Structure of Hydrated Kaolinite Edge Surfaces: DFT Results and Further Development of the ClayFF Classical Force Field with Metal-O-H Angle Bending Terms
Toward the development of classical force fields for the accurate modeling of clay mineral-water systems, we have extended the use of metalâ€“Oâ€“H (Mâ€“Oâ€“H) angle bending terms to describe surface Siâ€“Oâ€“H bending for hydrated kaolinite edge structures. Kaolinite, comprising linked octahedral Al and tetrahedral Si sheets, provides a rigorous test by combining aluminol and silanol groups with water molecules in hydrated edge structures. Periodic density functional theory and classical force fields were used with molecular dynamics to evaluate the structure, dynamics, hydrogen bonding, and power spectra for deriving optimum bending force constants and optimal equilibrium angles. Cleavage energies derived from density functional theory molecular dynamics calculations indicate the relative stabilities of both AC1 and AC2 edge terminations of kaolinite where Siâ€“OH and Alâ€“(OH2) or Siâ€“OH, Alâ€“OH, and Alâ€“(OH2) groups exist, respectively. Although not examined in this study, the new Siâ€“Oâ€“H angle bending parameter should allow for improved modeling of hydroxylated surfaces of silica minerals such as quartz and cristobalite, as well as amorphous silica-based surfaces and potentially those of other silicate and aluminosilicate phases.
Dust particles under certain conditions can acquire kinetic energy of the order of 10 eV and higher, far above the temperature of gas and temperatures of ions and electrons in the discharge. Furthermore, significant difference of mean horizontal and vertical energy is observed. Such difference can be explained by the energy transfer between degrees of freedom of a dusty plasma system. The proposed mechanism of energy transfer between vertical and horizontal motion is based on parametric resonance. A system of equations describing dust particles' motion with account of dust particle charge fluctuations and features of the discharge near-electrode layer is formulated. Molecular dynamics simulations of dust particles' system are performed. Dependences of magnitude of transferred energy and horizontal energy growth rate on system parameters are obtained.
Using molecular dynamics simulations, we investigate the effect of uniaxial elastostatic compression on the potential energy, structural relaxation, and mechanical properties of binary glasses. We consider the three-dimensional Kob-Andersen binary mixture, which was initially cooled from the liquid state to the glass phase with a slow rate at zero pressure. The glass was then loaded with a static stress at the annealing temperature during extended time intervals. It is found that the static stress below the yielding point induces large-scale plastic deformation and significant rejuvenation when the annealing temperature is smaller than a fraction of the glass transition temperature. By contrast, aging effects become dominant at sufficiently small values of the static stress and higher annealing temperatures. The mechanical tests after the elastostatic compression have shown that both the elastic modulus and the yield stress decrease in rejuvenated samples, while the opposite trend was observed for relaxed glasses. These results might be useful for the thermomechanical processing of metallic glasses with optimized mechanical properties.
This paper addresses hybrid ion exchange membranes fabricated by the synthesis of amorphous zirconium phosphate (dopant contents from 0.5 to 24 wt%) directly in the pore and channel system of heterogeneous cation-exchange membrane RALEX® CM (by in situ technique). The incorporation of zirconium phosphate nanoparticles into the membrane system of pores and channels leads to the displacement of the pore water. As a result, the cation transport numbers increase. The hybrid materials thus obtained are characterized by increased ionic resistance and enhanced monovalent ion selectivity. The former effect was eliminated by fabrication of a surface-modified membrane. The relative simplicity of modification, together with the benefits of the hybrid materials make them promising for some membrane processes. Using 31P MAS NMR and elemental analysis, considerable difference between the zirconium phosphate composition inside and outside the membrane was found.
The Callovo-Oxfordian clay formation (COx) is the potential host rock for long term nuclear waste repository in France. The clayey component of COx consists mostly of illite, smectite and interstratified illite/smectite (I/S) clay minerals. We performed a series of molecular dynamics (MD) computer simulations in order to quantify the molecular scale mechanisms responsible for the adsorption and transport of ions at the hydrated surfaces of illite, smectite, and I/S clays. New structural models of illite, smectite, and I/S allowed us to identify several structurally different adsorption sites at the basal surfaces of all three clay substrates. Adsorption free energy profiles above each individual adsorption site on each clay surface for a wide range of metal cations were then calculated and the metal sorption properties for the three clay surfaces are compared in terms of the preferable sorption sites and their surface distributions, most stable adsorption distances, and free energies of adsorption. The resulting equilibrium constants for surface adsorption and ion exchange were calculated and found in general agreement with available literature data. The observed discrepancies between the exchange energies obtained in the current MD simulations and the values obtained through the interpretation of recent X-ray reflectivity measurements can be attributed to the differences in the description of the exchange reaction equilibria between the experimental conditions and the simplified conditions of our simulations.
One of the key advances in genome assembly that has led to a significant improvement in contig lengths has been improved algorithms for utilization of paired reads (mate-pairs). While in most assemblers, mate-pair information is used in a post-processing step, the recently proposed Paired de Bruijn Graph (PDBG) approach incorporates the mate-pair information directly in the assembly graph structure. However, the PDBG approach faces difficulties when the variation in the insert sizes is high. To address this problem, we first transform mate-pairs into edge-pair histograms that allow one to better estimate the distance between edges in the assembly graph that represent regions linked by multiple mate-pairs. Further, we combine the ideas of mate-pair transformation and PDBGs to construct new data structures for genome assembly: pathsets and pathset graphs.
Papers about natural protection territories
Many environmental stimuli present a quasi-rhythmic structure at different timescales that the brain needs to decompose and integrate. Cortical oscillations have been proposed as instruments of sensory de-multiplexing, i.e., the parallel processing of different frequency streams in sensory signals. Yet their causal role in such a process has never been demonstrated. Here, we used a neural microcircuit model to address whether coupled theta–gamma oscillations, as observed in human auditory cortex, could underpin the multiscale sensory analysis of speech. We show that, in continuous speech, theta oscillations can flexibly track the syllabic rhythm and temporally organize the phoneme-level response of gamma neurons into a code that enables syllable identification. The tracking of slow speech fluctuations by theta oscillations, and its coupling to gamma-spiking activity both appeared as critical features for accurate speech encoding. These results demonstrate that cortical oscillations can be a key instrument of speech de-multiplexing, parsing, and encoding.
Neuronal nicotinic acetylcholine receptors (NNRs) of the α7 subtype have been shown to contribute to the release of dopamine in the nucleus accumbens. The site of action and the underlying mechanism, however, are unclear. Here we applied a circuit modeling approach, supported by electrochemical in vivo recordings, to clarify this issue. Modeling revealed two potential mechanisms for the drop in accumbal dopamine efflux evoked by the selective α7 partial agonist TC-7020. TC-7020 could desensitize α7 NNRs located predominantly on dopamine neurons or glutamatergic afferents to them or, alternatively, activate α7 NNRs located on the glutamatergic afferents to GABAergic interneurons in the ventral tegmental area. Only the model based on desensitization, however, was able to explain the neutralizing effect of coapplied PNU-120596, a positive allosteric modulator. According to our results, the most likely sites of action are the preterminal α7 NNRs controlling glutamate release from cortical afferents to the nucleus accumbens. These findings offer a rationale for the further investigation of α7 NNR agonists as therapy for diseases associated with enhanced mesolimbic dopaminergic tone, such as schizophrenia and addiction
Let G be a semisimple algebraic group whose decomposition into the product of simple components does not contain simple groups of type A, and P⊆G be a parabolic subgroup. Extending the results of Popov , we enumerate all triples (G, P, n) such that (a) there exists an open G-orbit on the multiple flag variety G/P × G/P × . . . × G/P (n factors), (b) the number of G-orbits on the multiple flag variety is finite.
I give the explicit formula for the (set-theoretical) system of Resultants of m+1 homogeneous polynomials in n+1 variables