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

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

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

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

On linear growth in COVID-19 cases

We present an elementary model of COVID-19 propagation that makes explicit the connection between testing strategies and rates of transmission and the linear growth in new cases observed in many parts of the world

Vaccination, asymptomatics and public health information in COVID-19

The dynamics of the COVID-19 pandemic are greatly influenced by vaccine quality, as well as by vaccination rates and the behaviour of infected individuals, both of which reflect public policy. We develop a model for the dynamics of relevant cohorts within a fixed population, taking extreme care to model the reduced social contact of infected individuals in a rigorous self-consistent manner. The basic reproduction number R0is then derived in terms of the parameters of the model. Analysis of R0 reveals two interesting possibilities, both of which are plausible based on known characteristics of COVID-19. Firstly, if the population in general moderates social contact, while infected individuals who display clinical symptoms tend not to isolate, then increased vaccination can drive the epidemic towards a disease-free equilibrium (DFE). However, if the reverse is true, then increased vaccination can destabilise the DFE and yield an endemic state. This surprising result is due to the fact that the vaccines are leaky, and can lead to an increase in asymptomatic individuals who unknowingly spread the disease. Therefore, this work shows that public policy regarding the monitoring and release of health information should be combined judiciously with vaccination policy to control COVID-19

Scaling of glycine nucleation kinetics with shear rate and glass-liquid interfacial area

The scaling of the nucleation kinetics of glycine was investigated in supersaturated aqueous solutions under isothermal conditions. Induction times were measured in a Couette cell with a wide range of average shear rates γ_avg (25-250 s^-1) and a range of glass-liquid interfacial areas A (2.5-10 cm^2 per ml solution). The probability distributions of induction times were found to scale with shear rate and glass-liquid interfacial area, with the characteristic timescale (γ_avg.A)^-1. Primary nucleation rates and growth times to reach detection (estimated from the probability distributions) were both dependent on this timescale. In-situ dynamic light scattering revealed mesoscale clusters in the solutions that increased in size over time at rates which also depended on this timescale. The increase in size was thought to be due to the shear-enhanced aggregation or coalescence of mesoscale clusters leading to a higher number of larger mesoscale clusters, resulting in higher rates of primary nucleation

Critical role of tyrosine-20 in formation of gold nanoclusters within lysozyme : a molecular dynamics study

Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is currently a poor understanding of the physical characteristics of the Ly-AuNC complex. In this study we have employed fully atomistic molecular dynamics simulations to gain an understanding of the formation of Au clusters within the protein. It was found that in order to form AuNCs in the simulations, an approach of targeted insertion of Au atoms at a critical surface residue was needed. Tyrosine is known to be crucial for the reduction of Au salts experimentally, and our simulations showed that Tyr20 is the key residue for the formation of an AuNC beneath the protein surface in the α-helical domain. It is hoped these observations will aid future improvements and modification of Ly-AuNCs via alterations of the alpha-helix domain or Tyr20

Protein interactions with negatively charged inorganic surfaces

Protein adsorption on charged inorganic solid materials has recently attracted enormous interest owing to its various possible applications, including drug delivery and biomaterial design. The need to combine experimental and computational approaches to get a detailed picture of the adsorbed protein properties is increasingly recognised and emphasised in this review. We discuss the methods frequently used to study protein adsorption and the information they can provide. We focus on model systems containing a silica surface, which is negatively charged and hydrophilic at physiological pH, and two contrasting proteins: bovine serum albumin (BSA) and lysozyme (LSZ) that are both water soluble. At pH 7, BSA has a net negative charge, whereas LSZ is positive. In addition, BSA is moderately sized and flexible, whereas LSZ is small and relatively rigid. These differences in charge and structural nature capture the role of electrostatics and hydrophobic interactions on the adsorption of these proteins, along with the impact of adsorption on protein orientation and function. Understanding these model systems will undoubtedly enhance the potential to extrapolate our knowledge to other systems of interest