Molecular packing and chemical association in liquid water simulated using ab initio hybrid Monte Carlo and different exchange-correlation functionals

In the free energy of hydration of a solute, the chemical contribution is given by the free energy required to expel water molecules from the coordination sphere and the packing contribution is given by the free energy required to create the solute-free coordination sphere (the observation volume) in bulk water. With the SPC/E water model as a reference, we examine the chemical and packing contributions in the free energy of water simulated using different electron density functionals. The density is fixed at a value corresponding to that for SPC/E water at a pressure of 1 bar. The chemical contribution shows that water simulated at 300 K with BLYP is somewhat more tightly bound than water simulated at 300 K with the revPBE functional or at 350 K with the BLYP and BLYP-D functionals. The packing contribution for various radii of the observation volume is studied. In the size range where the distribution of water molecules in the observation volume is expected to be Gaussian, the packing contribution is expected to scale with the volume of the observation sphere. Water simulated at 300 K with the revPBE and at 350 K with BLYP-D or BLYP conforms to this expectation, but the results suggest an earlier onset of system size effects in the BLYP 350 K and revPBE 300 K systems than that observed for either BLYP-D 350 K or SPC/E. The implication of this observation for constant pressure simulations is indicated. For water simulated at 300 K with BLYP, in the size range where Gaussian distribution of occupation is expected, we instead find non-Gaussian behavior, and the packing contribution scales with surface area of the observation volume, suggesting the presence of heterogeneities in the system

The Lense-Thirring effect in the Jovian system of the Galilean satellites and its measurability

In this paper we investigate the possibility of measuring the post-Newtonian general relativistic gravitomagnetic Lense-Thirring effect in the Jovian system of its Galilean satellites Io, Europa, Ganymede and Callisto in view of recent developments in processing and modelling their optical observations spanning a large time interval (125 years). The present day best observations have an accuracy between several kilometers to few tens of kilometers, which is just the order of magnitude of the Lense-Thirring shifts of the orbits of the Galilean satellites over almost a century. From a comparison between analytical development and numerical integration it turns out that, unfortunately, most of the secular component of the gravitomagnetic signature is removed in the process of fitting the initial conditions. Indeed, an estimation of the magnitude of the Lense-Thirring effect in the ephemerides residuals is given; the resulting residuals have a maximum magnitude of 20 meters only (over 125 years).Comment: Latex, 10 pages, 4 tables, 3 figures, 27 references. Invited paper for a Special Issue of Int. J. Mod. Phys. D on the Lense-Thirring effect, D. Grumiller edito

Distraction from pain and executive functioning: an experimental investigation of the role of inhibition, task switching and working memory

Although many studies have investigated the effectiveness of distraction as a method of pain control, the cognitive processes by which attentional re-direction is achieved, remain unclear. In this study the role of executive functioning abilities (inhibition, task switching and working memory) in the effectiveness of distraction is investigated. We hypothesized that the effectiveness of distraction in terms of pain reduction would be larger in participants with better executive functioning abilities. Ninety-one undergraduate students first performed executive functioning tasks, and subsequently participated in a cold pressor task (CPT). Participants were randomly assigned to (1) a distraction group, in which an attention-demanding tone-detection task was performed during the CPT, or (2) a control group, in which no distraction task was performed. Participants in the distraction group reported significantly less pain during the CPT, but the pain experience was not influenced by executive functioning abilities. However, the performance on the distraction task improved with better inhibition abilities, indicating that inhibition abilities might be important in focussing on a task despite the pain

Ab initio linear scaling response theory: Electric polarizability by perturbed projection

A linear scaling method for calculation of the static {\em ab inito} response within self-consistent field theory is developed and applied to calculation of the static electric polarizability. The method is based on density matrix perturbation theory [Niklasson and Challacombe, cond-mat/0311591], obtaining response functions directly via a perturbative approach to spectral projection. The accuracy and efficiency of the linear scaling method is demonstrated for a series of three-dimensional water clusters at the RHF/6-31G** level of theory. Locality of the response under a global electric field perturbation is numerically demonstrated by approximate exponential decay of derivative density matrix elements.Comment: 4.25 pages in PRL format, 2 figure

Solvent contribution to the stability of a physical gel characterized by quasi-elastic neutron scattering

The dynamics of a physical gel, namely the Low Molecular Mass Organic Gelator {\textit Methyl-4,6-O-benzylidene-$\alpha$ -D-mannopyranoside ($\alpha$-manno)} in water and toluene are probed by neutron scattering. Using high gelator concentrations, we were able to determine, on a timescale from a few ps to 1 ns, the number of solvent molecules that are immobilised by the rigid network formed by the gelators. We found that only few toluene molecules per gelator participate to the network which is formed by hydrogen bonding between the gelators' sugar moieties. In water, however, the interactions leading to the gel formations are weaker, involving dipolar, hydrophobic or $\pi-\pi$ interactions and hydrogen bonds are formed between the gelators and the surrounding water. Therefore, around 10 to 14 water molecules per gelator are immobilised by the presence of the network. This study shows that neutron scattering can give valuable information about the behaviour of solvent confined in a molecular gel.Comment: Langmuir (2015

Giant capsids from lattice self-assembly of cyclodextrin complexes

Proteins can readily assemble into rigid, crystalline and functional structures such as viral capsids and bacterial compartments. Despite ongoing advances, it is still a fundamental challenge to design and synthesize protein-mimetic molecules to form crystalline structures. Here we report the lattice self-assembly of cyclodextrin complexes into a variety of capsidlike structures such as lamellae, helical tubes and hollow rhombic dodecahedra. The dodecahedral morphology has not hitherto been observed in self-assembly systems. The tubes can spontaneously encapsulate colloidal particles and liposomes. The dodecahedra and tubes are respectively comparable to and much larger than the largest known virus. In particular, the resemblance to protein assemblies is not limited to morphology but extends to structural rigidity and crystallinity-a well-defined, 2D rhombic lattice of molecular arrangement is strikingly universal for all the observed structures. We propose a simple design rule for the current lattice self-assembly, potentially opening doors for new protein-mimetic materials

Idiosyncratic features in tRNAs participating in bacterial cell wall synthesis

The FemXWv aminoacyl transferase of Weissella viridescens initiates the synthesis of the side chain of peptidoglycan precursors by transferring l-Ala from Ala-tRNAAla to UDP-MurNAc-pentadepsipeptide. FemXWv is an attractive target for the development of novel antibiotics, since the side chain is essential for the last cross-linking step of peptidoglycan synthesis. Here, we show that FemXWv is highly specific for incorporation of l-Ala in vivo based on extensive analysis of the structure of peptidoglycan. Comparison of various natural and in vitro-transcribed tRNAs indicated that the specificity of FemXWv depends mainly upon the sequence of the tRNA although additional specificity determinants may include post-transcriptional modifications and recognition of the esterified amino acid. Site-directed mutagenesis identified cytosines in the G1–C72 and G2–C71 base pairs of the acceptor stem as critical for FemXWv activity in agreement with modeling of tRNAAla in the catalytic cavity of the enzyme. In contrast, semi-synthesis of Ala-tRNAAla harboring nucleotide substitutions in the G3–U70 wobble base pair showed that this main identity determinant of alanyl-tRNA synthetase is non-essential for FemXWv. The different modes of recognition of the acceptor stem indicate that specific inhibition of FemXWv could be achieved by targeting the distal portion of tRNAAla for the design of substrate analogues

Assessing Communities of Practice in health policy : A conceptual framework as a first step towards empirical research

Peer reviewe

Les Houches 2011: Physics at TeV Colliders New Physics Working Group Report

We present the activities of the "New Physics" working group for the "Physics at TeV Colliders" workshop (Les Houches, France, 30 May-17 June, 2011). Our report includes new agreements on formats for interfaces between computational tools, new tool developments, important signatures for searches at the LHC, recommendations for presentation of LHC search results, as well as additional phenomenological studies.Comment: 243 pages, report of the Les Houches 2011 New Physics Group; fix three figure