Elucidating the mechanisms of nanodiamond-promoted structural disruption of crystallised lipid

YesThe removal or structural disruption of crystallised lipid is a pivotal but energy-intensive step in a wide range of industrial and biological processes. Strategies to disrupt the structure of crystallised lipid in aqueous solution at lower temperatures are much needed, where nanoparticle-based strategies show enormous promise. Using the aqueous tristearin bilayer as a model for crystallised lipid, we demonstrate that the synergistic use of surfactant and detonation nanodiamonds can depress the onset temperature at which disruption of the crystallised lipid structure occurs. Our simulations reveal the molecular-scale mechanisms by which this disruption takes place, indicating that the nanodiamonds serve a dual purpose. First, the nanodiamonds are predicted to facilitate delivery of surfactant to the lipid/water interface, and second, nanodiamond adsorption acts to roughen the lipid/water interface, enhancing ingress of surfactant into the bilayer. We find the balance of the hydrophobic surface area of the nanodiamond and the nanodiamond surface charge density to be a key determinant of the effectiveness of using nanodiamonds to facilitate lipid disruption. For the nanodiamond size considered here, we identify a moderate surface charge density, that ensures the nanodiamonds are neither too hydrophobic nor too hydrophilic, to be optimal

Simultaneous Embeddability of Two Partitions

We study the simultaneous embeddability of a pair of partitions of the same underlying set into disjoint blocks. Each element of the set is mapped to a point in the plane and each block of either of the two partitions is mapped to a region that contains exactly those points that belong to the elements in the block and that is bounded by a simple closed curve. We establish three main classes of simultaneous embeddability (weak, strong, and full embeddability) that differ by increasingly strict well-formedness conditions on how different block regions are allowed to intersect. We show that these simultaneous embeddability classes are closely related to different planarity concepts of hypergraphs. For each embeddability class we give a full characterization. We show that (i) every pair of partitions has a weak simultaneous embedding, (ii) it is NP-complete to decide the existence of a strong simultaneous embedding, and (iii) the existence of a full simultaneous embedding can be tested in linear time.Comment: 17 pages, 7 figures, extended version of a paper to appear at GD 201

Sequence-dependent structure/function relationships of catalytic peptide-enabled gold nanoparticles generated under ambient synthetic conditions

YesPeptide-enabled nanoparticle (NP) synthesis routes can create and/or assemble functional nanomaterials under environmentally friendly conditions, with properties dictated by complex interactions at the biotic/abiotic interface. Manipulation of this interface through sequence modification can provide the capability for material properties to be tailored to create enhanced materials for energy, catalysis, and sensing applications. Fully realizing the potential of these materials requires a comprehensive understanding of sequence-dependent structure/function relationships that is presently lacking. In this work, the atomic-scale structures of a series of peptide-capped Au NPs are determined using a combination of atomic pair distribution function analysis of high-energy X-ray diffraction data and advanced molecular dynamics (MD) simulations. The Au NPs produced with different peptide sequences exhibit varying degrees of catalytic activity for the exemplar reaction 4-nitrophenol reduction. The experimentally derived atomic-scale NP configurations reveal sequence-dependent differences in structural order at the NP surface. Replica exchange with solute-tempering MD simulations are then used to predict the morphology of the peptide overlayer on these Au NPs and identify factors determining the structure/catalytic properties relationship. We show that the amount of exposed Au surface, the underlying surface structural disorder, and the interaction strength of the peptide with the Au surface all influence catalytic performance. A simplified computational prediction of catalytic performance is developed that can potentially serve as a screening tool for future studies. Our approach provides a platform for broadening the analysis of catalytic peptide-enabled metallic NP systems, potentially allowing for the development of rational design rules for property enhancemenAir Force Office for Scientific Research (Grant #FA9550-12-1-0226, RRN; AFOSR LRIR) and DOE-BES grant DE-SC0006877, fellowship support from the National Research Council Research Associateshi

Competition between decay and dissociation of core-excited OCS studied by X-ray scattering

We show the first evidence of dissociation during resonant inelastic soft X-ray scattering. Carbon and oxygen K-shell and sulfur L-shell resonant and non-resonant X-ray emission spectra were measured using monochromatic synchrotron radiation for excitation and ionization. After sulfur, L2,3 -> {\pi}*, {\sigma}* excitation, atomic lines are observed in the emission spectra as a consequence of competition between de-excitation and dissociation. In contrast the carbon and oxygen spectra show weaker line shape variations and no atomic lines. The spectra are compared to results from ab initio calculations and the discussion of the dissociation paths is based on calculated potential energy surfaces and atomic transition energies.Comment: 12 pages, 6 pictures, 2 tables, http://link.aps.org/doi/10.1103/PhysRevA.59.428

Distinct differences in peptide adsorption on palladium and gold: introducing a polarizable model for Pd(111)

YesMaterials-binding peptides offer promising routes to the production of tailored Pd nanomaterials in aqueous media, enabling the optimization of catalytic properties. However, the atomic-scale details needed to make these advances are relatively scarce and challenging to obtain. Molecular simulations can provide key insights into the structure of peptides adsorbed at the aqueous Pd interface, provided that the force-field can appropriately capture the relevant bio-interface interactions. Here, we introduce and apply a new polarizable force field, PdP-CHARMM, for the simulation of biomolecule–Pd binding under aqueous conditions. PdP-CHARMM was parametrized with density functional theory (DFT) calculations, using a process compatible with similar polarizable force-fields created for Ag and Au surfaces, ultimately enabling a direct comparison of peptide binding modes across these metal substrates. As part of our process for developing PdP-CHARMM, we provide an extensive study of the performance of ten different dispersion-inclusive DFT functionals in recovering biomolecule–Pd(111) binding. We use the functional with best all-round performance to create PdP-CHARMM.We then employ PdP-CHARMM and metadynamics simulations to estimate the adsorption free energy for a range of amino acids at the aqueous Pd(111) interface. Our findings suggest that only His and Met favor direct contact with the Pd substrate, which we attribute to a remarkably robust interfacial solvation layering. Replica-exchange with solute tempering molecular dynamics simulations of two experimentally-identified Pd-binding peptides also indicate surface contact to be chiefly mediated by His and Met residues at aqueous Pd(111). Adsorption of these two peptides was also predicted for the Au(111) interface, revealing distinct differences in both the solvation structure and modes of peptide adsorption at the Au and Pd interfaces. We propose that this sharp contrast in peptide binding is largely due to the differences in interfacial solvent structuring.Air Force Office for Scientfi c Research (Grant #FA9550-12-1-0226

Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices

YesThe operation of many nanostructured biomolecular sensors and catalysts critically hinges on the manipulation of non-covalent adsorption of biomolecules on unfunctionalised noble-metal nanoparticles (NMNPs). Molecular-level structural details of the aqueous biomolecule/NMNP interface are pivotal to the successful realisation of these technologies, but such experimental data are currently scarce and challenging to obtain. Molecular simulations can generate these details, but are limited by the assumption of non-preferential adsorption to NMNP features. Here, via first principles calculations using a vdW-DF functional, and based on nanoscale sized NMNPs, we demonstrate that adsorption preferences to NP features vary with adsorbate chemistry. These results show a clear distinction between hydrocarbons, that prefer adsorption to facets over edges/vertices, over heteroatomic molecules that favour adsorption onto vertices over facets. Our data indicate the inability of widely used force-fields to correctly capture the adsorption of biomolecules onto NMNP surfaces under aqueous conditions. Our findings introduce a rational basis for the development of new force-fields that will reliably capture these phenomena

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

YesInvestigation 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.vesk

Probing nano-patterned peptide self-organisation at the aqueous graphene interface

YesThe peptide sequence GrBP5, IMVTESSDYSSY, is found experimentally to bind to graphene, and ex situ atomic force microscopy indicates the formation of an ordered over-layer on graphite. However, under aqueous conditions neither the molecular conformations of the adsorbed peptide chains, nor the molecular-level spatial ordering of the over-layer, has been directly resolved. Here, we use advanced molecular dynamics simulations of GrBP5, and related mutant sequences, to elucidate the adsorbed structures of both the peptide and the adsorbed peptide over-layer at the aqueous graphene interface. In agreement with a previous hypothesis, we find GrBP5 binds at the aqueous graphene interface chiefly via the tyrosine-rich C-terminal region. Our simulations of the adsorbed peptide over-layers reveal that the peptide chains form an aggregate that does not evolve further into ordered patterns. Instead, we find that the inter-chain interactions are driven by hydrogen bonding and charge–charge interactions that are not sufficiently specific to support pattern formation. Overall, we suggest that the experimentally-observed over-layer pattern may be due to the drying of the sample, and may not be prevalent at the solvated interface. However, our simulations indicate sequence modifications of GrBP5 to promote over-layer ordering under aqueous conditions

Tristearin bilayers: structure of the aqueous interface and stability in the presence of surfactants

YesWe report results of atomistic molecular dynamics simulations of an industrially-relevant, exemplar triacylglycerol (TAG), namely tristearin (TS), under aqueous conditions, at different temperatures and in the presence of an anionic surfactant, sodium dodecylbenzene sulphonate (SDBS). We predict the TS bilayers to be stable and in a gel phase at temperatures of 350 K and below. At 370 K the lipid bilayer was able to melt, but does not feature a stable liquid–crystalline phase bilayer at this elevated temperature. We also predict the structural characteristics of TS bilayers in the presence of SDBS molecules under aqueous conditions, where surfactant molecules are found to spontaneously insert into the TS bilayers. We model TS bilayers containing different amounts of SDBS, with the presence of SDBS imparting only a moderate effect on the structure of the system. Our study represents the first step in applying atomistic molecular dynamics simulations to the investigation of TAG-aqueous interfaces. Our results suggest that the CHARMM36 force-field appears suitable for the simulation of such systems, although the phase behaviour of the system may be shifted to lower temperatures than is the case for the actual system. Our findings provide a foundation for further simulation studies of the TS-aqueous interface.vesk

Measurement of D*+/- meson production in jets from pp collisions at sqrt(s) = 7 TeV with the ATLAS detector

This paper reports a measurement of D*+/- meson production in jets from proton-proton collisions at a center-of-mass energy of sqrt(s) = 7 TeV at the CERN Large Hadron Collider. The measurement is based on a data sample recorded with the ATLAS detector with an integrated luminosity of 0.30 pb^-1 for jets with transverse momentum between 25 and 70 GeV in the pseudorapidity range |eta| < 2.5. D*+/- mesons found in jets are fully reconstructed in the decay chain: D*+ -> D0pi+, D0 -> K-pi+, and its charge conjugate. The production rate is found to be N(D*+/-)/N(jet) = 0.025 +/- 0.001(stat.) +/- 0.004(syst.) for D*+/- mesons that carry a fraction z of the jet momentum in the range 0.3 < z < 1. Monte Carlo predictions fail to describe the data at small values of z, and this is most marked at low jet transverse momentum.Comment: 10 pages plus author list (22 pages total), 5 figures, 1 table, matches published version in Physical Review