Phase Behavior of the Patchy Colloids Confined in the Patchy Porous Media

A simple model for functionalized disordered porous media is proposed and the effects of confinement on self-association, percolation and phase behavior of a fluid of patchy particles are studied. The media is formed by a randomly distributed hard-sphere obstacles fixed in space and decorated by a certain number of off-center square-well sites. The properties of the fluid of patchy particles, represented by the fluid of hard spheres each bearing a set of the off-center square-well sites, are studied using an appropriate combination of the scaled particle theory for the porous media, Wertheim's thermodynamic perturbation theory, and the Flory-Stockmayer theory. To assess the accuracy of the theory a set of computer simulations have been performed. In general, predictions of the theory appear to be in a good agreement with computer simulation results. Confinement and competition between the formation of bonds connecting the fluid particles, and connecting fluid particles and obstacles of the matrix, give rise to a re-entrant phase behavior with three critical points and two separate regions of the liquid-gas phase coexistence

The oscillatory damped behaviour of incommensurate double-walled carbon nanotubes

Abstract The mechanical properties of sliding carbon nanotubes have been investigated by classical molecular dynamics simulations in the canonical ensemble. In particular we have studied damped oscillations in the separation between the centres of mass of the inner and outer tubes of double-walled carbon nanotubes (DWCN). Incommensurate DWCNs forming (7, 0)@(9, 9) structures were simulated for systems at 298.15 K with axial lengths from 12.21 to 98.24 nm. The oscillations exhibited frequencies in the range of gigahertz with the frequency decreasing as the length of the system increases. The time until oscillations become negligible exhibited a nearly linear dependence on the length of the system. Two macroscopic models were developed in order to understand the forces involved in terms of macroscopic properties like friction and shear. The first model considered constant restoring forces during the whole event, while in the second the value of these constant restoring forces depended on the initial conditions of each oscillation. Both models reproduced the oscillations quite well, while the second model allows us to predict the dynamic shear strength in terms of the axial length of the system for tubes with the same diameters. The calculated dynamic shear strength exhibited monotonic behaviour with an inverse dependence on the length of the system. For systems with unequal axial lengths, the restoring force, which drives the oscillation, is reduced compared to the system with equal lengths, regardless of whether the outer nanotube is longer or shorter. M This article contains online multimedia enhancement

Swift Observations of GRB 050603: An afterglow with a steep late time decay slope

We report the results of Swift observations of the Gamma Ray Burst GRB 050603. With a V magnitude V=18.2 about 10 hours after the burst the optical afterglow was the brightest so far detected by Swift and one of the brightest optical afterglows ever seen. The Burst Alert Telescope (BAT) light curves show three fast-rise-exponential-decay spikes with $T_{90}$=12s and a fluence of 7.6$\times 10^{-6}$ ergs cm$^{-2}$ in the 15-150 keV band. With an $E_{\rm \gamma, iso} = 1.26 \times 10^{54}$ ergs it was also one of the most energetic bursts of all times. The Swift spacecraft began observing of the afterglow with the narrow-field instruments about 10 hours after the detection of the burst. The burst was bright enough to be detected by the Swift UV/Optical telescope (UVOT) for almost 3 days and by the X-ray Telescope (XRT) for a week after the burst. The X-ray light curve shows a rapidly fading afterglow with a decay index $\alpha$=1.76$^{+0.15}_{-0.07}$. The X-ray energy spectral index was $\beta_{\rm X}$=0.71\plm0.10 with the column density in agreement with the Galactic value. The spectral analysis does not show an obvious change in the X-ray spectral slope over time. The optical UVOT light curve decays with a slope of $\alpha$=1.8\plm0.2. The steepness and the similarity of the optical and X-ray decay rates suggest that the afterglow was observed after the jet break. We estimate a jet opening angle of about 1-2$^{\circ}$Comment: 14 pages, accepted for publication in Ap

Experimental and theoretical justifications for the observed discriminations between enantiomers of prochiral alcohols by chirally blind EI-MS

To all appearances, electron impact mass spectrometer (EI-MS) is considered a "chirally blind" instrument. Yet, numerous non-identical R (right) and S (left) configurations of prochiral alcohols' mass spectra alcohols have appeared in the literature with almost no justification. Such observations are often attributed to impurities, experimental circumstances, inaccurate measurements, etc. In an experimental attempt to explain this phenomenon, here we have avoided the above mentioned pitfalls by conducting control experiments using different pure enantiomers under the same circumstances. Hence, we report the mass spectra of R- and S-enantiomers of 2-octanol (1R, 1S) and 1-octyn-3-ol (2R, 2S) collected by running 20 independent experiments for each R- and S-enantiomer. Statistical analyses confirmed that the peak intensities were significant to an acceptable level of confidence. The 1R and 1S enantiomers were separated reasonably in the PC space, implying that the chirally blind EI-MS is able to discriminate between R and S prochiral alcohols. Theoretically, self-complexation through H-bonding for S (or R) appears to give a new chiral center at the H-bonded oxygen atom, producing a new dimeric pair of diastereomers SRS and SSS (or RRR and RSR) before ionization, and SRS.+ and SSS.+ (or RRR.+ and RSR.+) after ionization. The results of our calculations have explicitly shown that these hydrogen bonds formed. Interestingly, the latter four ionized diastereomers appear with different structural and thermodynamic parameters at the M06-2X/6-311++g (d,p) level of theory

Formalizing Atom-typing and the Dissemination of Force Fields with Foyer

A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models. Ambiguity in molecular models often stems from the dissemination of molecular force fields in a format that is not directly usable or is ambiguously documented via a non-machine readable mechanism. Specifically, the lack of a general tool for performing automated atom-typing under the rules of a particular force field facilitates errors in model parameterization that may go unnoticed if other researchers are unable reproduce this process. Here, we present Foyer, a Python tool that enables users to define force field atom-typing rules in a format that is both machine- and human-readable thus eliminating ambiguity in atom-typing and additionally providing a framework for force field dissemination. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type. Herein we describe the underlying methodology of the Foyer package, highlighting its advantages over typical atom-typing approaches and demonstrate is application in several use-cases.Comment: 39 Page, 4 Figures, 8 Listing