Extracting quantitative structural parameters for disordered polymers from neutron scattering data

The organization of non-crystalline polymeric materials at a local level, namely on a spatial scale between a few and 100 a, is still unclear in many respects. The determination of the local structure in terms of the configuration and conformation of the polymer chain and of the packing characteristics of the chain in the bulk material represents a challenging problem. Data from wide-angle diffraction experiments are very difficult to interpret due to the very large amount of information that they carry, that is the large number of correlations present in the diffraction patterns.We describe new approaches that permit a detailed analysis of the complex neutron diffraction patterns characterizing polymer melts and glasses. The coupling of different computer modelling strategies with neutron scattering data over a wide Q range allows the extraction of detailed quantitative information on the structural arrangements of the materials of interest. Proceeding from modelling routes as diverse as force field calculations, single-chain modelling and reverse Monte Carlo, we show the successes and pitfalls of each approach in describing model systems, which illustrate the need to attack the data analysis problem simultaneously from several fronts.

Substitutional Impurities in PPV Crystals: An Intrinsic Donor-Acceptor System for High V(oc) Photovoltaic Devices

Defects are usually present in organic polymer films and are commonly invoked to explain the low efficiency obtained in organic-based optoelectronic devices. We propose that controlled insertion of substitutional impurities may, on the contrary, tune the optoelectronic properties of the underivatized organic material and, in the case studied here, maximize the efficiency of a solar cell. We investigate a specific oxygen-impurity substitution, the keto-defect -(CH(2)-C=O)- in underivatized crystalline poly(p-phenylenevinylene) (PPV), and its impact on the electronic structure of the bulk film, through a combined classical (force-field) and quantum mechanical (DFT) approach. We find defect states which suggest a spontaneous electron hole separation typical of a donor acceptor interface, optimal for photovoltaic devices. Furthermore, the inclusion of oxygen impurities does not introduce defect states in the gap and thus, contrary to standard donor-acceptor systems, should preserve the intrinsic high open circuit voltage (V(oc)) that may be extracted from PPV-based devices.

Classical simulation of deposition of thiophene oligomers on TiO(2)-anatase: Relevance of long-range electrostatic interactions

We performed classical molecular dynamics simulations of the vapor-deposition of alpha-T4 oligomers on the TiO(2)-anatase (101) surface, comparing different sets of charges associated with the atoms of the model. The potential energy surfaces for alpha-T4 and TiO(2) were described by re-parametrizations of the Universal force field with charges given by the charge equilibration (QEq) scheme, or with fixed charges obtained by an ab initio method using the Hirshfeld partition. The two sets of charges lead to completely different results for the interface formation, and for the characteristics of the organic film, with a clearly defined alpha-T4 contact layer in the QEq case, and a more homogeneous molecular distribution when using Hirshfeld charges. The main reason for the discrepancy was found to be the incorrect charge assignment given by QEq to the sulfur and alpha-carbon atoms in thiophenes, and highlight the relevance of long-range interactions in the organization of molecular films. (C) 2009 Elsevier B.V. All rights reserved.

Ligand dissociation from estrogen receptor is mediated by receptor dimerization: Evidence from molecular dynamics simulations

Estrogen Receptor (ER) is an important target for pharmaceutical design. Like other ligand-dependent transcription factors, hormone binding regulates ER transcriptional activity. Nevertheless, the mechanisms by which ligands enter and leave ERs and other nuclear receptors remain poorly understood. Here, we report results of locally enhanced sampling molecular dynamics simulations to identify dissociation pathways of two ER ligands [the natural hormone 17 beta-estradiol (E-2) and the selective ER modulator raloxifene (RAL)] from the human ER alpha ligand-binding domain in monomeric and dimeric forms. E-2 dissociation occurs via three different pathways in ER monomers. One resembles the mousetrap mechanism (Path I), involving repositioning of helix 12 (H12), others involve the separation of H8 and H11 (Path II), and a variant of this pathway at the bottom of the ligand-binding domain (Path II`). RAL leaves the receptor through Path I and a Path I variant in which the ligand leaves the receptor through the loop region between H11 and H12 (Path I`). Remarkably, ER dimerization strongly suppresses Paths II and II` for E-2 dissociation and modifies RAL escape routes. We propose that differences in ligand release pathways detected in the simulations for ER monomers and dimers provide an explanation for previously observed effects of ER quaternary state on ligand dissociation rates and suggest that dimerization may play an important, and hitherto unexpected, role in regulation of ligand dissociation rates throughout the nuclear receptor family.

Flexibility and inhibitor binding in Cdc25 phosphatases

Cdc25 phosphatases involved in cell cycle checkpoints are now active targets for the development of anti-cancer therapies. Rational drug design would certainly benefit from detailed structural information for Cdc25s. However, only apo- or sulfate-bound crystal structures of the Cdc25 catalytic domain have been described so far. Together with previously available crystalographic data, results from molecular dynamics simulations, bioinformatic analysis, and computer-generated conformational ensembles shown here indicate that the last 30-40 residues in the C-terminus of Cdc25B are partially unfolded or disordered in solution. The effect of C-terminal flexibility upon binding of two potent small molecule inhibitors to Cdc25B is then analyzed by using three structural models with variable levels of flexibility, including an equilibrium distributed ensemble of Cdc25B backbone conformations. The three Cdc25B structural models are used in combination with flexible docking, clustering, and calculation of binding free energies by the linear interaction energy approximation to construct and validate Cdc25B-inhibitor complexes. Two binding sites are identified on top and beside the Cdc25B active site. The diversity of interaction modes found increases with receptor flexibility. Backbone flexibility allows the formation of transient cavities or compact hydrophobic units on the surface of the stable, folded protein core that are unexposed or unavailable for ligand binding in rigid and densely packed crystal structures. The present results may help to speculate on the mechanisms of small molecule complexation to partially unfolded or locally disordered proteins.

Host-guest system of 4-nerolidylcatechol in 2-hydroxypropyl-beta-cyclodextrin: preparation, characterization and molecular modeling

The interaction of 4-nerolidylcatechol (4-NRC), a potent antioxidant agent, and 2-hydroxypropyl-beta-cyclodextrin (HP-beta-CD) was investigated by the solubility method using Fourier transform infrared (FTIR) methods in addition to UV-Vis, (1)H-nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. The inclusion complexes were prepared using grinding, kneading and freeze-drying methods. According to phase solubility studies in water a B(S)-type diagram was found, displaying a stoichiometry complexation of 2:1 (drug:host) and stability constant of 6494 +/- A 837 M(-1). Stoichiometry was established by the UV spectrophotometer using Job`s plot method and, also confirmed by molecular modeling. Data from (1)H-NMR, and FTIR, experiments also provided formation evidence of an inclusion complex between 4-NRC and HP-beta-CD. 4-NRC complexation indeed led to higher drug solubility and stability which could probably be useful to improve its biological properties and make it available to oral administration and topical formulations.

Shielding of ionic interactions by sulfur dioxide in an ionic liquid

The effect of adding SO(2) on the structure and dynamics of 1-butyl-3-methylimidazolium bromide (BMIBr) was investigated by low-frequency Raman spectroscopy and molecular dynamics (MD) simulations. The MD simulations indicate that the long-range structure of neat BMIBr is disrupted resulting in a liquid with relatively low viscosity and high conductivity, but strong correlation of ionic motion persists in the BMIBr-SO(2) mixture due to ionic pairing. Raman spectra within the 5 < omega < 200 cm(-1) range at low temperature reveal the short-time dynamics, which is consistent with the vibrational density of states calculated by MD simulations. Several time correlation functions calculated by MD simulations give further insights on the structural relaxation of BMIBr-SO(2).

Total syntheses of trikentrins and of herbindoles

CNPq

Modelling water adsorption on Au(210) surfaces: II. Monte Carlo simulations

Canonical Monte Carlo simulations for the Au(210)/H(2)O interface, using a force field recently proposed by us, are reported. The results exhibit the main features normally observed in simulations of water molecules in contact with different noble metal surfaces. The calculations also assess the influence of the surface topography on the structural aspects of the adsorbed water and on the distribution of the water molecules in the direction normal to the metal surface plane. The adsorption process is preferential at sites in the first layer of the metal. The analysis of the density profiles and dipole moment distributions points to two predominant orientations. Most of the molecules are adsorbed with the molecular plane parallel to surface, while others adsorb with one of the O-H bonds parallel to the surface and the other bond pointing towards the bulk liquid phase. There is also evidence of hydrogen bond formation between the first and second solvent layers at the interface. (c) 2007 Elsevier B.V. All rights reserved.

Haptic guidance for microrobotic intracellular injection

The ability for a bio-operator to utilise a haptic device to manipulate a microrobot for intracellular injection offers immense benefits. One significant benefit is for the bio-operator to receive haptic guidance while performing the injection process. In order to address this, this paper investigates the use of haptic virtual fixtures for cell injection and proposes a novel force field virtual fixture. The guidance force felt by the bio-operator is determined by force field analysis within the virtual fixture. The proposed force field virtual fixture assists the bio-operator when performing intracellular injection by limiting the micropipette tip's motion to a conical volume as well as recommending the desired path for optimal injection. A virtual fixture plane is also introduced to prevent the bio-operator from moving the micropipette tip beyond the deposition target inside the cell. Simulation results demonstrate the operation of the guidance system.

Haptic microrobotic intracellular injection assistance using virtual fixtures

In manual cell injection the operator relies completely on visual information for task feedback and is subject to extended training times as well as poor success rates and repeatability. From this perspective, enhancing human-in-the-loop intracellular injection through haptic interaction offers significant benefits. This paper outlines two haptic virtual fixtures aiming to assist the human operator while performing cell injection. The first haptic virtual fixture is a parabolic force field designed to assist the operator in guiding the micropipette's tip to a desired penetration point on the cell's surface. The second is a planar virtual fixture which attempts to assist the operator from moving the micropipette's tip beyond the deposition target location inside the cell. Preliminary results demonstrate the operation of the haptically assisted microrobotic cell injection system.

Evaluating the stability of disulfide bridges in proteins: a torsional potential energy surface for diethyl disulfide

Disulfide bonds formed by the oxidation of cysteine residues in proteins are the major form of intra- and inter-molecular covalent linkages in the polypeptide chain. To better understand the conformational energetics of this linkage, we have used the MP2(full)/6-31G(d) method to generate a full potential energy surface (PES) for the torsion of the model compound diethyl disulfide (DEDS) around its three critical dihedral angles (χ2, χ3, χ2′). The use of ten degree increments for each of the parameters resulted in a continuous, fine-grained surface. This allowed us to accurately predict the relative stabilities of disulfide bonds in high resolution structures from the Protein Data Bank. The MP2(full) surface showed significant qualitative differences from the PES calculated using the Amber force field. In particular, a different ordering was seen for the relative energies of the local minima. Thus, Amber energies are not reliable for comparison of the relative stabilities of disulfide bonds. Surprisingly, the surface did not show a minimum associated with χ2 − 60°, χ390, χ2′ − 60°. This is due to steric interference between Hα atoms. Despite this, significant populations of disulfides were found to adopt this conformation. In most cases this conformation is associated with an unusual secondary structure motif, the cross-strand disulfide. The relative instability of cross-strand disulfides is of great interest, as they have the potential to act as functional switches in redox processes.

Shifting ground in some Australian photography

This is a report of a practice-as-research project. The chapter outlines McArdle's discoveries of means by which the pre-conscious processes of binocular vision and steropsis can be made visible in an effect which with one-eyed vision renders the scene 3-dimensional.

In the book's introduction editor Mehigan writes "[The] will to creation is only assayable once we estimate the role of the observer in the construction of space. McArdle's contribution, in engaging with the question of the animating presence of the observer focuses not just on what is caught in the lens of the photographer at the moment of depiction, but how the photographer's movement through space is the 'force field' that insinuates itself into the landscape and enters into a reciprocal relationship with it. The schematism of Euclidean geometry, for this reason, cannot account for the truth of the photographer's images; McArdle's metaphors are singularly non-Euclidean in their description of how objects are held together in the imaginative space of mental awareness."

The future of diversity and difference : can the national curriculum for English be hospitable?

This chapter explores the context of constructing the Australian Curriculum: English and how it represents and responds to the diversity of students. It starts with the brief genealogy of neoliberal standards-based reforms as a way of managing differences. In doing so, the chapter situates the national agenda of curriculum reforms in the semiotic order of ‘risk societies’ (Beck, 1992) through which various risks are both manufactured and managed. The semiotic order of managing educational risks through reforms is presented as a discursive force-field that both creates ‘moral panics’ and provides solutions, thereby appealing to the broader public and securing its consent. This discussion prepares the ground for the reading of texts produced in the lead-up to the actual release of the national curriculum for English and statements about diversity in these documents as well as in the curriculum itself. The chapter then goes on to explore what might be possible in the process of the curriculum implementation, by drawing on ideas of hospitality, responsibility and dialogism. In conclusion, this essay argues that no national curriculum can be successfully implemented unless it is sensitive to the textual and cultural practices of other groups and unless it wins their political consent. Equally, no national curriculum can be ethically implemented unless it recognises and responds to difference and unless it creates a possibility of transcending the logic of the Same.

Dossier Chris Marker : the suffering image

Dossier Chris Marker: The Suffering Image is a study of a late-modern chiasmus, impersonal-personal agency, as it comes to expression in the works of French artist and filmmaker, Chris Marker, as the dynamic interplay of political and subjective agency. As chiasmus, the complementary halves of this often-apocalyptic dynamis (a semi-catastrophic, temporal or historical force-field) also – arguably – secretly agree to meet, through the work of art, in the futural. Consistent with the classical figure of concordia discors, these irreducible warring aspects of life experience are, in fact, resolved in an atemporal and ahistorical moment that inhabits the work of art from its inception. This redemptive aspect in art is also the ultimate gesture of the artwork as “mask” or “screen” for forces that reside beyond the frame of the image or work, as its proverbial Other, or within the frame, as other to that Other. A topological “knot,” or ontological “problem,” it is this very conflict that animates all of Marker’s extensive works – filmic and otherwise.