Distributional fixed point equations for island nucleation in one dimension: a retrospective approach for capture zone scaling

The distributions of inter-island gaps and captures zones for islands nucleated on a one-dimensional substrate during submonolayer deposition are considered using a novel retrospective view. This provides an alternative perspective on why scaling occurs in this continuously evolving system. Distributional fixed point equations for the gaps are derived both with and without a mean field approximation for nearest neighbour gap size correlation. Solutions to the equations show that correct consideration of fragmentation bias justifies the mean field approach which can be extended to provide closed-from equations for the capture zones. Our results compare favourably to Monte Carlo data for both point and extended islands using a range of critical island size $i=0,1,2,3$. We also find satisfactory agreement with theoretical models based on more traditional fragmentation theory approaches.Comment: 9 pages, 7 figures and 1 tabl

Asymptotics of capture zone distributions in a fragmentation-based model of submonolayer deposition

We consider the asymptotics of the distribution of the capture zones associated with the islands nucleated during submonolayer deposition onto a one-dimensional substrate. We use a convolution of the distribution of inter-island gaps, the asymptotics of which is known for a class of nucleation models, to derive the asymptotics for the capture zones. The results are in broad agreement with published Monte Carlo simulation data (O'Neill et al., 2012) [13]

Capture-zone distribution in one-dimensional sub-monolayer film growth: a fragmentation theory approach

The distribution of capture zones formed during the nucleation and growth of point islands on a one-dimensional substrate during monomer deposition is considered for general critical island size $i$. A fragmentation theory approach yields the small and (for $i=0$) large size asymptotics for the capture zone distribution (CZD) under the assumption of no neighbour-neighbour gap size correlation. These CZD asymptotic forms are different to those of the Generalised Wigner Surmise which has recently been proposed for island nucleation and growth models, and we discuss the reasons for the discrepancies.Comment: 12 pages, uses equation.st

Probing the sudlow binding site with warfarin : how does gold nanocluster growth alter human serum albumin?

The search for new fluorescent molecules is vital to the advancement of molecular imaging and sensing for the benefit of medical and biological studies. One such class of new fluorescent molecule is fluorescent gold nanoclusters encapsulated in Human Serum Albumin (HSA-AuNC). In order to use this new fluorescent molecule as a sensor or fluorescent marker in biological imaging both in vitro and in vivo it is important to understand whether/how the proteins function is changed by the synthesis and presence of the gold nanoclusters inside the protein. Natural HSA acts as the main drug carrier in the blood stream, carrying a multitude of molecules in two major binding sites (Sudlow I and II). To test the effects of gold on the ability of HSA to act as a drug carrier we employed warfarin, an anticoagulant drug, as a fluorescent probe to detect changes between natural HSA and HSA-AuNCs. AuNCs are found to inhibit the take up of warfarin by HSA. Evidence for this is found from fluorescence spectral and lifetime measurements. Interestingly, the presence of warfarin bound to HSA also inhibits the formation of gold nanoclusters within protein. This research provides valuable insight into how protein function can change upon synthesis of AuNCs and how that will affect their use as a fluorescent probe

Locating the nucleation sites for protein encapsulated gold nanoclusters : a molecular dynamics and fluorescence study

Fluorescent gold nanoclusters encapsulated by proteins have attracted considerable attention in recent years for their unique properties as new fluorescence probes for biological sensing and imaging. However, fundamental questions, such as the nucleation sites of gold nanoclusters within proteins and the fluorescence mechanism remain unsolved. Here we present a study of the location of gold nanoclusters within bovine serum albumin (BSA) combining both fully atomistic molecular dynamic (MD) simulations and fluorescence spectroscopic studies. The MD simulations show gold clusters growing close to a number of cysteine sites across all three domains of BSA, although just two major sites in domains IIB and IA were found to accommodate large clusters comprising more than 12 atoms. The dependence of the fluorescence on pH is found to be compatible with possible nucleation sites in domains IIB and IA. Furthermore, the energy transfer between tryptophan and gold nanoclusters reveals a separation of 29.7 Å, further indicating that gold nanoclusters were most likely located in the major nucleation site in domain IIB. The disclosure of the precise location of the gold nanoclusters and their surrounding amino acid residues should help better understanding of their fluorescence mechanism and aid their optimization as fluorescent nanoprobes

Aggregation of model asphaltenes – a molecular dynamics study

Natural asphaltenes are defined as polyaromatic compounds whose chemical composition and structure is dependent on its geological origin and production history, hence are regarded as complex molecules with aromatic cores and aliphatic tails that occur in the heaviest fraction of crude oil. The aggregation of asphaltenes presents a range of technical challenges to the production and processing of oil. In this work we study the behaviour of the model asphaltene-like molecule hexa-tert-butylhexa-peri-hexabenzocoronene (HTBHBC) using molecular dynamics simulation. It was found that the regular arrangement of the tert-butyl side chains prevents the formation of strongly-bound dimers by severely restricting the configurational space of the aggregation pathway. In contrast, a modified molecule with only 3 side chains is readily able to form dimers. This work therefore confirms the influence of the molecular structure of polyaromatic compounds on their aggregation mechanism, and reveals the unexpected design rules required for model systems that can mimic the behavior of asphaltenes

Surface and interstitial Ti diffusion at the rutile TiO2(110) surface

Diffusion of Ti through the TiO2 (110) rutile surface plays a key role in the growth and reactivity of TiO2. To understand the fundamental aspects of this important process, we present an analysis of the diffusion of Ti adspecies at the stoichiometric TiO2(110) surface using complementary computational methodologies of density functional theory corrected for on-site Coulomb interactions (DFT+U) and a charge equilibration (QEq) atomistic potential to identify minimum energy pathways. We find that diffusion of Ti from the surface to subsurface (and vice versa) follows an intersticialcy exchange mechanism, involving exchange of surface Ti with the 6-fold coordinated Ti below the bridging oxygen rows. Diffusion in the subsurface between layers also follows an interstitialcy mechanism. The diffusion of Ti is discussed in light of continued attempts to understand the re-oxidation of non-stoichiometric TiO2(110) surfaces

Rotons and Quantum Evaporation from Superfluid 4He

The probability of evaporation induced by $R^+$ and $R^-$ rotons at the surface of superfluid helium is calculated using time dependent density functional theory. We consider excitation energies and incident angles such that phonons do not take part in the scattering process. We predict sizable evaporation rates, which originate entirely from quantum effects. Results for the atomic reflectivity and for the probability of the roton change-mode reflection are also presented.Comment: 11 pages, REVTEX, 3 figures available upon request or at http://anubis.science.unitn.it/~dalfovo/papers/papers.htm

Magic Islands and Barriers to Attachment: A Si/Si(111)7x7 Growth Model

Surface reconstructions can drastically modify growth kinetics during initial stages of epitaxial growth as well as during the process of surface equilibration after termination of growth. We investigate the effect of activation barriers hindering attachment of material to existing islands on the density and size distribution of islands in a model of homoepitaxial growth on Si(111)7x7 reconstructed surface. An unusual distribution of island sizes peaked around "magic" sizes and a steep dependence of the island density on the growth rate are observed. "Magic" islands (of a different shape as compared to those obtained during growth) are observed also during surface equilibration.Comment: 4 pages including 5 figures, REVTeX, submitted to Physical Review