Abstract: The role of the Cu atoms sputtered from the cathode material in a cylindrical hollow cathode discharge (HCD) and the corresponding Cu+ ions are studied with a self-consistent model based on the principle of Monte Carlo (MC) and fluid simulations. In order to obtain a more realistic view of the discharge processes, this model is coupled with other submodels, which describe the behavior of electrons, fast Ar atoms, Ar+ ions, and Ar metastable atoms, also based on the principles of MC and fluid simulations. Typical results are, among others, the thermalization profile of the Cu atoms, the fast Cu atom, the thermal Cu atom and Cu+ ion fluxes and densities, and the energy distribution of the Cu+ ions. It was found that the contribution of the Ar+ ions to the sputtering was the most significant, followed by the fast Ar atoms. At the cathode bottom, there was no net sputtered flux but a net amount of redeposition. Throughout the discharge volume, at all the conditions investigated, the largest concentration of Cu atoms was found in the lower half of the HCD, close to the bottom. Penning ionization was found the main ionization mechanism for the Cu atoms. The ionization degree of copper atoms was found to be in the same order as for the argon atoms (10-4). (c) 2005 American Institute of Physics.

Abstract: The nucleation and growth of titanium dioxide (TiO2) and zinc oxide (ZnO) thin films on Fe2O3 (hematite), Al2O3 (á-alumina) and SiO2 (á-quartz) are studied by molecular dynamics simulations. The results show the formation of a strong interface region between the substrate and the film in the six systems studied here. A combination of polycrystalline and amorphous phases are observed in the TiO2 films grown on the three substrates. ZnO deposition on the Fe2O3 and Al2O3 crystals yields a monocrystalline film growth. The ZnO film deposited on the SiO2 crystal exhibits less crystallinity. The simulation results are compared with experimental results available in the literature.

Abstract: A pulsed microwave surfaguide discharge operating at 2.45 GHz was used for the conversion of molecular nitrogen into valuable compounds in several gas mixtures: N2 :O2 , N2 :O2 :CO2 and N2 :CO2 . The ro-vibrational absorption bands of the molecular species were monitored by a Fourier transform infrared apparatus in the post-discharge region in order to evaluate the relative number density of species, specifically NO production. The effects of specific energy input, pulse frequency, gas flow fraction, gas admixture and gas flow rate were studied for better understanding and optimization of the NO production yield and the corresponding energy cost (EC). By both the experiment and modelling, a highest NO yield is obtained at N2 :O2 (1:1) gas ratio in N2 :O2 mixture. The NO yield reveals a small growth followed by saturation when pulse repetition frequency increases. The energy efficiency start decreasing after the energy input reaches about 5 eV/molec, whereas the NO yield rises steadily at the same time. The lowest EC of about 8 MJ mol−1 corresponding to the yield and the energy efficiency of about 7% and 1% are found, respectively, in an optimum discharge condition in our case.

Abstract: Triple-modal imaging magnetic nanocapsules, encapsulating hydrophobic superparamagnetic iron oxide nanoparticles, are formulated and used to magnetically target solid tumours after intravenous administration in tumour-bearing mice. The engineered magnetic polymeric nanocapsules m-NCs are ~200 nm in size with negative Zeta potential and shown to be spherical in shape. The loading efficiency of superparamagnetic iron oxide nanoparticles in the m-NC was ~100%. Up to ~3- and ~2.2-fold increase in tumour uptake at 1 and 24 h was achieved, when a static magnetic field was applied to the tumour for 1 hour. m-NCs, with multiple imaging probes (e.g. indocyanine green, superparamagnetic iron oxide nanoparticles and indium-111), were capable of triple-modal imaging (fluorescence/magnetic resonance/nuclear imaging) in vivo. Using triple-modal imaging is to overcome the intrinsic limitations of single modality imaging and provides complementary information on the spatial distribution of the nanocarrier within the tumour. The significant findings of this study could open up new research perspectives in using novel magnetically-responsive nanomaterials in magnetic-drug targeting combined with multi-modal imaging.

Abstract: Simulations are carried out based on the dynamical mean-field theory (DMFT) in order to investigate the properties of correlated thin films for various values of the chemical potential, temperature, interaction strength, and applied transverse electric field. Application of a sufficiently strong field to a thin film at half filling leads to the appearance of conducting regions near the surfaces of the film, whereas in doped slabs the application of a field leads to a conductivity enhancement on one side of the film and a gradual transition to the insulating state on the opposite side. In addition to the inhomogeneous DMFT, a local density approximation (LDA) is considered in which the particle density n, quasiparticle residue Z, and spectral weight at the Fermi level A(ω=0) of each layer are approximated by a homogeneous bulk environment. A systematic comparison between the two approaches reveals that the less expensive LDA results are in good agreement with the DMFT approach, except close to the metal-to-insulator transition points and in the layers immediately at the film surfaces. LDA values for n are overall more reliable than those for Z and A(ω=0). The hysteretic behavior (memory effect) characteristic of the bulk doping driven Mott transition persists in the slab.

Abstract: When Fe(II) bearing groundwaters surface in streams, particulate authigenic Fe-rich material is produced by oxidation. Such freshly precipitated Fe minerals may be transported as suspended sediment and have a profound impact on the fate of trace metals and nutrients in rivers. The objective of this study was to monitor changes in mineralogy and composition of authigenic material from its source to streams of increasing order. Groundwaters, surface waters, and suspended sediment in streams of different order were sampled in the Kleine Nete catchment (Belgium), a lowland with Fe-rich groundwaters (3.5-53.8 mg Fe/L; pH 6.3-6.9). Fresh authigenic material (>0.45 mu m) was produced by oxidising filtered (<0.45 mu m) groundwater and surface water. This material contained, on average, 44% Fe, and smaller concentrations of C, P, and Ca. Iron EXAFS (Extended X-ray Absorption Fine Structure) spectroscopy showed that the Fe was present as poorly crystalline hydrous ferric oxides with a structure similar to that of ferrihydrite. The Fe concentration in the suspended sediment samples decreased to 36-40% (stream order 2), and further to 18-26% (stream order 4 and 5). Conversely, the concentrations of organic C, Ca, Si, and trace metals increased with increasing stream order, suggesting mixing of authigenic material with suspended sediment from a different source. The Fe speciation in the suspended sediment was similar to that in fresh authigenic material, but more Fe-Fe interactions were observed, i.e. it was increasingly hydrolysed, suggesting ageing reactions. The suspended sediment in the streams of order 4 and 5 is estimated to contain between 31% and 59% of authigenic material, but more data are needed to refine this estimate. The authigenic material is an important sink for P in these streams which may alleviate the eutrophication risk in this catchment. (C) 2013 Elsevier Ltd. All rights reserved.

Abstract: The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems.

Abstract: We present an approach to incorporate the effect of vibrational nonequilibrium in molecular dynamics (MD) simulations. A perturbed canonical ensemble, in which selected modes are excited to higher temperature while all others remain equilibrated at low temperature, is simulated by applying a specifically tailored bias potential. Our method can be readily applied to any (classical or quantum mechanical) MD setup at virtually no additional computational cost and allows the study of reactions of vibrationally excited molecules in nonequilibrium environments such as plasmas. In combination with enhanced sampling methods, the vibrational efficacy and mode selectivity of vibrationally stimulated reactions can then be quantified in terms of chemically relevant observables, such as reaction rates and apparent free energy barriers. We first validate our method for the prototypical hydrogen exchange reaction and then show how it can capture the effect of vibrational excitation on a symmetric SN2 reaction and radical addition on CO2.

Abstract: Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.

Abstract: Uniform-acceptance force-bias Monte Carlo (fbMC) methods have been shown to be a powerful technique to access longer timescales in atomistic simulations allowing, for example, phase transitions and growth. Recently, a new fbMC method, the time-stamped force-bias Monte Carlo (tfMC) method, was derived with inclusion of an estimated effective timescale; this timescale, however, does not seem able to explain some of the successes the method. In this contribution, we therefore explicitly quantify the effective timescale tfMC is able to access for a variety of systems, namely a simple single-particle, one-dimensional model system, the Lennard-Jones liquid, an adatom on the Cu(100) surface, a silicon crystal with point defects and a highly defected graphene sheet, in order to gain new insights into the mechanisms by which tfMC operates. It is found that considerable boosts, up to three orders of magnitude compared to molecular dynamics, can be achieved for solid state systems by lowering of the apparent activation barrier of occurring processes, while not requiring any system-specific input or modifications of the method. We furthermore address the pitfalls of using the method as a replacement or complement of molecular dynamics simulations, its ability to explicitly describe correct dynamics and reaction mechanisms, and the association of timescales to MC simulations in general.

Abstract: Atomistic simulations can in principle provide an unbiased description of all mechanisms, intermediates, and products of complex chemical processes. However, due to the severe time scale limitation of conventional simulation techniques, unrealistically high simulation temperatures are usually applied, which are a poor approximation of most practically relevant low-temperature applications. In this work, we demonstrate the direct observation at the atomic scale of the pyrolysis and oxidation of n-dodecane at temperatures as low as 700 K through the use of a novel simulation technique, collective variable-driven hyperdynamics (CVHD). A simulated timescale of up to 39 seconds is reached. Product compositions and dominant mechanisms are found to be strongly temperature-dependent, and are consistent with experiments and kinetic models. These simulations provide a first atomic-level look at the full dynamics of the complicated fuel combustion process at industrially relevant temperatures and time scales, unattainable by conventional molecular dynamics simulations.

Abstract: Optimization of catalytic materials for a given application is greatly constrained by linear scaling relations. Recently, however, it has been demonstrated that it is possible to reversibly modulate the chemisorption of molecules on nanomaterials by charging (i.e., injection or removal of electrons) and hence reversibly and selectively modify catalytic activity beyond structure−activity correlations. The fundamental physical relation between the properties of the material, the charging process, and the chemisorption energy, however, remains unclear, and a systematic exploration and optimization of charge-switchable sorbent materials is not yet possible. Using hybrid DFT calculations of CO2 chemisorption on hexagonal boron nitride nanosheets with several types of defects and dopants, we here reveal the existence of fundamental correlations between the electron affinity of a material and charge-induced chemisorption, show how defect engineering can be used to modulate the strength and efficiency of the adsorption process, and demonstrate that excess electrons stabilize many topological defects. We then show how these insights could be exploited in the development of new electrocatalytic materials and the synthesis of doped nanomaterials. Moreover, we demonstrate that calculated chemical properties of charged materials are highly sensitive to the employed computational methodology because of the self-interaction error, which underlines the theoretical challenge posed by such systems.

Abstract: We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.