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]

Multi-scale chemistry modelling for spacecraft atmospheric re-entry

We aim to develop a model capable of simulating the surface chemistry and material erosion involved when a re-entry vehicle descends through the atmosphere. Our starting point is to simulate the erosion of a fcc crystal slab due to cluster bombardment, using the model Lennard-Jones potential. From this, we plan to scale up towards Direct Monte Carlo Simulation approaches for the gas dynamics above the surface

Asymptotic Capture-Number and Island-Size Distributions for One-Dimensional Irreversible Submonolayer Growth

Using a set of evolution equations [J.G. Amar {\it et al}, Phys. Rev. Lett. {\bf 86}, 3092 (2001)] for the average gap-size between islands, we calculate analytically the asymptotic scaled capture-number distribution (CND) for one-dimensional irreversible submonolayer growth of point islands. The predicted asymptotic CND is in reasonably good agreement with kinetic Monte-Carlo (KMC) results and leads to a \textit{non-divergent asymptotic} scaled island-size distribution (ISD). We then show that a slight modification of our analytical form leads to an analytic expression for the asymptotic CND and a resulting asymptotic ISD which are in excellent agreement with KMC simulations. We also show that in the asymptotic limit the self-averaging property of the capture zones holds exactly while the asymptotic scaled gap distribution is equal to the scaled CND.Comment: 4 pages, 1 figure, submitted to Phys. Rev.

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

Antibody-protein binding and conformational changes : identifying allosteric signalling pathways to engineer a better effector response

Numerous monoclonal antibodies have been developed successfully for the treatment of various diseases. Nevertheless, the development of biotherapeutic antibodies is complex, expensive, and time-consuming, and to facilitate this process, careful structural analysis beyond the antibody binding site is required to develop a more efficacious antibody. In this work, we focused on protein antigens, since they induce the largest antibody changes, and provide interesting cases to compare and contrast. The structures of 15 anti-protein antibodies were analysed to compare the antigen-bound/unbound forms. Surprisingly, three different classes of binding-induced changes were identified. In class (B1), the antigen binding fragment distorted significantly, and we found changes in the loop region of the heavy chain’s constant domain; this corresponds well with expected allosteric movements. In class (B2), we found changes in the same loop region without the overall distortion. In class (B3), these changes did not present, and only local changes at the complementarity determining regions were found. Consequently, structural analysis of antibodies is crucial for therapeutic development. Careful evaluation of allosteric movements must be undertaken to develop better effector responses, especially during the transformation of these antibodies from small fragments at the discovery stage to full antibodies at the subsequent development stages

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

Spatial regularity of InAs-GaAs quantum dots: quantifying the dependence of lateral ordering on growth rate.

The lateral ordering of arrays of self-assembled InAs-GaAs quantum dots (QDs) has been quantified as a function of growth rate, using the Hopkins-Skellam index (HSI). Coherent QD arrays have a spatial distribution which is neither random nor ordered, but intermediate. The lateral ordering improves as the growth rate is increased and can be explained by more spatially regular nucleation as the QD density increases. By contrast, large and irregular 3D islands are distributed randomly on the surface. This is consistent with a random selection of the mature QDs relaxing by dislocation nucleation at a later stage in the growth, independently of each QD's surroundings. In addition we explore the statistical variability of the HSI as a function of the number N of spatial points analysed, and we recommend N > 10(3) to reliably distinguish random from ordered arrays

Structural analysis of anti-hapten antibodies to identify long-range structural movements induced by hapten binding

Antibodies are well known for their high specificity that has enabled them to be of significant use in both therapeutic and diagnostic applications. Antibodies can recognize different antigens, including proteins, carbohydrates, peptides, nucleic acids, lipids, and small molecular weight haptens that are abundantly available as hormones, pharmaceuticals, and pesticides. Here we focus on a structural analysis of hapten-antibody couples and identify potential structural movements originating from the hapten binding by comparison with unbound antibody, utilizing 40 crystal structures from the Protein Data Bank. Our analysis reveals three binding surface trends; S1 where a pocket forms to accommodate the hapten, S2 where a pocket is removed when the hapten binds, and S3 where no pockets changes are found. S1 and S2 are expected for induced-fit binding, whereas S3 indicates that a pre-existing population of optimal binding antibody conformation exists. The structural analysis reveals four classifications of structural reorganization, some of which correlate to S2 but not to the other binding surface changes. These observations demonstrate the complexity of the antibody-antigen interaction, where structural changes can be restricted to the binding sites, or extend through the constant domains to propagate structural changes. This highlights the importance of structural analysis to ensure successful and compatible transformation of small antibody fragments at the early discovery stage into full antibodies during the subsequent development stages, where long-range structural changes are required for an Fc effector response

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