A molecular interpretation of vitreous boron oxide dynamics

The mobility of vitreous boron oxide is studied by molecular dynamics simulation. A polarization model that incorporates induced dipoles arising both from charges and from other induced dipoles on atoms with nonzero polarizability is used to simulate boron oxide glass at various temperatures above the glass transition temperature. Particle mobility is investigated through the calculation of the self-intermediate scattering function and the mean-squared displacement. The calculations clearly reveal a two-step relaxation with a plateau at intermediate times for all investigated temperatures. With respect to atomic species, boron atoms are less mobile than oxygen atoms at all temperatures within the plateau region. Through analyzing particle trajectories, it is revealed that BO(3) groups move as one unit and follow each other in a stringlike manner. Three connected BO(3) groups comprise a six-membered boroxol ring, which is shown to move in a collective manner, requiring the simultaneous movement of all ring atoms. The boroxol ring is observed to be confined, or caged, during the plateau region, and jumps to a new location at longer times. This observation is linked to the concept of strong versus fragile glass formers and the potential energy landscape. In addition to the caging feature, an overshoot or dip occurs in the plateau regions of the mean-squared displacement and self-intermediate scattering functions respectively. These features are followed by a ringing pattern, previously associated with finite size effects in other strong glass formers, which persist for the duration of the plateau region. Both features are shown to be consistent with the bending of atomic "cages" from the plane of the boroxol ring, and arise due to the displacement of atoms from local minimum energy configurations.     

The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting

Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white‐beam X‐ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady‐state and millisecond time‐resolved footprinting experiments based on the production of hydroxyl radicals by X‐rays. Footprinting studies of nucleic acids are routinely conducted with X‐ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein–protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches.     

Temperature dependence of the colloidal agglomeration inhibition: computer simulation study

There exist experimental evidences that the structure and extension of colloidal aggregates in suspensions change dramatically with temperature. This results in an associated change in the suspension rheology. Experimental studies of the inhibitor applications to control the particle clustering have revealed some unexpected tendencies. Namely, the heating of colloidal suspensions has provoked either extension or reduction of the colloidal aggregates. To elucidate the origin of this behavior, we investigate the influence of temperature on the stabilizing effect of the inhibitor, applying an associative two-component fluid model. Our results of the canonical Monte Carlo simulations indicate that the anomalous effect of the temperature may not be necessarily explained by the temperature dependent changes in the inhibitor tail conformation, as has been suggested recently by Won et al. [Langmuir 21, 924 (2005)]. We show that the competition between colloid-colloid and colloid-inhibitor associations, which, in turn, depends on the temperature and the relative concentrations, may be one of the main reasons for the unexpected temperature dependence of inhibitor efficacy.     

Can we live in the bulk without a brane?

We suggest a braneless scenario that still hides large-volume extra dimensions. Ordinarily the strength of bulk gauge interactions would be diluted over the large internal volume, making all the four-dimensional forces weak. We use the fact that if the gauge fields result from the dimensional reduction of pure higher-dimensional gravity, then the strengths of the four-dimensional gauge interactions are related to the sizes of corresponding cycles averaged over the compact internal manifold. Therefore, if a gauge force is concentrated over a small cycle it will not be diluted over the entire manifold. Gravity, however, remains diluted over the large volume. Thus large-volume, large mass-gap extra dimensions with small cycles can remain hidden and result in a hierarchy between gravity and the other forces. However, problematically, the cycles are required to be smaller than the higher-dimensional Planck length and this raises concern over quantum gravity corrections. We speculate on possible cures.     

Influence of thermal history and humidity on the ionic conductivity of nanoparticle‐filled solid polymer electrolytes

The crystallinity and conductivity of nanoparticle‐filled solid polymer electrolytes (SPEs) are investigated as a function of thermal history and water content. Our objective is to evaluate how performance is affected by the conditions under which the SPEs are handled and tested. The samples consist of polyethylene oxide (PEO), LiClO₄, and Al₂O₃ nanoparticles. At low humidity, SPEs at ether oxygen to lithium ratios of 8:1 do not crystallize immediately; instead, 3 days are required for crystallization to occur, and this does not depend strongly on the presence of nanoparticles. The conductivity is improved by the addition of nanoparticles at low humidity, but only at an ether oxygen to lithium ratio of 10:1, which corresponds to the eutectic concentration. At high humidity, the recrystallization time is delayed for 3 weeks, and the conductivity increases in both filled and unfilled SPEs beyond that of the low humidity samples. Although we observe that water amplifies the influence of nanoparticles on conductivity, we also find that nanoparticles inhibit water uptake—but only in the presence of lithium. Because Li⁺ strongly absorbs water, this result suggests that nanoparticles may interact directly with Li⁺ ions to prevent water uptake. In filled samples at the eutectic concentration (10:1), more water is absorbed compared to the nanoparticle‐filled 8:1 samples, even though less lithium is present. This suggests that nanoparticles may segregate to lithium‐poor regions in the 10:1 samples, and this scenario is supported by the morphology that would be expected at the eutectic concentration. © 2011 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 49: 1496–1505, 2011     

Future directions of structural mass spectrometry using hydroxyl radical footprinting

Hydroxyl radical protein footprinting coupled to mass spectrometry has been developed over the last decade and has matured to a powerful method for analyzing protein structure and dynamics. It has been successfully applied in the analysis of protein structure, protein folding, protein dynamics, and protein–protein and protein–DNA interactions. Using synchrotron radiolysis, exposure of proteins to a ‘white’ X‐ray beam for milliseconds provides sufficient oxidative modification to surface amino acid side chains, which can be easily detected and quantified by mass spectrometry. Thus, conformational changes in proteins or protein complexes can be examined using a time‐resolved approach, which would be a valuable method for the study of macromolecular dynamics. In this review, we describe a new application of hydroxyl radical protein footprinting to probe the time evolution of the calcium‐dependent conformational changes of gelsolin on the millisecond timescale. The data suggest a cooperative transition as multiple sites in different molecular subdomains have similar rates of conformational change. These findings demonstrate that time‐resolved protein footprinting is suitable for studies of protein dynamics that occur over periods ranging from milliseconds to seconds. In this review, we also show how the structural resolution and sensitivity of the technology can be improved as well. The hydroxyl radical varies in its reactivity to different side chains by over two orders of magnitude, thus oxidation of amino acid side chains of lower reactivity are more rarely observed in such experiments. Here we demonstrate that the selected reaction monitoring (SRM)‐based method can be utilized for quantification of oxidized species, improving the signal‐to‐noise ratio. This expansion of the set of oxidized residues of lower reactivity will improve the overall structural resolution of the technique. This approach is also suggested as a basis for developing hypothesis‐driven structural mass spectrometry experiments. Copyright © 2010 John Wiley & Sons, Ltd.     

Neumann heat flow and gradient flow for the entropy on non-convex domains

For large classes of non-convex subsets Y in \(\mathbb R^n\) or in Riemannian manifolds (M, g) or in RCD-spaces (X, d, m) we prove that the gradient flow for the Boltzmann entropy on the restricted metric measure space \((Y,d_Y,m_Y)\) exists—despite the fact that the entropy is not semiconvex—and coincides with the heat flow on Y with Neumann boundary conditions.     

Metal- and ligation-dependent fragmentation of [M(1,10-Phenanthroline)(1,2,3)]2+ cations with M = Mn, Fe, Co, Ni, Cu, and Zn: Comparison between the gas phase and solution

The core ions [ML(n)]2+ with n = 1-3, where L = 1,10-phenanthroline and M is a first-row transition metal, have been successfully transferred from aqueous solution into the gas phase by electrospraying and then probed for their stabilities by collision-induced dissociation in a triple quadrupole mass spectrometer. The triply ligated metal dications [ML3]2+ were observed to dissociate by the extrusion of a neutral ligand, while ligand loss from both [ML2]2+ and [ML]2+ was accompanied by electron transfer. Comparisons are provided between gas-phase stabilities and stabilities for ligand loss measured in aqueous solution at 298 K. The measured onset for ligand loss from [ML3]2+ is quite insensitive to the metal, while a distinct stability order has been reported for aqueous solution. Low level density functional theory (DFT) calculations predict an intrinsic stability order for loss of ligand from [ML2]2+, but it differs from that in aqueous solution. Substantial agreement was obtained for the stability order for the loss of ligand from [ML]2+ deduced from onset energies measured for charge separation, computed with DFT, and reported for aqueous solution where hydration seems less decisive in influencing this stability order. A qualitative potential-energy diagram is presented that allows the energy for charge separation to be related to the energy for neutral ligand loss from [ML]2+ and shows that IE(M+) is decisive in determining the intrinsic stability order for loss of ligand from [ML]2+.