also be used to explain the spin phase diagram.

Journal Article↗

PubMed2001

Neural-network analysis of the vibrational spectra of N-acetyl L-alanyl N'-methyl amide conformational states.

Density-functional theory (DFT) calculations utilizing the Becke 3LYP hybrid functional have been carried out for N-acetyl L-alanine N'-methylamide and examined with respect to the effect of water on the structure, the vibrational frequencies, vibrational absorption (VA), vibrational circular dichroism (VCD), Raman spectra, and Raman optical activity (ROA) intensities. The large changes due to hydration in the structures, and the relative stability of the conformer, reflected in the VA, VCD, Raman spectra, and ROA spectra observed experimentally, are reproduced by the DFT calculations. A neural network has been constructed for reproducing the inverse scattering data (we infer the structural coordinates from spectroscopic data) that the DFT method could produce. The purpose of the network has also been to generate the large set of conformational states associated with each set of spectroscopic data for a given conformer of the molecule by interpolation. Finally the neural network performances are used to monitor a sensitivity analysis of the importance of secondary structures and the influence of the solvent. The neural network is shown to be good in distinguishing the different conformers of the small alanine peptide, especially in the gas phase.

Alanine↗

PubMed2001

Do arsenic interstitials really exist in As-rich GaAs?

To investigate the lattice distortion caused by point defects in As-rich GaAs, we make use of a self-consistent-charge density-functional based tight-binding method. Both relevant defects, the As antisite and the As interstitial, cause significant lattice distortion. In contrast to As interstitials, isolated As antisites lead to lattice strain as well as displacement of nearest neighbor As lattice atoms into the <110> channels, in excellent agreement with experiments. Therefore, our result gives powerful evidence for As antisites being the dominating defect in as-grown As-rich GaAs.

Journal Article↗

PubMed2001

Aggregation kinetics of thermal double donors in silicon.

A general kinetic model based on accurate density-functional-theoretic total-energy calculations is introduced to describe the aggregation kinetics of oxygen-related thermal double donors (TDD's) in silicon. The calculated kinetics, which incorporates the reactions of associations, dissociations, and isomerizations of all relevant oxygen complexes, is in agreement with experimental annealing studies. The aggregation of TDD's takes place through parallel-consecutive reactions where both mobile oxygen dimers and fast migrating chainlike TDD's capture interstitial oxygen atoms.

Journal Article↗

PubMed2001

Effect of potential energy distribution on the melting of clusters.

We find that the potential energy distribution of atoms in clusters can consistently explain many important phenomena related to the phase changes of clusters, such as the nonmonotonic variation of melting temperature with size, the dependence of melting, boiling, and sublimation temperatures on the interatomic potentials, the existence of a surface-melted phase, and the absence of a premelting peak in heat capacity curves. We also find a new type of premelting mechanism in double icosahedral Pd19 clusters, where one of the two internal atoms escapes to the surface at the premelting temperature.

Journal Article↗