Adaptive Resolution Molecular Dynamics Technique: Down to the Essential

We investigate the role of the thermodynamic (TD) force, as an essential and sufficient technical ingredient for an efficient and accurate adaptive resolution algorithm. Such a force applied in the coupling region of an adaptive resolution Molecular Dynamics (MD) set-up, assures thermodynamic equilibrium between atomistically resolved and coarse-grained regions, allowing the proper exchange of molecules. We numerically prove that indeed for systems as relevant as liquid water and 1,3-dimethylimidazolium chloride ionic liquid, the combined action of the TD force and thermostat allows for computationally efficient and numerically accurate simulations, beyond the current capabilities of adaptive resolution set-ups, which employ switching functions in the coupling region

Error in hydraulic head and gradient time-series measurements: a quantitative appraisal

&amp;lt;p&amp;gt;&amp;lt;strong&amp;gt;Abstract.&amp;lt;/strong&amp;gt; Hydraulic head and gradient measurements underpin practically all investigations in hydro(geo)logy. There is sufficient information in the literature to suggest that head measurement errors may be so large that flow directions can not be inferred reliably, and that their magnitude can have as great an effect on the uncertainty of flow rates as the hydraulic conductivity. Yet, educational text books contain limited content regarding measurement techniques and studies rarely report on measurement errors. The objective of our study is to review currently-accepted standard operating procedures in hydrological research and to determine the smallest head gradients that can be resolved. To this aim, we first systematically investigate the systematic and random measurements errors involved in collecting time series information on hydraulic head at a given location: (1) geospatial position, (2) point of head, (3) depth to water, and (4) water level time series. Then, by propagating the random errors, we find that with current standard practice, horizontal head gradients&amp;amp;#8201;&amp;lt;&amp;amp;#8201;10&amp;lt;sup&amp;gt;&amp;amp;#8722;4&amp;lt;/sup&amp;gt; are resolvable at distances&amp;amp;#8201;&amp;amp;#10886;&amp;amp;#8201;170&amp;amp;#8201;m. Further, it takes extraordinary effort to measure hydraulic head gradients&amp;amp;#8201;&amp;lt;&amp;amp;#8201;10&amp;lt;sup&amp;gt;&amp;amp;#8722;3&amp;lt;/sup&amp;gt; over distances&amp;amp;#8201;&amp;lt;&amp;amp;#8201;10&amp;amp;#8201;m. In reality, accuracy will be worse than our theoretical estimates because of the many possible systematic errors. Regional flow on a scale of kilometres or more can be inferred with current best-practice methods, but processes such as vertical flow within an aquifer cannot be determined until more accurate and precise measurement methods are developed. Finally, we offer a concise set of recommendations for water level, hydraulic head and gradient time series measurements. We anticipate that our work contributes to progressing the quality of head time series data in the hydro(geo)logical sciences, and provides a starting point for the development of universal measurement protocols for water level data collection.&amp;lt;/p&amp;gt; </jats:p

Hierarchical supercrystalline nanocomposites through the self-assembly of organically-modified ceramic nanoparticles

Biomaterials often display outstanding combinations of mechanical properties thanks to their hierarchical structuring, which occurs through a dynamically and biologically controlled growth and self-assembly of their main constituents, typically mineral and protein. However, it is still challenging to obtain this ordered multiscale structural organization in synthetic 3D-nanocomposite materials. Herein, we report a new bottom-up approach for the synthesis of macroscale hierarchical nanocomposite materials in a single step. By controlling the content of organic phase during the self-assembly of monodisperse organically-modified nanoparticles (iron oxide with oleyl phosphate), either purely supercrystalline or hierarchically structured supercrystalline nanocomposite materials are obtained. Beyond a critical concentration of organic phase, a hierarchical material is consistently formed. In such a hierarchical material, individual organically-modified ceramic nanoparticles (Level 0) self-assemble into supercrystals in face-centered cubic superlattices (Level 1), which in turn form granules of up to hundreds of micrometers (Level 2). These micrometric granules are the constituents of the final mm-sized material. This approach demonstrates that the local concentration of organic phase and nano-building blocks during self-assembly controls the final material's microstructure, and thus enables the fine-tuning of inorganic-organic nanocomposites' mechanical behavior, paving the way towards the design of novel high-performance structural materials.The authors gratefully acknowledge the financial support from the German Research Foundation (DFG) via the SFB 986-M3, projects A1, A6, Z2, and Z3. We thank Dr. F. Beckmann (Helmholtz-Zentrum Geesthacht, Geesthacht, Germany) for scanning the sample with the technique SRµCT and for reconstructing the slices, and Dr. I. Greving (Helmholtz-Zentrum Geesthacht, Geesthacht, Germany) for her inputs on SRµCT. Dr. F. Brun (National Institute of Nuclear Physics, Trieste, Italy) is acknowledged for the discussion regarding quantitative analysis using Pore3d

Dataset of ptychographic X-ray computed tomography of inverse opal photonic crystals produced by atomic layer deposition

This data article describes the detailed parameters for synthesizing mullite inverse opal photonic crystals via Atomic Layer Deposition (ALD), as well as the detailed image analysis routine used to interpret the data obtained by the measurement of such photonic crystals, before and after the heat treatment, via Ptychographic X-ray Computed Tomography (PXCT). The data presented in this article are related to the research article by Furlan and co-authors entitled "Photonic materials for high-temperature applications: Synthesis and characterization by X-ray ptychographic tomography" (Furlan et al., 2018). The data include detailed information about the ALD super-cycle process to generate the ternary oxides inside a photonic crystal template, the raw data from supporting characterization techniques, as well as the full dataset obtained from PXCT. All the data herein described is publicly available in a Mendeley Data archive "Dataset of synthesis and characterization by PXCT of ALD-based mullite inverse opal photonic crystals" located at https://data.mendeley.com/datasets/zn49dsk7x6/1 for any academic, educational, or research purposes

First Evidence of Reproductive Adaptation to “Island Effect” of a Dwarf Cretaceous Romanian Titanosaur, with Embryonic Integument In Ovo

<div><h3>Background</h3><p>The Cretaceous vertebrate assemblages of Romania are famous for geographically endemic dwarfed dinosaur taxa. We report the first complete egg clutches of a dwarf lithostrotian titanosaur, from Toteşti, Romania, and its reproductive adaptation to the “island effect”.</p> <h3>Methodology/Findings</h3><p>The egg clutches were discovered in sequential sedimentary layers of the Maastrichtian Sânpetru Formation, Toteşti. The occurrence of 11 homogenous clutches in successive strata suggests philopatry by the same dinosaur species, which laid clutches averaging four ∼12 cm diameters eggs. The eggs and eggshells display numerous characters shared with the positively identified material from egg-bearing level 4 of the Auca Mahuevo (Patagonia, Argentina) nemegtosaurid lithostrotian nesting site. Microscopic embryonic integument with bacterial evidences was recovered in one egg. The millimeter-size embryonic integument displays micron size dermal papillae implying an early embryological stage at the time of death, likely corresponding to early organogenesis before the skeleton formation.</p> <h3>Conclusions/Significance</h3><p>The shared oological characters between the Haţeg specimens and their mainland relatives suggest a highly conservative reproductive template, while the nest decrease in egg numbers per clutch may reflect an adaptive trait to a smaller body size due to the “island effect”. The combined presence of the lithostrotian egg and its embryo in the Early Cretaceous Gobi coupled with the oological similarities between the Haţeg and Auca Mahuevo oological material evidence that several titanosaur species migrated from Gondwana through the Haţeg Island before or during the Aptian/Albian. It also suggests that this island might have had episodic land bridges with the rest of the European archipelago and Asia deep into the Cretaceous.</p> </div

Nitrate Reduction Functional Genes and Nitrate Reduction Potentials Persist in Deeper Estuarine Sediments. Why?

Denitrification and dissimilatory nitrate reduction to ammonium (DNRA) are processes occurring simultaneously under oxygen-limited or anaerobic conditions, where both compete for nitrate and organic carbon. Despite their ecological importance, there has been little investigation of how denitrification and DNRA potentials and related functional genes vary vertically with sediment depth. Nitrate reduction potentials measured in sediment depth profiles along the Colne estuary were in the upper range of nitrate reduction rates reported from other sediments and showed the existence of strong decreasing trends both with increasing depth and along the estuary. Denitrification potential decreased along the estuary, decreasing more rapidly with depth towards the estuary mouth. In contrast, DNRA potential increased along the estuary. Significant decreases in copy numbers of 16S rRNA and nitrate reducing genes were observed along the estuary and from surface to deeper sediments. Both metabolic potentials and functional genes persisted at sediment depths where porewater nitrate was absent. Transport of nitrate by bioturbation, based on macrofauna distributions, could only account for the upper 10 cm depth of sediment. A several fold higher combined freeze-lysable KCl-extractable nitrate pool compared to porewater nitrate was detected. We hypothesised that his could be attributed to intracellular nitrate pools from nitrate accumulating microorganisms like Thioploca or Beggiatoa. However, pyrosequencing analysis did not detect any such organisms, leaving other bacteria, microbenthic algae, or foraminiferans which have also been shown to accumulate nitrate, as possible candidates. The importance and bioavailability of a KCl-extractable nitrate sediment pool remains to be tested. The significant variation in the vertical pattern and abundance of the various nitrate reducing genes phylotypes reasonably suggests differences in their activity throughout the sediment column. This raises interesting questions as to what the alternative metabolic roles for the various nitrate reductases could be, analogous to the alternative metabolic roles found for nitrite reductases

Detrimental proarrhythmogenic interaction of Ca2+/calmodulin-dependent protein kinase II and NaV1.8 in heart failure

An interplay between Ca2+/calmodulin-dependent protein kinase IIδc (CaMKIIδc) and late Na+ current (INaL) is known to induce arrhythmias in the failing heart. Here, we elucidate the role of the sodium channel isoform NaV1.8 for CaMKIIδc-dependent proarrhythmia. In a CRISPR-Cas9-generated human iPSC-cardiomyocyte homozygous knock-out of NaV1.8, we demonstrate that NaV1.8 contributes to INaL formation. In addition, we reveal a direct interaction between NaV1.8 and CaMKIIδc in cardiomyocytes isolated from patients with heart failure (HF). Using specific blockers of NaV1.8 and CaMKIIδc, we show that NaV1.8-driven INaL is CaMKIIδc-dependent and that NaV1.8-inhibtion reduces diastolic SR-Ca2+ leak in human failing cardiomyocytes. Moreover, increased mortality of CaMKIIδc-overexpressing HF mice is reduced when a NaV1.8 knock-out is introduced. Cellular and in vivo experiments reveal reduced ventricular arrhythmias without changes in HF progression. Our work therefore identifies a proarrhythmic CaMKIIδc downstream target which may constitute a prognostic and antiarrhythmic strategy