Table of contents

The Second International Conference 'Dynamics of Systems on the Nanoscale' (DySoN 2012) took place in Saint Petersburg, Russia between 30 September and 4 October 2012. The venue was the Courtyard by Marriott St Petersburg Vasilievsky Hotel, 2nd line of Vasilievsky Island 61/30A, 199178. The conference was organized by the Frankfurt Institute for Advanced Studies – Goethe University, A F Ioffe Physical-Technical Institute and Saint Petersburg State Polytechnic University.

This DySoN conference has been built upon a series of International Symposia 'Atomic Cluster Collisions: structure and dynamics from the nuclear to the biological scale' (ISACC 2003, ISACC 2007, ISACC 2008, ISACC 2009 and ISACC 2011). During these meetings it has become clear that there is a need for an interdisciplinary conference covering a broader range of topics than just atomic cluster collisions, related to the Dynamics of Systems on a Nanoscale. Therefore, in 2010 it was decided to launch a new conference series under the title 'Dynamics of Systems on the Nanoscale'. The first DySoN conference took place at the National Research Council, Rome, Italy in 2010. The DySoN 2012 is the second conference in this series.

The DySoN 2012 Conference promoted the growth and exchange of interdisciplinary scientific information on the structure, formation and dynamics of animate and inanimate matter on the nanometer scale. There are many examples of complex many-body systems of micro- and nanometer scale size exhibiting unique features, properties and functions. These systems may have very different nature and origin, e.g. atomic and molecular clusters, nanoobjects, ensembles of nanoparticles, nanostructures, biomolecules, biomolecular and mesoscopic systems. A detailed understanding of the structure and dynamics of these systems on the nanometer scale is an important fundamental task, the solution of which is necessary in numerous applications of nano- and biotechnology, material science and medicine.

Although mesoscopic, nano- and biomolecular systems differ in their nature and origin, a number of fundamental problems are common to all of them: what are the underlying principles of self-organization and self-assembly of matter on the micro- and nanoscale? Are these principles classical or quantum? How does function emerge on the nano- and the mesoscale in systems of different origin? What criteria govern the stability of these systems? How do their properties change as a function of size and composition? How are their properties altered by their environment? Seeking answers to these questions is at the core of a new interdisciplinary field that lies at the intersection of physics, chemistry and biology, a field called Meso-Bio-Nano (MBN) Science.

Both experimental and theoretical aspects of the mentioned problems were discussed at the DySoN 2012 Conference. Particular attention was devoted to dynamical phenomena and many-body effects taking place in various MBN systems, which include problems of structure formation, fusion and fission, collision and fragmentation, collective electron excitations, reactivity, nanoscale phase transitions, nanoscale insights into biodamage, channeling phenomena and many more.

This volume is a collection of the contributions received from the participants of the DySoN 2012 Conference. It provides an overview of the topics, new results and ideas that have been discussed at the conference. I would like to thank all the authors of these proceedings, as well as all the participants of the conference for making it so successful.

The third DySoN Conference will be held in Edinburgh in May 2014.

A V Solov'yov Frankfurt Institute for Advanced Studies, Ruth-Moufang Str. 1, 60438, Frankfurt am Main, Germany On leave from A F Ioffe Physical-Technical Institute, Polytechnicheskaya 26, 194021, St. Petersburg, Russia E-mail: solovyov@fias.uni-frankfurt.de

The PDF contains further information about the conference.

All papers published in this volume of Journal of Physics: Conference Series have been peer reviewed through processes administered by the proceedings Editors. Reviews were conducted by expert referees to the professional and scientific standards expected of a proceedings journal published by IOP Publishing.

Quantum Confinement is in some sense a new subject. International meetings dedicated to Quantum Confinement have occurred only recently in Mexico City (the first in 2010 and the second, in September 2011). However, at least in principle, the subject has existed since a very long time. Surprisingly perhaps, it lay dormant for many years, for want of suitable experimental examples. However, when one looks carefully at its origin, it turns out to have a long and distinguished history. In fact, the problem of quantum confinement raises a number of very interesting issues concerning boundary conditions in elementary quantum mechanics and how they should be applied to real problems. Some of these issues were missed in the earliest papers, but are implicit in the structure of quantum mechanics, and lead to the notion of Confinement Resonances, the existence of which was predicted theoretically more than ten years ago. Although, for several reasons, these resonances remained elusive for a very long time, they have now been observed experimentally, which puts the whole subject in much better shape and, together with the advent of metallofullerenes, has contributed to its revival.

Theoretical studies have been carried out to investigate the unusual reactivity of Ag⁺₁₅ cations with oxygen. Our previous work has shown that the reactivity of free metal clusters with oxygen entails a spin excitation that causes reduced reactivity in clusters with filled electronic shells and large HOMO-LUMO gaps. Earlier experiments on Ag⁺₁₅ have shown that the cluster exhibits remarkable resistance to reactivity with oxygen despite having a valence electron count that is not expected to result in a filled electronic shell within the spherical jellium model. It is shown that Ag⁺₁₅, Ag₁₄, and Ag⁻₁₃ clusters with 14 valence electrons, all have oblate bilayer atomic structures that lead to a splitting of the superatomic D-shell in a manner analogous to crystal field splitting of d-states in transition metals. The importance of the oblate structure is demonstrated by showing a correlation between an oblate deformation coefficient and the HOMO-LUMO gap of the different structures of Ag⁺₁₅. The oblate deformation results in the splitting of the electronic subshells and leads to an unusually large HOMO-LUMO gap and the unusual resistance of the cationic species to oxidation.

The mechanism of CO oxidation by O₂ on Au atoms supported on the pristine and defected hexagonal boron nitride (h-BN) surface has been studied theoretically using density functional theory. Two possible routes for catalytic oxidation are considered. The first route consists in a preliminary dissociation of the adsorbed O₂ followed by consequential oxidation of a reactant molecule by atomic oxygen. Although the presence of h-BN surface can change the O₂ dissociation barrier, it remains relatively high. The second route is a direct oxidation reaction between the activated molecular oxygen and the reactant. We have found two different pathways for CO oxidation: a two-step pathway where two CO₂ molecules are formed independently, and a self-promotion pathway where oxidation of the first CO molecule is promoted by the second CO molecule. Interaction of Au with the defect-free and defected h-BN surface considerably affects the CO oxidation reaction pathways and barriers. Therefore, Au supported on the h-BN surface (pristine or defected) cannot be considered as pseudo-free atom and support effects have to be taken into account, even when the interaction of Au with the support is weak.

An apparatus has been developed for measuring catalytic activities of uni-atomic-composition bi-element clusters supported on a solid substrate. The cluster sample is prepared by irradiating a cluster-ion beam having the uni-atomic composition onto the substrate on a soft-landing condition in an ultra-high vacuum. The catalytic activity is measured by temperature-programmed desorption (TPD) mass analysis. Molecules at a density as low as <10³ cm⁻³ have been detected with an ultrahigh-sensitive TPD mass spectrometer consisting of a cylindrical electron gun, a quadrupole mass filter and a micro-channel-plate ion-detector. The high reproducibility has been achieved by careful calibration of the TPD mass spectrometer. As a benchmark example, thermal oxidation of CO catalysed on Pt₃₀ disks supported on a silicon surface was studied. The CO₂ products have been successfully observed at the Pt₃₀ density as low as 3 × 10¹² clusters in a circular area of 8 mm in diameter at the ramping rate of the sample temperature as low as 0.3 K s⁻¹.

Size selected metal oxide, sulfide and oxynitride clusters, soft-landed onto highly ordered pyrolytic graphite (HOPG) at room temperature, have been studied in this work. Based on their size and chemical compositions, the deposited clusters have exhibited various surface structures as illustrated by in situ Scanning Tunnelling Microscope (STM) and ex situ Atomic Force Microscope (AFM). In contrast to pure metal clusters, size selected metal compound clusters have shown different surface behaviours due to their different cluster-surface interactions.

One of the goals of nanotechnology is the development of controlled, reproducible, and industrially transposable nanostructured materials. In this context, controlling of the final architecture of such materials by tuneable parameters is one of the fundamental problems. Post-growth processes occurring in patterns grown on a surface were studied using a multi-purpose computer code MBN EXPLORER introduced in the present paper. The package allows to model molecular systems of varied level of complexity, and in the present paper was used, in particular, to study dynamics of silver nanofractal formation and fragmentation on graphite surface. We demonstrate that the detachment of particles from the fractal and their diffusion within the fractal and over the surface determines the shape of the islands remaining on a surface after the fractal fragmentation.

We report on collisions of highly charged Xe²⁰⁺ ions with weakly bound clusters of water molecules and water/adenine mixtures. Singly and doubly charged water clusters are observed in the size range of n=1 to 65 and n=49 to 61, respectively. In contrast to other comparable systems, the dominant monomer fragment (H₃O⁺) is formed with very low kinetic energy, hence indicating that it is formed by evaporation processes. Larger fragments are produced with larger kinetic energies due to charge-separating processes. Furthermore, water clusters are found to be protonated, only a very small amount of the non protonated dimer (H₂O)₂⁺ is observed. Excited mixed adenine/water clusters fragment by the loss of the surrounding water molecules, thus, adenine fragments are formed without water molecules attached. In addition, the adenine monomer is found to be partly protonated.

The model of water clusters formation has been developed for the direct simulation Monte Carlo method. The model describes hierarchy of reactions which lead to growth and decay of water clusters including initial processes of dimer formation by triple and binary collisions of water molecules. The algorithm takes into account internal state of clusters and energy exchange processes accompanying clusterization kinetics. The model was applied for the research of condensation process in the rarefied flows of water molecules typical for the inner atmospheres of comets.

Application of the jellium model for investigation of the electronic structure and photoionization of metal clusters and fullerenes is discussed. The valence electrons are considered either within the Hartree-Fock and the local density approximations. The random phase approximation is utilized to account for the many-electron correlations in the response of a system to an external field. It is shown that the photodetachment cross section and photoelectron angular distribution in metal cluster anions are described reasonably well within the jellium model. Its application to fullerenes requires the use of corrections for a better description of the ground state electron density.

We analyze electron emission from irradiated clusters by means of time-dependent density-functional theory (TDDFT) in real time. We focus on photo-electron spectra (PES) which deliver an invaluable tool to explore static and dynamical properties of irradiated species. We discuss, in particular, the role of resonances in the PES once the laser frequency is below the emission threshold which implies multiphoton processes. We show that the resonances in the electronic spectrum lead to the occurrence of several peaks in the PES and also strongly affect the standard scaling relations between ionization and the number of required photons for electronic emission.

We study collective electron excitations (also referred to as plasmons) in the C₆₀ fullerene in the processes of photoionization and electron inelastic scattering. To reveal the contribution of collective electron excitations, we utilize the plasmon resonance approximation. It is shown that within this framework the photoionization cross section is described as a sum of two contributions, which represent two coupled modes of the surface plasmon. The electron energy loss spectra of C₆₀ are described by three contributions, namely by the two modes of the surface plasmon and the volume plasmon. The results of calculations are in good agreement with experimental data on photoionization and electron inelastic scattering of C₆₀. We show that the collective excitations play a significant role in the ionization process and provide a dominant contribution to the spectra.

Differential and integral electron scattering cross section from some Ar clusters (dimer, trimer and tetramer) are calculated for incident energies ranging from 1 to 500 eV by using a screening corrected additivity rule based on an independent atom representation (IAM-SCAR). The possibility of using this method to derive electron scattering cross section in the liquid phase is discussed and electron scattering cross section data for Ar liquid are provided.

The vibrations of ordered counterions around right- and left-handed DNA double helix are studied. To determine the modes of DNA conformational vibrations the structure of the double helix with counterions is considered as ionic lattice (ion-phosphate lattice). Using the developed approach the frequencies and Raman intensities for right-handed B-form and left-handed Z-form of the double helix with Na⁺, K⁺, Rb⁺, Cs⁺, and Mg²⁺ counterions are calculated. The obtained frequencies of vibrations of internal structure elements of the double helix (<100 cm⁻¹) weakly depend on counterion type. In contrast, the vibrations of the ion-phosphate lattice are determined by counterion mass and charge. The frequencies of ion-phosphate vibrations of alkali metal counterions decrease from 180 to 100 cm⁻¹, while their Raman intensities increase as the counterion mass increases for the both B- and Z-DNA. In the case of Z-DNA new mode of ion-phosphate vibrations near 150 cm⁻¹ is found. This mode is characterized by vibrations of Mg²⁺ counterions with respect to the phosphates of different strands of the double helix. Our results explain the experimental Raman spectra of Z-DNA.

A multiscale approach to the physics of ion-beam cancer therapy, an approach suggested in order to understand the interplay of a large number of phenomena involved in radiation damage scenario occurring on a range of temporal, spatial, and energy scales, is being reviewed. The scenario is described along with a variety of effects that take place on different temporal, spatial, and energy scales and play major roles in the scenario of interaction of ions with tissue. The understanding of these effects leads to a quantitative assessment of relative biological effectiveness that relates the physical quantities, such as dose, to the biological values, such as the probability of cell survival.

In this work we review and further develop a semiempirical model recently proposed for the ion impact ionization of complex biological media. The model is based on the dielectric formalism, and makes use of a semiempirical parametrization of the optical energy-loss function of bioorganic compounds, allowing the calculation of single and total ionization cross sections and related quantities for condensed biological targets, such as liquid water, DNA and its components, proteins, lipids, carbohydrates or cell constituents. The model shows a very good agreement with experimental data for water, adenine and uracil, and allows the comparison of the ionization efficiency of different biological targets, and also the average kinetic energy of the ejected secondary electrons.

Ion beam therapy offers the possibility of excellent dose localization for treatment of malignant tumours, minimizing radiation damage in normal tissue, while maximizing cell killing within the tumour. However, as the underlying dependent physical, chemical and biological processes are too complex to treat them on a purely analytical level, most of our current and future understanding will rely on computer simulations, based on mathematical equations, algorithms and last, but not least, on the available atomic and molecular data. The viability of the simulated output and the success of any computer simulation will be determined by these data, which are treated as the input variables in each computer simulation performed. The radiation research community lacks a complete database for the cross sections of all the different processes involved in ion beam induced damage: ionization and excitation cross sections for ions with liquid water and biological molecules, all the possible electron – medium interactions, dielectric response data, electron attachment to biomolecules etc. In this paper we discuss current progress in the creation of such a database, outline the roadmap of the project and review plans for the exploitation of such a database in future simulations.

The phenomenon of channeling and the basic features of channeling radiation emission are introduced in a pedestrian way. Both, radiation spectra as well as dechanneling length measurements at electron beam energies between 195 and 855 MeV feature quantum state phenomena for the (110) planar potential of the silicon single crystals. Radiation from a crystalline undulator, produced at the Aarhus University (UAAR), has been investigated at the Mainz Microtron electron accelerator facility MAMI. The 4-period epitaxially grown strained layer Si_1−xGe_x undulator had a period length λ_u = 9.9 μm. At a beam energy of 375 MeV a broad excess yield around the theoretically expected photon energy of 0.132 MeV has been observed. Model calculations on the basis of synchrotron-like radiation emission suggest that evidence for a weak undulator effect has been observed.

Preliminary results of numerical simulations of electron and positron channeling and emission spectra are reported for straight, uniformly bent and periodically bent silicon crystal. The projectile trajectories are computed using the newly developed module [1] of the MBN Explorer package [2,3]. The electron and positron channeling along Si(110) and Si(111) crystallographic planes are studied for the projectile energies 195-855 MeV.

We report on the results of theoretical simulations of the electron channeling in a bent silicon crystal. The dynamics of ultra-relativistic electrons in the crystal is computed using the newly developed part [1] of the MBN Explorer package [2,3], which simulates classical trajectories of in a crystalline medium by integrating the relativistic equations of motion with account for the interaction between the projectile and crystal atoms. A Monte Carlo approach is employed to sample the incoming electrons and to account for thermal vibrations of the crystal atoms. The electron channeling along Si(110) crystallographic planes are studied for the projectile energies 195–855 MeV and different curvatures of the bent crystal.

Phase competition at TiNb-based Ni-free shape memory alloys caused by changes of alloying, temperature, external stresses is considered by analysis of experimental results on elastic modulus determination, X-ray diffraction, thermal analysis, mechanical tensile and indentation testing. Martensitic β↔α" transformation undergoes due to a reversible displacements of atoms at (002) plane of orthorhombic unit cell. The martensitic structure has high stability against thermal and mechanical cycling.

We present the results of molecular dynamics simulations of nanoindentation of a bimetallic nickel-titanium crystal in the austenitic (cubic) B2 phase. By considering three different types of indenters, namely of square, conical and spherical shapes, we observe the dependence of deformations of the crystalline structure on the type of the indenter. Various load-displacement curves are observed for different indenter types. We perform the molecular dynamics simulations of a full indentation cycle, which includes the loading and unloading stages. On the basis of such simulations we evaluate mechanical properties of the material, namely we calculate hardness and reduced Young's modulus. We observe variation of the calculated parameters depending on the indenter type and discuss the origin of occurring discrepancies.