Efficient simulations of the aqueous bio-interface of graphitic nanostructures with a polarisable model.

To fully harness the enormous potential offered by interfaces between graphitic nanostructures and biomolecules, detailed connections between adsorbed conformations and adsorption behaviour are needed. To elucidate these links, a key approach, in partnership with experimental techniques, is molecular simulation. For this, a force-field (FF) that can appropriately capture the relevant physics and chemistry of these complex bio-interfaces, while allowing extensive conformational sampling, and also supporting inter-operability with known biological FFs, is a pivotal requirement. Here, we present and apply such a force-field, GRAPPA, designed to work with the CHARMM FF. GRAPPA is an efficiently implemented polarisable force-field, informed by extensive plane-wave DFT calculations using the revPBE-vdW-DF functional. GRAPPA adequately recovers the spatial and orientational structuring of the aqueous interface of graphene and carbon nanotubes, compared with more sophisticated approaches. We apply GRAPPA to determine the free energy of adsorption for a range of amino acids, identifying Trp, Tyr and Arg to have the strongest binding affinity and Asp to be a weak binder. The GRAPPA FF can be readily incorporated into mainstream simulation packages, and will enable large-scale polarisable biointerfacial simulations at graphitic interfaces, that will aid the development of biomolecule-mediated, solution-based graphene processing and self-assembly strategies.

Binding affinities of amino acid analogues at the charged aqueous titania interface : implications for titania-binding peptides

Despite the extensive utilization of biomolecule-titania interfaces, biomolecular recognition and interactions at the aqueous titania interface remain far from being fully understood. Here, atomistic molecular dynamics simulations, in partnership with metadynamics, are used to calculate the free energy of adsorption of different amino acid side chain analogues at the negatively-charged aqueous rutile TiO2 (110) interface, under conditions corresponding with neutral pH. Our calculations predict that charged amino acid analogues have a relatively high affinity to the titania surface, with the arginine analogue predicted to be the strongest binder. Interactions between uncharged amino acid analogues and titania are found to be repulsive or weak at best. All of the residues that bound to the negatively-charged interface show a relatively stronger adsorption compared with the charge-neutral interface, including the negatively-charged analogue. Of the analogues that are found to bind to the titania surface, the rank ordering of the binding affinities is predicted to be "arginine" > "lysine" ≈ aspartic acid > "serine". This is the same ordering as was found previously for the charge-neutral aqueous titania interface. Our results show very good agreement with available experimental data and can provide a baseline for the interpretation of peptide-TiO2 adsorption data.

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. Here, the structures of such citrate overlayers adsorbed at the aqueous Au(111) interface at pH 7 are predicted and characterized using atomistic molecular dynamics simulations, for a range of citrate surface densities. We find that the overlayers are disordered in the surface density range considered, and that many of their key characteristics are invariant with surface density. In particular, we predict the overlayers to have 3-D, rather than 2-D, morphologies, with the anions closest to the gold surface being oriented with their carboxylate groups pointing away from the surface. We predict both striped and island morphologies for our overlayers, depending on the citrate surface density, and in all cases we find bare patches of the gold surface are present. Our simulations suggest that both citrate-gold adsorption and citrate-counterion pairing contribute to the stability of these citrate overlayer morphologies. We also calculate the free energy of adsorption at the aqueous Au(111) interface of a single citrate molecule, and compare this with the corresponding value for a single arginine molecule. These findings enable us to predict the conditions under which ligand displacement of surface-adsorbed citrate by arginine may take place. Our findings represent the first steps toward elucidating a more elaborate, detailed atomistic-scale model relating to the biofunctionalization of citrate-capped AuNPs.

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. To provide these molecular-scale details, here we explore current hypotheses regarding the possible subdomain organization of n16N, as related to these three interfaces in nacre, by combining outcomes of Replica Exchange with Solute Tempering molecular dynamics simulations with NMR experiments, to investigate the conformational ensemble of n16N in solution. We verify that n16N lacks a well-defined secondary structure, both with and without the presence of Ca(2+) ions, as identified from previous experiments. Our data support the presence of three different, functional subdomains within n16N. Our results reveal that tyrosine, chiefly located in the center of the peptide, plays a multifunctional role in stabilizing conformations of n16N, for intrapeptide and possibly interpeptide interactions. Complementary NMR spectroscopy data confirm the participation of tyrosine in this stabilization. The C-terminal half of n16N, lacking in tyrosine and highly charged, shows substantive conformational diversity and is proposed as a likely site for nucleation of calcium carbonate. Finally, dominant structures from our predicted conformational ensemble suggest the presentation of key residues thought to be critical to the selective binding to β-chitin surfaces.

What makes a good graphene-binding peptide? Adsorption of amino acids and peptides at aqueous graphene interfaces

Investigation of the non-covalent interaction of biomolecules with aqueous graphene interfaces is a rapidly expanding area. However, reliable exploitation of these interfaces in many applications requires that the links between the sequence and binding of the adsorbed peptide structures be clearly established. Molecular dynamics (MD) simulations can play a key role in elucidating the conformational ensemble of peptides adsorbed at graphene interfaces, helping to elucidate these rules in partnership with experimental characterisation. We apply our recently-developed polarisable force-field for biomolecule-graphene interfaces, GRAPPA, in partnership with advanced simulation approaches, to probe the adsorption behaviour of peptides at aqueous graphene. First we determine the free energy of adsorption of all twenty naturally occurring amino acids (AAs) via metadynamics simulations, providing a benchmark for interpreting peptide-graphene adsorption studies. From these free energies, we find that strong-binding amino acids have flat and/or compact side chain groups, and we relate this behaviour to the interfacial solvent structuring. Second, we apply replica exchange with solute tempering simulations to efficiently and widely sample the conformational ensemble of two experimentally-characterised peptide sequences, P1 and its alanine mutant P1A3, in solution and adsorbed on graphene. For P1 we find a significant minority of the conformational ensemble possesses a helical structure, both in solution and when adsorbed, while P1A3 features mostly extended, random-coil conformations. In solution this helical P1 configuration is stabilised through favourable intra-peptide interactions, while the adsorbed structure is stabilised via interaction of four strongly-binding residues, identified from our metadynamics simulations, with the aqueous graphene interface. Our findings rationalise the performance of the P1 sequence as a known graphene binder.

Understanding water and ion transport behaviour and permeability through poly(amide) thin film composite membrane

Molecular dynamics (MD) together with the adaptive biasing force (ABF) and metadynamics free energy calculation methods was used to investigate the permeation properties of salt water through poly(amide) thin film composite reverse osmosis membranes. The thin films were generated by annealing an amorphous cell of poly(amide) chains through an MD method. The MD results showed they have typical structural properties of the active layer of thin film composite membranes and comparable water diffusivity (2.13×10^-5cm²/s for the film with a density of 1.06g/cm³) and permeability (9.27×10^-15cm³cm/cm²sPa) to experimental data. The simulations of water permeation through the films under different transmembrane pressures revealed the behaviours of water molecules in the thin films and the dynamic regimes of water permeation, including Brownian diffusion, flush and jump diffusion regimes. The intermolecular interactions of water and ions with poly(amide) chains showed a strong dependence on the local structure of films. The attraction between water and ploy(amide) molecules can be up to 8.5kcal/mol in dense polymer regions and 5kcal/mol in the pores of about 3nm. The ABF and metadynamics simulations produced the profiles of free energy potential of water and ions along the depth of the thin films, which provided important information for quantitatively determining the barrier energy required for water permeation and rejection of ions. The thin film with a density of 1.06g/cm³ and a thickness of 6nm offers a rejection to Na⁺ but a slight absorption of Cl^- (0.25kcal/mol) at 0.3-0.4nm distance to its surface. Water molecules must overcome 63kcal/mol energy to move to the centre of the film. The dependences of the barrier energy and the water-polymer interaction energy on the local free volume size in the thin film were analysed. The simulations of water permeation under high transmembrane pressures showed a nonlinear response of the concentration and distribution of water molecules in the film to the imposed pressure. Compaction of the film segments close to the porous substrate and water congestion in dense regions significantly influenced the water permeation when the membrane was operated under pressures of more than 3.0MPa.

Improving the description of interactions between Ca2+ and protein carboxylate groups, including γ-carboxyglutamic acid: revised CHARMM22∗ parameters

A reliable description of ion pair interactions for biological systems, particularly those involving polyatomic ions such as carboxylate and divalent ions such as Ca²⁺, using biomolecular force-fields is essential for making useful predictions for a range of protein functions. In particular, the interaction of divalent ions with the double carboxylate group present in γ-carboxyglutamic acid (Gla), relevant to the function of many proteins, is relatively understudied using biomolecular force-fields. Using force-field based metadynamics simulations to predict the free energy of binding between Ca²⁺ and the carboxylate group in liquid water, we show that a widely-used biomolecular force-field, CHARMM22∗, substantially over-estimates the binding strength between Ca²⁺ and the side-chains of both glutamic acid (Glu) and Gla, compared with experimental data obtained for the analogous systems of aqueous calcium-acetate and calcium-malonate. To correct for this, we propose and test a range of modifications to the σ value of the heteroatomic Lennard-Jones interaction between Ca²⁺ and the oxygen of the carboxylate group. Our revised parameter set can recover the same three association modes of this aqueous ion pair as the standard parameter set, and yields free energies of binding for the carboxylate-Ca²⁺ interaction in good agreement with experimental data. The revised parameter set recovers other structural properties of the ion pair in agreement with the standard CHARMM22∗ parameter set.

Enhancement of the antifouling properties and filtration performance of poly(ethersulfone) ultrafiltration membranes by incorporation of nanoporous titania nanoparticles

Nanoporous titania nanoparticles (NTNs) were synthesized and used as an additive at a low concentration of 0.1-1 wt % in the fabrication of poly(ethersulfone) (PES) ultrafiltration membranes via non-solvent-induced phase separation. The structure and properties of nanoparticles were characterized using nitrogen sorption, X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The NTNs have a size distribution with a particle size of mainly <100 nm and have a Brunauer, Emmett, and Teller surface area of ∼100 m2 g-1. The modified membranes were fabricated and investigated in terms of their pure water flux, solute rejection, and fouling resistance. The water permeability and molecular weight cutoffs (MWCOs) of membranes were determined under constant-pressure filtration in dead-end mode at 100 kPa. The membrane fouling resistance was characterized under constant flux operation using bovine serum albumin as a model foulant. The membranes were characterized in terms of morphology, porosity, pore size distribution, energy-dispersive X-ray spectroscopy, contact angle goniometry, surface free energy, and viscosity of the dope solution. Overall, the modified membrane showed increased wettability and reduced surface free energy and pore size. The modified UF membrane with 0.5 wt % NTN loading exhibited improved fouling resistance (fouling rate of 0.58 kPa/min compared to a rate of 0.70 kPa/min for the control membrane) with ∼80% water flux recovery. The same membrane showed an ∼20% increase in water flux, an improvement in MWCO, and a narrower pore size distribution.

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 via molecular simulation. A current unmet challenge lies in forging links between predicted adsorption free energies derived from enhanced sampling simulations with the conformational ensemble of the peptide and the water structure at the surface. To meet this challenge, here we use an in situ combination of Replica Exchange with Solute Tempering with Metadynamics simulations to predict the adsorption free energy of a gold-binding peptide sequence, AuBP1, at the aqueous Au(111), Au(100)(1 × 1) and Au(100)(5 × 1) interfaces. We find adsorption to the Au(111) surface is stronger than to Au(100), irrespective of the reconstruction status of the latter. Our predicted free energies agree with experiment, and correlate with trends in interfacial water structuring. For gold, surface hydration is predicted as a chief determining factor in peptide-surface recognition. Our findings can be used to suggest how shaped seed-nanocrystals of Au, in partnership with AuBP1, could be used to control AuNP nanoparticle morphology.

Pyrolysis of municipal green waste: a modelling, simulation and experimental analysis

Pyrolysis is the thermo-chemical conversion of carbonaceous feedstock in the absence of oxygen to produce bio-fuel (bio-oil, bio-char and syn-gas). Bio-fuel production from municipal green waste (MGW) through the pyrolysis process has attracted considerable attention recently in the renewable energy sector because it can reduce greenhouse gas emissions and contribute to energy security. This study analyses properties of MGW feedstock available in Rockhampton city of Central Queensland, Australia, and presents an experimental investigation of producing bio-fuel from that MGW through the pyrolysis process using a short sealed rotary furnace. It was found from the experiment that about 19.97% bio-oil, 40.83% bio-char and 29.77% syn-gas can be produced from the MGW. Then, a four-stage steady state simulation model is developed for pyrolysis process performance simulation using Aspen Plus software. In the first stage, the moisture content of the MGW feed is reduced. In the second stage, the MGW is decomposed according to its elemental constituents. In the third stage, condensate material is separated and, finally, the pyrolysis reactions are modelled using the Gibbs free energy minimisation approach. The MGW's ultimate and proximate analysis data were used in the Aspen Plus simulation as input parameters. The model is validated with experimentally measured data. A good agreement between simulation and experimental results was found. More specifically, the variation of modelling and experimental elemental compositions of the MGW was found to be 7.3% for carbon, 15.82% for hydrogen, 7.04% for nitrogen and 5.56% for sulphur. The validated model is used to optimise the biofuel production from the MGW as a function of operating variables such as temperature, moisture content, particle size and process heat air-fuel ratio. The modelling and optimisation results are presented, analysed and discussed.

A survey on mechanisms and critical parameters on solidification of selective laser melting during fabrication of Ti-6Al-4V prosthetic acetabular cup

Additive Manufacturing (AM) includes a range of approaches that correlate with computer aided design (CAD) and manufacturing by fabrication via precise layers and is a promising method for the production of medical tools. In this study, different aspects and mechanisms of solidification for curved surfaces based on equilibrium at curved interfaces, Monge patch, interfacial and Gibbs energy will be discussed. Also, the effect of capillarity, geometry, substrate temperature, cooling rate and scanning parameters in the solidification of a prosthetic acetabular cup (PAC) using selective laser melting (SLM) is analysed. The contributions of this work are analysing solidification and effective factors in this process to produce parts with a higher quality and mechanical properties such as strength, strain, porosity, relative density and hardness. Results indicate that due to the surface to volume (S/V) ratio, and the increasing effect of the radius on Monge patch, thermal stresses and surface forces are more prevalent on outer surfaces. Moreover, solidification and mechanical properties are related to capillarity, geometry, substrate temperature, cooling rate, scanning power and speed. The results also indicate the interaction of solute diffusion and heat transfer with interatomic forces in large S/V ratio and at small scales tend to improve solidification.

Flipper strokes can predict energy expenditure and locomotion costs in free-ranging northern and Antarctic fur seals

Flipper strokes have been proposed as proxies to estimate the energy expended by marine vertebrates while foraging at sea, but this has never been validated on free-ranging otariids (fur seals and sea lions). Our goal was to investigate how well flipper strokes correlate with energy expenditure in 33 foraging northern and Antarctic fur seals equipped with accelerometers, GPS, and time-depth recorders. We concomitantly measured field metabolic rates with the doubly-labelled water method and derived activity-specific energy expenditures using fine-scale time-activity budgets for each seal. Flipper strokes were detected while diving or surface transiting using dynamic acceleration. Despite some inter-species differences in flipper stroke dynamics or frequencies, both species of fur seals spent 3.79 ± 0.39 J/kg per stroke and had a cost of transport of ~1.6-1.9 J/kg/m while diving. Also, flipper stroke counts were good predictors of energy spent while diving (R(2) = 0.76) and to a lesser extent while transiting (R(2) = 0.63). However, flipper stroke count was a poor predictor overall of total energy spent during a full foraging trip (R(2) = 0.50). Amplitude of flipper strokes (i.e., acceleration amplitude × number of strokes) predicted total energy expenditure (R(2) = 0.63) better than flipper stroke counts, but was not as accurate as other acceleration-based proxies, i.e. Overall Dynamic Body Acceleration.

Assessing body condition and energy budget components by scoring abdominal profiles in free-ranging pink-footed geese Anser brachyrhynchus

An abdominal profile index (API) was developed for pink-footed geese Anser brachyrhynchus as a measure of body condition. On basis of carcass analysis of 56 adult geese with known API prior to collection, we found significant linear relationships between API against body mass, abdominal fat and total energy content. Hence, changes in API reflect net energy intake rates. As an example of the applicability of the calibration, we compared APIs of individually marked geese before and after long migration episodes and estimated the cost of flight at 8.9 kJ/km. In addition we estimated gain rates at three major staging sites along the spring flyway indicating an increase in fueling rates with latitude. Calibration of APIs and energy contents offers new opportunities for field studies of waterfowl energetics.