Simulation of reconstructions of the polar ZnO (0001) surfaces

Surface reconstructions on the polar ZnO(0001) surface are investigated using empirical potential models. Several possible reconstructions based around triangular motifs are investigated. The quenching of the dipole moment in the material dominates the energetics of the surface patterns so that no one particular size of surface triangular island or pit is strongly favoured. We employ Monte Carlo simulations to explore which patterns emerge from a high temperature quench and during deposition of additional ZnO monolayers. The simulations show that a range of triangular islands and pits evolve in competition with one another. The surface patterns we discover are qualitatively similar to those observed experimentally

Characterising submonolayer deposition via visibility graphs

We use visibility graphs as a tool to analyse the results of kinetic Monte Carlo (kMC) simulations of submonolayer deposition in a one-dimensional point island model. We introduce an efficient algorithm for the computation of the visibility graph resulting from a kMC simulation and show that from the properties of the visibility graph one can determine the critical island size, thus demonstrating that the visibility graph approach, which implicitly combines size and spatial data, can provide insights into island nucleation and growth processes

Fluctuations and scaling in models for particle aggregation

We consider two sequential models of deposition and aggregation for particles. The first model (No Diffusion) simulates surface diffusion through a deterministic capture area, while the second (Sequential Diffusion) allows the atoms to diffuse up to \ell steps. Therefore the second model incorporates more fluctuations than the first, but still less than usual (Full Diffusion) models of deposition and diffusion on a crystal surface. We study the time dependence of the average densities of atoms and islands and the island size distribution. The Sequential Diffusion model displays a nontrivial steady-state regime where the island density increases and the island size distribution obeys scaling, much in the same way as the standard Full Diffusion model for epitaxial growth. Our results also allow to gain insight into the role of different types of fluctuations.Comment: 25 pages. Minor changes in the main text and in some figures. Accepted for publication in Surface Scienc

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

Fibronectin module FNIII9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics

The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FNIII9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (?1e), FN III9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FNIII9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FNIII9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved

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

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]

How negatively charged proteins adsorb to negatively charged surfaces - a molecular dynamics study of BSA adsorption on silica

How proteins adsorb to inorganic material surfaces is critically important for the development of new biotechnologies, since the orientation and structure of the adsorbed proteins impacts their functionality. Whilst it is known that many negatively charged proteins readily adsorb to negatively charged oxide surfaces, a detailed understanding of how this process occurs is lacking. In this work we study the adsorption of BSA, an important transport protein that is negatively charged at physiological conditions, to a model silica surface that is also negatively charged. We use fully atomistic Molecular Dynamics to provide detailed understanding of the non-covalent interactions that bind the BSA to the silica surface. Our results provide new insight into the competing roles of long-range electrostatics and short-range forces, and the consequences this has for the orientation and structure of the adsorbed proteins

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.

Steering protein adsorption at charged surfaces : electric fields and ionic screening

Protein adsorption at charged surfaces is a common process in the development of functional technological devices. Accurately reproducing the environment above the surface in simulations is essential for understanding how the adsorption process can be influenced and utilised. Here we present a simulation strategy that includes the electric field above the charged surface as well as the screening ions in solution, using standard molecular dynamics tools. With this approach we investigate the adsorption of Hen Egg White Lysozyme (HEWL) onto a model charged silica surface. We find that the screening effects of the ions slow down the adsorption process, giving the protein more time to find its optimal orientation as it adsorbs. Furthermore, we find that the concentrated ionic region directly above the surface helps to stabilise the protein structure in its adsorbed state. Together these effects imply that the adsorbed HEWL might retain its biological activity, with its active site exposed to solution rather than to the surface. Furthermore, this work shows how the steering effects of the electric field, coupled to the ionic screening, might be used to develop general strategies for surface functionalization through protein adsorption for technological applications