Abstract: We introduce a simple enhanced sampling approach for the calculation of free energy differences and barriers along a one-dimensional reaction coordinate. First, a small number of short nonequilibrium simulations are carried out along the reaction coordinate, and the Jarzynski equality is used to learn an approximate free energy surface from the nonequilibrium work distribution. This free energy estimate is represented in a compact form as an artificial neural network and used as an external bias potential to accelerate rare events in a subsequent molecular dynamics simulation. The final free energy estimate is then obtained by reweighting the equilibrium probability distribution of the reaction coordinate sampled under the influence of the external bias. We apply our reweighted Jarzynski sampling recipe to four processes of varying scales and complexities.spanning chemical reaction in the gas phase, pair association in solution, and droplet nucleation in supersaturated vapor. In all cases, we find reweighted Jarzynski sampling to be a very efficient strategy, resulting in rapid convergence of the free energy to high precision.

Abstract: Many natural objects exhibit radial or axial symmetry in a single plane. However, a universal tool for simulating and fitting the shapes of such objects is lacking. Herein, we present an R package called 'biogeom' that simulates and fits many shapes found in nature. The package incorporates novel universal parametric equations that generate the profiles of bird eggs, flowers, linear and lanceolate leaves, seeds, starfish, and tree-rings, and three growth-rate equations that generate the profiles of ovate leaves and the ontogenetic growth curves of animals and plants. 'biogeom' includes several empirical datasets comprising the boundary coordinates of bird eggs, fruits, lanceolate and ovate leaves, tree rings, seeds, and sea stars. The package can also be applied to other kinds of natural shapes similar to those in the datasets. In addition, the package includes sigmoid curves derived from the three growth-rate equations, which can be used to model animal and plant growth trajectories and predict the times associated with maximum growth rate. 'biogeom' can quantify the intra- or interspecific similarity of natural outlines, and it provides quantitative information of shape and ontogenetic modification of shape with important ecological and evolutionary implications for the growth and form of the living world.

Abstract: Dry deposition is an important process determining pollutant concentrations, especially when studying the influence of urban green infrastructure on particulate matter (PM) levels in cities. Computational fluid dynamics (CFD) models of PM capture by vegetation are useful tools to increase their applicability. The meso-scale models of Zhang et al. (Atmos Environ 35:549-560, 2001) and Petroff and Zhang (Geosci Model Dev 3(2):753-769, 2010) have often been adopted in CFD models, however a comparison of these models with measurements including all PM particle sizes detrimental to health has been rarely reported and certainly not for green wall species. This study presents dry deposition experiments on real grown Hedera helix in a wind tunnel setup with wind speeds from 1 to 4 m s(-1) and PM consisting of a mixture of soot (0.02 – 0.2 mu mu m) and dust particles (0.3 – 10 mu mu m). Significant factors determining the collection efficiency (%) were particle diameter and wind speed, but relative air humidity and the type of PM (soot or dust) did not have a significant influence. Zhang's model outperformed Petroff's model for particles < 0.3 mu mu m, however the inclusion of turbulent impaction in Petroff's model resulted in better agreement with the measurements for particles > 2 – 3 mu mu m. The optimised model had an overall root-mean-square-error of similar to 4% for collection efficiency (CE) and 0.4 cm s-1 for deposition velocity (nu d), which was shown to be highly competitive against previously described models. It can thus be used to model PM deposition on other plant species, provided the correct parameterisation of the drag by this species. A detailed description of the spatial distribution of the vegetation could solve the underestimation for particle sizes of 0.3 – 2 mu mu m.

Abstract: The Darcy–Forchheimer method is used for modelling the airflow through vegetation. Seven tree and shrub species with contrasting leaf morphologies were installed in a wind tunnel to allow pressure loss measurements across the plant section. Aerodynamic parameters derived from this experiment were inserted into a COMSOL Multiphysics computational fluid dynamics model. The model was confirmed to be a good predictor for airflow through vegetation (R2 = 0.98), regardless of plant morphology. Moreover, supplementing these data with results from a previous study (which considered herbaceous species) revealed a pattern of pressure loss data, that was already been normalised for plant area density. Although we propose further research into kinetic energy transfer in vegetation, this study provides sufficient interesting information for further applications and modelling to describe and predict urban ecology.

Abstract: Over the last two decades, three-dimensional (3D) imaging by transmission electron microscopy or “electron tomography” has evolved into a powerful tool to investigate a variety of nanomaterials in different fields, such as life sciences, chemistry, solid-state physics, and materials science. Most of these results were obtained with nanometer-scale resolution, but different approaches have recently pushed the resolution to the atomic level. Such information is a prerequisite to understand the specific relationship between the atomic structure and the physicochemical properties of (nano) materials. We provide an overview of the latest progress in the field of atomic-resolution electron tomography. Different imaging and reconstruction approaches are presented, and state-of-the-art results are discussed. This article demonstrates the power and importance of electron tomography with atomic-scale resolution.

Abstract: In this study the uptake of ZnO and CuO nanoparticles by Daphnia magna was tested. Daphnids were exposed during 48 h to acute concentrations of the nanoparticles and corresponding metal salts. The Daphnia zinc and copper concentration was measured and the nanoparticles were localized using electron microscopy. The aggregation and dissolution in the medium was characterized. A fast dissolution of ZnO in the medium was observed, while most CuO formed large aggregates and only a small fraction dissolved. The Daphnia zinc concentration was comparable for the nanoparticles and salts. Contrarily, a much higher Daphnia copper concentration was observed in the CuO exposure, compared to the copper salt. CuO nanoparticles adsorbed onto the carapace and occurred in the gut but did not internalize in the tissues. The combined dissolution and uptake results indicate that the toxicity of both nanoparticle types was caused by metal ions dissolved from the particles in the medium.

Abstract: Direct mercury (Hg) speciation was assessed for soil samples with a Hg concentration ranging from 7 up to 240 mg kg1. Hg chemical forms were identified and quantified by sequential extractions and bulkand micro-analytical techniques exploiting synchrotron generated X-rays. In particular, microspectroscopic techniques such as m-XRF, m-XRD and m-XANES were necessary to solve bulk Hg speciation, in both soil fractions <2 mm and <2 mm. The main Hg-species found in the soil samples were metacinnabar (b-HgS), cinnabar (a-HgS), corderoite (Hg3S2Cl2), and an amorphous phase containing Hg bound to chlorine and sulfur. The amount of metacinnabar and amorphous phases increased in the fraction <2 mm. No interaction among Hg-species and soil components was observed. All the observed Hgspecies originated from the slow weathering of an inert Hg-containing waste material (K106, U.S. EPA) dumped in the area several years ago, which is changing into a relatively more dangerous source of pollution.

Abstract: Riboflavin-producing lactic acid bacteria represent a promising and cost-effective strategy for food biofortification, but production levels are typically insufficient to support daily human requirements. In this study, we describe the novel human isolate Limosilactobacillus reuteri AMBV339 as a strong food biofortification candidate. This strain shows a high natural riboflavin (vitamin B2) overproduction of 18.36 mu g/ml, biomass production up to 6 x 10(10) colony-forming units/ml (in the typical range of model lactobacilli), and pH-lowering capacities to a pH as low as 4.03 in common plant-based (coconut, soy, and oat) and cow milk beverages when cultured up to 72 h at 37 degrees C. These properties were especially pronounced in coconut beverage and butter milk fermentations, and were sustained in co-culture with the model starter Streptococcus thermophilus. Furthermore, L. reuteri AMBV339 grown in laboratory media or in a coconut beverage survived in gastric juice and in a simulated gastrointestinal dialysis model with colon phase (GIDM-colon system) inoculated with fecal material from a healthy volunteer. Passive transport of L. reuteri AMBV339-produced riboflavin occurred in the small intestinal and colon stage of the GIDM system, and active transport via intestinal epithelial Caco-2 monolayers was also demonstrated. L. reuteri AMBV339 did not cause fecal microbiome perturbations in the GIDM-colon system and inhibited enteric bacterial pathogens in vitro. Taken together, our data suggests that L. reuteri AMBV339 represents a promising candidate to provide riboflavin fortification of plant-based and dairy foods, and has a high application potential in the human gastrointestinal tract.

Abstract: Restoration of drained peatlands through rewetting has recently emerged as a prevailing strategy to mitigate excessive greenhouse gas emissions and re-establish the vital carbon sequestration capacity of peatlands. Rewetting can help to restore vegetation communities and biodiversity, while still allowing for extensive agricultural management such as paludiculture. Belowground processes governing carbon fluxes and greenhouse gas dynamics are mediated by a complex network of microbial communities and processes. Our understanding of this complexity and its multi-factorial controls in rewetted peatlands is limited. Here, we summarize the research regarding the role of soil microbial communities and functions in driving carbon and nutrient cycling in rewetted peatlands including the use of molecular biology techniques in understanding biogeochemical processes linked to greenhouse gas fluxes. We emphasize that rapidly advancing molecular biology approaches, such as high-throughput sequencing, are powerful tools helping to elucidate the dynamics of key biogeochemical processes when combined with isotope tracing and greenhouse gas measuring techniques. Insights gained from the gathered studies can help inform efficient monitoring practices for rewetted peatlands and the development of climate-smart restoration and management strategies.

Abstract: A facile, “one-pot”, chemical approach to synthesize gold-based nanoparticles finely dispersed on porous activated carbon (Norit) was demonstrated in this work. The pH of the synthesis bath played a critical role in determining the optimal gold-carbon interaction, which enabled a successful deposition of the gold nanoparticles onto the carbon matrix with a maximized metal utilization of 93 %. The obtained AuNP/C nanocomposite was characterized using SEM, HAADF-STEM electron tomography and electrochemical techniques. It was found that the Au nanoparticles, with diameters between 5 and 20 nm, were evenly distributed over the carbon matrix, both inside and outside the pores. Electrochemical characterization indicated that the composite had a very large electroactive surface area (EASA), as high as 282.4 m2 gAu-1. By exploiting its very high EASA, the catalyst was intended to boost the productivity of glucaric acid in the electrooxidation of its precursor, gluconic acid. However, cyclic voltammetry experiments revealed a very limited reactivity towards gluconic acid oxidation, due to the spacial hindrance of gluconic acid molecule which prevented diffusion inside the catalyst nanopores. On the other hand, the as-synthesized nanocomposite promises to be effective towards the ORR, and might thus find potential application as anode catalyst for fuel cells as well as for the scalability of all those electrochemical reactions involving small molecules with high diffusivity and catalysed by noble metals (i. e. CO2, CH4, N2, etc..). Electrocatalysis: Gold nanoparticles with diameter between 5 and 20 nm evenly distributed onto porous activated carbon (Norit) were obtained using a facile “one-pot” chemical synthesis technique with very high metal utilization. The AuNP/C nanocomposite was characterized using SEM, HAADF-STEM electron tomography and electrochemical techniques, revealing a very large electroactive surface area (EASA). The figure shows the HAADF-STEM image (a) and the respective EDX elemental distribution (b) for the AuNP/C composite with 9.3 % Au-loading developed in this work (Au is marked in red and C in green).image

Abstract: Recently, interlayer and intralayer excitons in transition metal dichalcogenide heterobilayers have been studied both experimentally and theoretically. In spite of a growing interest, these layer-resolved excitons in the presence of external stimuli, such as strain, remain not fully understood. Here, using density-functional theory calculations with many-body effects, we explore the excitonic properties of vertically stacked MoSe2/WSe2 heterobilayer in the presence of in-plane biaxial strain of up to 5%. We calculate the strain dependence of exciton absorption spectrum, oscillator strength, wave function, and binding energy by solving the Bethe-Salpeter equation on top of the standard GW approach. We identify the interlayer and intralayer excitons by analyzing their electron-hole weights and spatial wave functions. We show that with the increase in strain magnitude, the absorption spectrum of the interlayer and intralayer excitons is red-shifted and re-ordered, and the binding energies of these layer-resolved excitons decrease monotonically and almost linearly. We derive the sensitivity of exciton binding energy to the applied strain and find that the intralayer excitons are more sensitive to strain than the interlayer excitons. For instance, a sensitivity of -7.9 meV/% is derived for the intra-MoSe2-layer excitons, which is followed by -7.4 meV/% for the intra-WSe2-layer excitons, and by -4.2 meV/% for the interlayer excitons. Our results indicate that interlayer and intralayer excitons in vertically stacked MoSe2/WSe2 heterobilayer are efficiently tunable by in-plane biaxial strain.

Abstract: The metal-insulator transition (MIT) in strongly correlated oxides is a topic of great interest for its potential applications, such as Mott field effect transistors and sensors. We report that the MIT in high quality epitaxial SrVO3 (SVO) thin films is present as the film thickness is reduced, lowering the dimensionality of the system, and electron-electron correlations start to become the dominant interactions. The critical thickness of 3 u.c is achieved by avoiding effects due to off-stoichiometry using optimal growth conditions and excluding any surface effects by a STO capping layer. Compared to the single SVO thin films, conductivity enhancement in SVO/STO superlattices is observed. This can be explained by the interlayer coupling effect between SVO sublayers in the superlattices. Magnetoresistance and Hall measurements indicate that the dominant driving force of MIT is the electron–electron interaction.

Abstract: Two-dimensional transition-metal dinitrides have attracted considerable attention in recent years due to their rich magnetic properties. Here, we focus on rare-earth-metal elements and propose a monolayer of lanthanum dinitride with a 1T structural phase, 1T-LaN2. Using first-principles calculations, we systematically investigated the structure, stability, magnetism, and band structure of this material. It is a flexible and stable monolayer exhibiting a low lattice thermal conductivity, which is promising for future thermoelectric devices. The monolayer shows the ferromagnetic ground state with a spin-polarized band structure. Two linear spin-polarized bands cross at the Fermi level forming a Dirac point, which is formed by the p atomic orbitals of the N atoms, indicating that monolayer 1T-LaN2 is a Dirac spin-gapless semiconductor of p-state. When the spin-orbit coupling is taken into account, a large nontrivial indirect bandgap (86/354meV) can be opened at the Dirac point, and three chiral edge states are obtained, corresponding to a high Chern number of C=3, implying that monolayer 1T-LaN2 is a Chern insulator. Importantly, this kind of band structure is expected to occur in more monolayers of rare-earth-metal dinitride with a 1T structural phase.

Abstract: Using Floquet-Bloch theory, we propose to realize chiral topological phases in two-dimensional (2D) hexagonal FeX2 (X=Cl, Br, I) monolayers under irradiation of circularly polarized light. Such 2D FeX2 monolayers are predicted to be dynamically stable and exhibit both ferromagnetic and semiconducting properties. To capture the full topological physics of the magnetic semiconductor under periodic driving, we adopt ab initio Wannier-based tight-binding methods for the Floquet-Bloch bands, with the light-induced bandgap closings and openings being obtained as the light field strength increases. The calculations of slabs with open boundaries show the existence of chiral edge states. Interestingly, the topological transitions with branches of chiral edge states changing from zero to one and from one to two by tuning the light amplitude are obtained, showing that the topological Floquet phase of high Chern number can be induced in the present Floquet-Bloch systems. Published under license by AIP Publishing.

Abstract: Thermal-catalytic gas processing is integral to many current industrial processes. Ever-increasing demands on conversion and energy efficiencies are a strong driving force for the development of alternative approaches. Similarly, synthesis of several functional materials (such as nanowires and nanotubes) demands special processing conditions. Plasma catalysis provides such an alternative, where the catalytic process is complemented by the use of plasmas that activate the source gas. This combination is often observed to result in a synergy between plasma and catalyst. This Review introduces the current state-of-the-art in plasma catalysis, including numerous examples where plasma catalysis has demonstrated its benefits or shows future potential, including CO2 conversion, hydrocarbon reforming, synthesis of nanomaterials, ammonia production, and abatement of toxic waste gases. The underlying mechanisms governing these applications, as resulting from the interaction between the plasma and the catalyst, render the process highly complex, and little is known about the factors leading to the often-observed synergy. This Review critically examines the catalytic mechanisms relevant to each specific application.