Morphology, energetics and growth kinetics of diphenylalanine fibres.

Diphenylalanine (FF) has been shown to self-assemble from water into heterogeneous fibres that are among the stiffest biomaterials known. How and why the fibres form has, however, not been clear. In this work, the nucleation and growth of FF fibres was investigated in a combined experimental and theoretical study.

SCORE: Shared care of Colorectal cancer survivors: protocol for a randomised controlled trial.

Background: Colorectal cancer (CRC) is the most common cancer affecting both men and women. Survivors of CRC often experience various physical and psychological effects arising from CRC and its treatment. These effects may last for many years and adversely affect QoL, and they may not be adequately addressed by standard specialist-based follow-up.

Organic-Silica Interactions in Saline: Elucidating the Structural Influence of Calcium in Low-Salinity Enhanced Oil Recovery.

Enhanced oil recovery using low-salinity solutions to sweep sandstone reservoirs is a widely-practiced strategy. The mechanisms governing this remain unresolved. Here, we elucidate the role of Ca by combining chemical force microscopy (CFM) and molecular dynamics (MD) simulations.

A classical view on nonclassical nucleation.

Understanding and controlling nucleation is important for many crystallization applications. Calcium carbonate (CaCO) is often used as a model system to investigate nucleation mechanisms. Despite its great importance in geology, biology, and many industrial applications, CaCO nucleation is still a topic of intense discussion, with new pathways for its growth from ions in solution proposed in recent years.

Predictors of functional status at service entry and discharge among young people with first episode psychosis.

Objective: Most patients with first episode psychosis (FEP) are neither studying nor employed (have a poor functional status) when first accessing care. Knowledge of the characteristics of patients with poor functioning and the features influencing functional status over time may pave the way to better treatment.

Method: A medical file audit was used to collect data on premorbid, entry, treatment and 18-month outcome characteristics on 661 FEP patients who consecutively attended the Early Psychosis Prevention and Intervention Centre, Melbourne, Australia, between 1998 and 2000.

Sodium Binding Sites and Permeation Mechanism in the NaChBac Channel: A Molecular Dynamics Study.

NaChBac was the first discovered bacterial sodium voltage-dependent channel, yet computational studies are still limited due to the lack of a crystal structure. In this work, a pore-only construct built using the NavMs template was investigated using unbiased molecular dynamics and metadynamics. The potential of mean force (PMF) from the unbiased run features four minima, three of which correspond to sites IN, CEN, and HFS discovered in NavAb.

Improved estimation of density of states for Monte Carlo sampling via MBAR.

We present a new method to calculate the density of states using the multistate Bennett acceptance ratio (MBAR) estimator. We use a combination of parallel tempering (PT) and multicanonical simulation to demonstrate the efficiency of our method in a statistical model of sampling from a two-dimensional normal mixture and also in a physical model of aggregation of lattice polymers. While MBAR has been commonly used for final estimation of thermodynamic properties, our numerical results show that the efficiency of estimation with our new approach, which uses MBAR as an intermediate step, often improves upon conventional use of MBAR.

Facet selectivity in gold binding peptides: exploiting interfacial water structure.

Peptide sequences that can discriminate between gold facets under aqueous conditions offer a promising route to control the growth and organisation of biomimetically-synthesised gold nanoparticles. Knowledge of the interplay between sequence, conformations and interfacial properties is essential for predictable manipulation of these biointerfaces, but the structural connections between a given peptide sequence and its binding affinity remain unclear, impeding practical advances in the field. These structural insights, at atomic-scale resolution, are not easily accessed with experimental approaches, but can be delivered molecular simulation.

How does an amorphous surface influence molecular binding?--ovocleidin-17 and amorphous calcium carbonate.

Atomistic molecular dynamics simulations of dehydrated amorphous calcium carbonate interacting with the protein ovocleidin-17 are presented. These simulations demonstrate that the amorphisation of the calcium carbonate surface removes water structure from the surface. This reduction of structure allows the protein to bind with many residues, unlike on crystalline surfaces where binding is strongest when only a few residues are attached to the surface.

Structure and properties of citrate overlayers adsorbed at the aqueous Au(111) interface.

One of the most common means of gold nanoparticle (AuNP) biofunctionalization involves the manipulation of precursor citrate-capped AuNPs via ligand displacement. However, the molecular-level structural characteristics of the citrate overlayer adsorbed at the aqueous Au interface at neutral pH remain largely unknown. Access to atomistic-scale details of these interfaces will contribute much needed insight into how AuNPs can be manipulated and exploited in aqueous solution.

Equilibrium conformational ensemble of the intrinsically disordered peptide n16N: linking subdomain structures and function in nacre.

n16 is a framework protein family associated with biogenic mineral stabilization, thought to operate at three key interfaces in nacre: protein/β-chitin, protein/protein, and protein/CaCO3. The N-terminal half of this protein, n16N, is known to be active in conferring this mineral stabilization and organization. While some details relating to the stabilization and organization of the mineral are known, the molecular mechanisms that underpin these processes are not yet established.

New insight into the stability of CaCO3 surfaces and nanoparticles via molecular simulation.

Using updated and improved atomistic models for the polymorphs of calcium carbonate and their constituent ions in solution, we revisit the question of surface energetics and nanoparticle stability. Using a simple lattice-based Monte Carlo scheme, we generate nanoparticle configurations in vacuum for all three biologically relevant polymorphs of calcium carbonate and establish that the bulk energetic ordering of polymorphs persists to the nanoscale. In aqueous environments, results based on surface enthalpy alone indicate that formation of mineral-water interfaces is marginally favorable in many cases.

Solubility of aqueous methane under metastable conditions: implications for gas hydrate nucleation.

To understand the prenucleation stage of methane hydrate formation, we measured methane solubility under metastable conditions using molecular dynamics simulations. Three factors that influence solubility are considered: temperature, pressure, and the strength of the modeled van der Waals attraction between methane and water. Moreover, the naturally formed water cages and methane clusters in the methane solutions are analyzed.

GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100).

Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field, compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and first-principles data.

Protein binding on stepped calcite surfaces: simulations of ovocleidin-17 on calcite {31.16} and {31.8}.

Simulations using classical molecular dynamics are reported on the binding of the protein Ovocleidin-17 to calcite stepped surfaces. vicinal surfaces ({31.8} and {31.

Applying the Z method to estimate temperatures of melting in structure II clathrate hydrates.

Equilibrium melting temperatures for structure II THF hydrate and argon/xenon (Ar/Xe) binary hydrate have been calculated using molecular dynamics using two melting techniques, namely the Z method [Belonoshko et al., Phys. Rev.

Sampling the structure of calcium carbonate nanoparticles with metadynamics.

Metadynamics is employed to sample the configurations available to calcium carbonate nanoparticles in water, and to map an approximate free energy as a function of crystalline order. These data are used to investigate the validity of bulk and ideal surface energies in predicting structure at the nanoscale. Results indicate that such predictions can determine the structure and morphology of particles as small as 3-4 nm in diameter.

Templates for wax deposition?

Molecular dynamics simulations have been used to study the behaviour of a liquid mixture of octacosane and heptane between two planar hematite surfaces; one of the surfaces was coated by a monolayer of an imidazoline-based corrosion inhibitor (CI). It was found that the octacosane could be inserted into the CI monolayer when it was aligned with the alkyl tails of the CIs, but the rate for such an insertion was slow. Potential of mean force calculations confirmed that there is a free energy barrier to insertion of octacosane into the CI film, and identified a secondary minimum about 13 A from the surface as a metastable intermediate for insertion.

Theoretical study of phase transitions in Kr and Ar clathrate hydrates from structure II to structure I under pressure.

The theory developed in our earlier papers is extended to predict dynamical and thermodynamic properties of clathrate structures by accounting for the possibility of multiple filling of cavities by guest molecules. The method is applied to the thermodynamic properties of argon and krypton hydrates, considering both structures I (sI) and II (sII), in which the small cages can be singly occupied and large cages of sII can be singly or doubly occupied. It was confirmed that the structure of the clathrate hydrate is determined by two main factors: intermolecular interaction between guest and host molecules and the configurational entropy.

Metadynamics simulations of calcite crystallization on self-assembled monolayers.

We show that recent developments in the application of metadynamics methods to direct simulations of crystallization make it possible to predict the orientation of crystals grown on self-assembled monolayers. In contrast to previous studies, the method allows for dynamic treatment of the organic component and the inclusion of explicit surface water without the need for computationally intensive interfacial energy calculations or prior knowledge of the interfacial structure. The method is applied to calcite crystallization on carboxylate terminated alkanethiols arrayed on Au (111).

Structural variations within group 1 (Li-Cs)+ (2,2,6,6-tetramethyl-1-piperidinyloxy)- complexes made via metallic reduction of the nitroxyl radical.

Treatment of 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) with a group 1 metal (Li, Na, K, Rb, or Cs), resulted in the reduction of this important radical to the TEMPO(-) anion--the first examples of elemental-metal single electron reduction of the radical to its anionic form. The synthesis and characterization of seven alkali metal TEMPO(-) complexes are reported. A variety of structural motifs are encountered depending on the choice of metal and/or solvent.

Isomer separation and gas-phase configurations of organoruthenium anticancer complexes: ion mobility mass spectrometry and modeling.

We have used ion mobility-mass spectrometry combined with molecular modeling for the separation and configurational analysis of three low-molecular-weight isomeric organoruthenium anticancer complexes containing ortho-, meta-, or para-terphenyl arene ligands. The isomers were separated using ion mobility based on traveling-wave technology and the experimentally determined collision cross sections were compared to theoretical calculations. Excellent agreement was observed between the experimentally and theoretically derived measurements.

Crystal-like low frequency phonons in the low-density amorphous and high-density amorphous ices.

The structure and vibrational properties of high- and low-density amorphous (HDA and LDA, respectively) ices have been determined using reverse Monte Carlo, molecular dynamics, and lattice dynamics simulations. This combined approach leads to a more accurate and detailed structural description of HDA and LDA ices when compared to experiment than was previously possible. The water molecules in these ices form well connected hydrogen-bond networks that exhibit modes of vibration that extend throughout the solid and can involve up to 70% of all molecules.