Molecular dynamics study of MscL interactions with a curved lipid bilayer

Mechanosensitivity is a ubiquitous sensory mechanism found in living organisms. The simplest known mechanotransducing mechanism is found in bacteria in the form of the mechanosensitive membrane channel of large conductance, MscL. This channel has been studied extensively using a variety of methods at a functional and structural level. The channel is gated by membrane tension in the lipid bilayer alone. It serves as a safety valve protecting bacterial cells against hypoosmotic shock. MscL of Escherichia coli embedded in bilayers composed of asymmetric amounts of single-tailed and double-tailed lipids has been shown to gate spontaneously, even in the absence of membrane tension. To gain insight into the effect of the lipid membrane composition and geometry on MscL structure, a fully solvated, all-atom model of MscL in a stress-free curved bilayer composed of double- and single-tailed lipids was studied using a 9.5-ns molecular dynamics simulation. The bilayer was modeled as a domed structure accommodating the asymmetric composition of the monolayers. During the course of the simulation a spontaneous restructuring of the periplasmic loops occurred, leading to interactions between one of the loops and phospholipid headgroups. Previous experimental studies of the role of the loops agree with the observation that opening starts with a restructuring of the periplasmic loop, suggesting an effect of the curved bilayer. Because of limited resources, only one simulation of the large system was performed. However, the results obtained suggest that through the geometry and composition of the bilayer the protein structure can be affected even on short timescales.

Scattering and tangential momentum accommodation at a 2D adsorbate-solid interface

We calculate tangential momentum coefficients for the exchange of momentum between molecules in transport and the internal surface of a membrane pore, modelled as a simple atomic structure. We introduce a local specular reflection (LSR) hypothesis, which states that impinging molecules undergo mirror-like reflection in a plane tangent to a surface atom at the point of impact. As a consequence, the components of the velocity, parallel to the direction of flow will (in general) change on impact. The overall effect is a loss of tangential momentum, since more is lost in the upstream direction than is gained in the downstream direction. The loss of tangential momentum is greater when the size ratio of fluid to solid atom is small, allowing more steeply inclined impact planes to become accessible to the fluid phase molecules. (c) 2005 Elsevier B.V. All rights reserved.

The hydration of paper studied with solid-state magnetisation-exchange H-1 NMR spectroscopy

The wide-line H-1 nuclear magnetic resonance (NMR) spectrum of paper in equilibrium with ambient humidity consists of super-imposed relatively broad and narrow lines. The narrower line is of the order of 2 kHz wide at half the maximum height, while the broader line is of the order of 40 kHz in width at half height. On the basis of these line widths, the narrow line is assigned to water sorbed to the paper, and the broad line to the polymeric constituents of the paper. It was not possible to distinguish between the various polymeric components of paper contributing to the H-1 NMR spectra. A modified Goldman-Shen pulse sequence was used to generate a spatial magnetisation gradient between the polymer and water phases. The exchange of magnetisation between protons associated with water and those associated with the macromolecules in paper was observed. The exchange of magnetisation is discussed within a heat transfer model for homonuclear dipolar coupling, with exchange being characterised by a spin-diffusion coefficient. Consideration of the magnitude of the initial rate of the exchange process and estimates of the spin-spin relaxation times based on H-1 line widths indicate that some water must exist in a sufficiently immobile state as to allow homonuclear dipolar interactions between adjacent polymer and water protons. Thus, water sorbed onto paper must exist in at least two states in mass exchange with each other. This observation allows certain conclusions to be drawn about the ratio of free/bound water as a function of moisture content and the dispersal of water within the polymer matrix.

Implementation of particle-scale rotation in the 3-d Lattice Solid Model

In this study, 3-D Lattice Solid Model (LSMearth or LSM) was extended by introducing particle-scale rotation. In the new model, for each 3-D particle, we introduce six degrees of freedom: Three for translational motion, and three for orientation. Six kinds of relative motions are permitted between two neighboring particles, and six interactions are transferred, i.e., radial, two shearing forces, twisting and two bending torques. By using quaternion algebra, relative rotation between two particles is decomposed into two sequence-independent rotations such that all interactions due to the relative motions between interactive rigid bodies can be uniquely decided. After incorporating this mechanism and introducing bond breaking under torsion and bending into the LSM, several tests on 2-D and 3-D rock failure under uni-axial compression are carried out. Compared with the simulations without the single particle rotational mechanism, the new simulation results match more closely experimental results of rock fracture and hence, are encouraging. Since more parameters are introduced, an approach for choosing the new parameters is presented.

Solid-phase combinatorial chemistry and scintillation proximity assays

The Scintillation Proximity Assay (SPA) is a method that is frequently used to detect and quantify the strength of intermolecular interactions between a biological receptor and ligand molecule in aqueous media. This thesis describes the synthesis of scintillant-tagged-compounds for application in a novel cell-based SPA. A series of 4-functianlised-2,5-diphenyloxazole molecules were synthesised. These 4-functionalised-2,5-diphenyloxazoles were evaluated by Sense Proteomic Ltd. Accordingly, the molecules were evaluated for the ability to scintillate in the presence of ionising radiation. In addition, the molecules were incorporated into liposomal preparations which were subsequently evaluated for the ability to scintillate in the presence of ionising radiation. The optimal liposomal preparation was introduced into the membrane of HeLa cells that were used successfully in a cell-based SPA to detect and quantify the uptake of [14C]methionine. This thesis also describes the synthesis and subsequent polymerisation of novel poly(oxyethylene glycol)-based monomers to form a series of new polymer supports. These Poly(oxyethylene glycol)-polymer (POP) supports were evaluated for the ability to swell and mass-uptake in a variety of solvents, demonstrating that POP-supports exhibit enhanced solvent compatibilities over several commercial resins. The utility of POP-supports in solid-phase synthesis was also demonstrated successfully. The incorporation of (4’-vinyl)-4-benzyl-2,5-diphenyloxazole in varying mole percentage into the monomer composition resulted in the production of chemically functionalised scintillant-containing poly(oxyethylene glycol) polymer (POP-Sc) supports. These materials are compatible with both aqueous and organic solvents and scintillate efficiently in the presence of ionising radiation. The utility of POP-Sc supports in solid-phase synthesis and subsequent in-situ SPA to detect and quantify, in real-time, the kinetic progress of a solid-phase reaction was exemplified successfully.In addition, POP-Sc supports were used successfully both in solid-phase combinatorial synthesis of a peptide nucleic acid (PNA)-library and subsequent screening of this library for the ability to hybridise with DNA, which was labelled with a suitable radio-isotape. This data was used to identify the dependence of the number and position of complimentary codon pairs upon the extent of hybridisation. Finally, a further SPA was used to demonstrate the excellent compatibility of POP-Sc supports for use in the detection and quantification of enzyme assays conducted within the matrix of the POP-Sc support.

Solid base catalysed 5-HMF oxidation to 2,5-FDCA over Au/hydrotalcites:fact or fiction?

Nanoparticulate gold has emerged as a promising catalyst for diverse mild and efficient selective aerobic oxidations. However, the mechanism of such atom-economical transformations, and synergy with functional supports, remains poorly understood. Alkali-free Mg-Al hydrotalcites are excellent solid base catalysts for the aerobic oxidation of 5-hydroxymethylfurfural (HMF) to 2,5-furan dicarboxylic acid (FDCA), but only in concert with high concentrations of metallic gold nanoparticles. In the absence of soluble base, competitive adsorption between strongly-bound HMF and reactively-formed oxidation intermediates site-blocks gold. Aqueous NaOH dramatically promotes solution phase HMF activation, liberating free gold sites able to activate the alcohol function within the metastable 5-hydroxymethyl-2-furancarboxylic acid (HMFCA) reactive intermediate. Synergistic effects between moderate strength base sites within alkali-free hydrotalcites and high gold surface concentrations can afford highly selective and entirely heterogeneous catalysts for aqueous phase aldehyde and alcohol cascade oxidations pertinent to biomass transformation.

Gas-solid coexistence of adhesive spheres

In this note, the authors investigate whether the gas-liquid critical point can remain stable with respect to solidification for narrow attractive interactions down to the Baxter limit. Using a crude cell theory, the authors estimate the necessary conditions for this to be true. Possible realizations are briefly discussed.

PEG-based solid dispersions enhanced the solubility and dissolution of eprosartan mesylate in-vitro

Abstract - This study investigates the effect of solid dispersions prepared from of polyethylene glycol (PEG) 3350 and 6000 Da alone or combined with the non-ionic surfactant Tween 80 on the solubility and dissolution rate of a poorly soluble drug eprosartan mesylate (ESM) in attempt to improve its bioavailability following its oral administration.

INTRODUCTION

ESM is a potent anti-hypertension [1]. It has low water solubility and is classified as a Class II drug as per the Biopharmaceutical Classification Systems (BCS) leading to low and variable oral bioavailability (approximately 13%). [2]. Thus, improving ESM solubility and/or dissolution rate would eventually improve the drug bioavailability. Solid dispersion is widely used technique to improve the water solubility of poorly water-soluble drugs employing various biocompatible polymers. In this study, we aimed to enhance the solubility and dissolution of EMS employing solid dispersion (SD) formulated from two grades of poly ethylene glycol (PEG) polymers (i.e. PEG 3350 & PEG 6000 Da) either individually or in combination with Tween 80.

MATERIALS AND METHODS

ESM SDs were prepared by solvent evaporation method using either PEG 3350 or PEG 6000 at various (drug: polymer, w/w) ratios 1:1, 1:2, 1:3, 1:4, 1:5 alone or combined with Tween 80 added at fixed percentage of 0.1 of drug by weight?. Physical mixtures (PMs) of drug and carriers were also prepared at same ratios. Drug solid dispersions and physical mixtures were characterized in terms of drug content, drug dissolution using dissolution apparatus USP II and assayed using HPLC method. Drug dissolution enhancement ratio (ER %) from SD in comparison to the plain drug was calculated. Drug-polymer interactions were evaluated using Differential Scanning Calorimetry (DSC) and FT-IR.

RESULTS AND DISCUSSION

The in vitro solubility and dissolution studies showed SDs prepared using both polymers produced a remarkable improvement (p<0.05) in comparison to the plain drug which reached around 32% (Fig. 1). The dissolution enhancement ratio was polymer type and concentration-dependent. Adding Tween 80 to the SD did not show further dissolution enhancement but reduced the required amount of the polymer to get the same dissolution enhancement. The DSC and FT-IR studies indicated that using SD resulted in transformation of drug from crystalline to amorphous form.

CONCLUSIONS

This study indicated that SDs prepared by using both polymers i.e. PEG 3350 and PEG 6000 improved the in-vitro solubility and dissolution of ESM remarkably which may result in improving the drug bioavailability in vivo.

Acknowledgments

This work is a part of MSc thesis of O.M. Ali at the Faculty of Pharmacy, Aleppo University, Syria.

REFERENCES

[1] Ruilope L, Jager B: Eprosartan for the treatment of hypertension. Expert Opin Pharmacother 2003; 4(1):107-14

[2] Tenero D, Martin D, Wilson B, Jushchyshyn J, Boike S, Lundberg, D, et al. Pharmacokinetics of intravenously and orally administered Eprosartan in healthy males: absolute bioavailability and effect of food. Biopharm Drug Dispos 1998; 19(6): 351- 6.

The use of binary polymeric networks in stabilising polyethylene oxide solid dispersions

The objective of this study was to determine if a high Tg polymer (Eudragit® S100) could be used to stabilize amorphous domains of polyethylene oxide (PEO) and hence improve the stability of binary polymer systems containing celecoxib (CX). We propose a novel method of stabilizing the amorphous PEO solid dispersion through inclusion of a miscible, high Tg polymer, namely, that can form strong inter-polymer interactions. The effects of inter-polymer interactions and miscibility between PEO and Eudragit S100 are considered. Polymer blends were first manufactured via hot-melt extrusion at different PEO/S100 ratios (70/30, 50/50, and 30/70 wt/wt). Differential scanning calorimetry and dynamic mechanical thermal analysis data suggested a good miscibility between PEO and S100 polymer blends, particularly at the 50/50 ratio. To further evaluate the system, CX/PEO/S100 ternary mixtures were extruded. Immediately after hot-melt extrusion, a single Tg that increased with increasing S100 content (anti-plasticization) was observed in all ternary systems. The absence of powder X-ray diffractometry crystalline Bragg’s peaks also suggested amorphization of CX. Upon storage (40°C/75% relative humidity), the formulation containing PEO/S100 at a ratio of 50:50 was shown to be most stable. Fourier transform infrared studies confirmed the presence of hydrogen bonding between Eudragit S100 and PEO suggesting this was the principle reason for stabilization of the amorphous CX/PEO solid dispersion system.

Direct observation of a long-lived single-atom catalyst chiseling atomic structures in graphene

Fabricating stable functional devices at the atomic scale is an ultimate goal of nanotechnology. In biological processes, such high-precision operations are accomplished by enzymes. A counterpart molecular catalyst that binds to a solid-state substrate would be highly desirable. Here, we report the direct observation of single Si adatoms catalyzing the dissociation of carbon atoms from graphene in an aberration-corrected high-resolution transmission electron microscope (HRTEM). The single Si atom provides a catalytic wedge for energetic electrons to chisel off the graphene lattice, atom by atom, while the Si atom itself is not consumed. The products of the chiseling process are atomic-scale features including graphene pores and clean edges. Our experimental observations and first-principles calculations demonstrated the dynamics, stability, and selectivity of such a single-atom chisel, which opens up the possibility of fabricating certain stable molecular devices by precise modification of materials at the atomic scale.

Modélisation d'éléments finis pour les interactions fluide-structure

Cette thèse concerne la modélisation des interactions fluide-structure et les méthodes numériques qui s’y rattachent. De ce fait, la thèse est divisée en deux parties. La première partie concerne l’étude des interactions fluide-structure par la méthode des domaines fictifs. Dans cette contribution, le fluide est incompressible et laminaire et la structure est considérée rigide, qu’elle soit immobile ou en mouvement. Les outils que nous avons développés comportent la mise en oeuvre d’un algorithme fiable de résolution qui intégrera les deux domaines (fluide et solide) dans une formulation mixte. L’algorithme est basé sur des techniques de raffinement local adaptatif des maillages utilisés permettant de mieux séparer les éléments du milieu fluide de ceux du solide que ce soit en 2D ou en 3D. La seconde partie est l’étude des interactions mécaniques entre une structure flexible et un fluide incompressible. Dans cette contribution, nous proposons et analysons des méthodes numériques partitionnées pour la simulation de phénomènes d’interaction fluide-structure (IFS). Nous avons adopté à cet effet, la méthode dite «arbitrary Lagrangian-Eulerian» (ALE). La résolution fluide est effectuée itérativement à l’aide d’un schéma de type projection et la structure est modélisée par des modèles hyper élastiques en grandes déformations. Nous avons développé de nouvelles méthodes de mouvement de maillages pour aboutir à de grandes déformations de la structure. Enfin, une stratégie de complexification du problème d’IFS a été définie. La modélisation de la turbulence et des écoulements à surfaces libres ont été introduites et couplées à la résolution des équations de Navier-Stokes. Différentes simulations numériques sont présentées pour illustrer l’efficacité et la robustesse de l’algorithme. Les résultats numériques présentés attestent de la validité et l’efficacité des méthodes numériques développées.

Dynamic fluid-structure interactions using finite volume unstructured mesh procedures

A three-dimensional finite volume, unstructured mesh (FV-UM) method for dynamic fluid–structure interaction (DFSI) is described. Fluid structure interaction, as applied to flexible structures, has wide application in diverse areas such as flutter in aircraft, wind response of buildings, flows in elastic pipes and blood vessels. It involves the coupling of fluid flow and structural mechanics, two fields that are conventionally modelled using two dissimilar methods, thus a single comprehensive computational model of both phenomena is a considerable challenge. Until recently work in this area focused on one phenomenon and represented the behaviour of the other more simply. More recently, strategies for solving the full coupling between the fluid and solid mechanics behaviour have been developed. A key contribution has been made by Farhat et al. [Int. J. Numer. Meth. Fluids 21 (1995) 807] employing FV-UM methods for solving the Euler flow equations and a conventional finite element method for the elastic solid mechanics and the spring based mesh procedure of Batina [AIAA paper 0115, 1989] for mesh movement. In this paper, we describe an approach which broadly exploits the three field strategy described by Farhat for fluid flow, structural dynamics and mesh movement but, in the context of DFSI, contains a number of novel features: a single mesh covering the entire domain, a Navier–Stokes flow, a single FV-UM discretisation approach for both the flow and solid mechanics procedures, an implicit predictor–corrector version of the Newmark algorithm, a single code embedding the whole strategy.

Materials design for ambipolar devices: tuning orbital energetics in oligothiophene-naphthalimides semiconductors

Ambipolar organic field-effect transistors (OFETs), which can efficiently transport both holes and electrons, using a single type of electrode, are currently of great interest due to their possible applications in complementary metal oxide semiconductor (CMOS)-like circuits, sensors, and in light-emitting transistors. Several theoretical and experimental studies have argued that most organic semiconductors should be able to transport both types of carrier, although typically unipolar behavior is observed. One factor that can compromise ambipolar transport in organic semiconductors is poor solid state overlap between the HOMO (p-type) or LUMO (n-type) orbitals of neighboring molecules in the semiconductor thin film. In the search of low-bandgap ambipolar materials, where the absence of skeletal distortions allows closer intermolecular π-π stacking and enhanced intramolecular π-conjugation, a new family of oligothiophene-naphthalimide assemblies have been synthesized and characterized, in which both donor and acceptor moieties are directly conjugated through rigid linkers. In previous works we found that oligothiophene-napthalimide assemblies connected through amidine linkers (NDI derivates) exhibit skeletal distortions (50-60º) arising from steric hindrance between the carbonyl group of the arylene core and the sulphur atom of the neighbored thiophene ring (see Figure 1). In the present work we report novel oligo- and polythiophene–naphthalimide analogues NAI-3T, NAI-5T and poly-NAI-8C-3T, in which the connections of the amidine linkage have been inverted in order to prevent steric interactions. Thus, the nitrogen atoms are directly connected to the naphthalene moiety in NAI derivatives while they were attached directly to the thiophene moiety in the previously investigated NDI-3T and NDI-5T. In Figure 1 is depicted the calculated molecular structure of NAI-3T together with that of NDI-3T showing how the steric interactions are not present in the novel NAI derivative. The planar skeletons in these new family induce higher degree of crystallinity and the carrier charge transport can be switched from n-type to ambipolar behaviour. The highest FET performance is achieved for vapor-deposited films of NAI-3T with mobilities of 1.95x10-4cm2V-1s-1 and 2.00x10-4cm2V-1s-1 for electrons and holes, respectively. Finally, these planar semiconductors are compared with their NDI derivates analogues, which exhibit only n-type mobility, in order to understand the origin of the ambipolarity in this new series of molecular semiconductors.

Theoretical and experimental study on electron interactions with chlorobenzene: Shape resonances and differential cross sections

In this work, we report theoretical and experimental cross sections for elastic scattering of electrons by chlorobenzene (ClB). The theoretical integral and differential cross sections (DCSs) were obtained with the Schwinger multichannel method implemented with pseudopotentials (SMCPP) and the independent atom method with screening corrected additivity rule (IAM-SCAR). The calculations with the SMCPP method were done in the static-exchange (SE) approximation, for energies above 12 eV, and in the static-exchange plus polarization approximation, for energies up to 12 eV. The calculations with the IAM-SCAR method covered energies up to 500 eV. The experimental differential cross sections were obtained in the high resolution electron energy loss spectrometer VG-SEELS 400, in Lisbon, for electron energies from 8.0 eV to 50 eV and angular range from 7 degrees to 110 degrees. From the present theoretical integral cross section (ICS) we discuss the low-energy shape-resonances present in chlorobenzene and compare our computed resonance spectra with available electron transmission spectroscopy data present in the literature. Since there is no other work in the literature reporting differential cross sections for this molecule, we compare our theoretical and experimental DCSs with experimental data available for the parent molecule benzene. Published by AIP Publishing.