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In this study, the adaption of the recently published molecular GFN-FF for periodic boundary conditions (pGFN-FF) is described through the use of neighbor lists combined with appropriate charge sums to handle any dimensionality from 1D polymers to 2D surfaces and 3D solids. Numerical integration over the Brillouin zone for the calculation of π bond orders of periodic fragments is also included. Aside from adapting the GFN-FF method to handle periodicity, improvements to the method are proposed in regard to the calculation of topological charges through the inclusion of a screened Coulomb term that leads to more physical charges and avoids a number of pathological cases. Short-range damping of three-body dispersion is also included to avoid collapse of some structures. Analytic second derivatives are also formulated with respect to both Cartesian and strain variables, including prescreening of terms to accelerate the dispersion/coordination number contribution to the Hessian. The modified pGFN-FF scheme is then applied to a wide range of different materials in order to examine how well this universal model performs.

Carbon dots are emerging in the nanotechnology field as the newest class of fluorescent probes, owing to their high water-solubility, good chemical and photo-stability and tunable photoluminescence. The ability of metal cations to quench carbon dots fluorescence is already well known. Anyway, a dedicated study directed to the rational design of the optimal carbon dot probe is still missing. Herein we present a novel synthetic method for the production of carbon nanodots from an economic and environmental polluting starting material: olive solid wastes. The obtained carbon dots are efficiently quenched in presence of Fe3+, allowing the cation detection. Starting from a comprehensive study on their quenching mechanism, we have been able to develop effective strategies to modulate the sensing properties of these carbon dots. The sensitivity and linear range of the probe have been tuned by modulating the surface functionalization of the nanoparticles. The selectivity toward Fe3+ has been improved by growing around the dots a porous microsphere of ion imprinted polymer. The results highlighted in this work demonstrate that the carbon dots sensing properties can be modulated to meet the requirement of the users, allowing the design of tailored probes for a wide range of applications.

The detection of cancer biomarkers at an early stage of tumor development is vital for effective diagnosis and treatment of cancer. Current diagnostic tools can often detect cancer only when the biomarker levels are already too high, so that the tumors have spread and treatments are less effective. It is urgent therefore to develop highly sensitive assays for the detection of such biomarkers at the lowest possible concentration. In this context, we developed a sandwich immunoassay based on surface-enhanced Raman scattering (SERS) for the ultrasensitive detection of alpha-fetoprotein (AFP), which is typically present in human serum as a biomarker indicative of early stages of hepatocellular carcinoma. In the immunoassay design, molybdenum disulfide (MoS2) modified with a monoclonal antibody was used as a capture probe for AFP. A secondary antibody linked to an SERS-encoded nanoparticle was employed as the Raman signal reporter, that is, the transducer for AFP detection. The sandwich immunocomplex "capture probe/target/SERS tag" was deposited on a silicon wafer and decorated with silver-coated gold nanocubes to increase the density of "hot spots" on the surface of the immunosensor. The developed SERS immunosensor exhibits a wide linear detection range (1 pg mL(-1) to 10 ng mL(-1)) with a limit of detection as low as 0.03 pg mL(-1) toward AFP with good reproducibility (RSD < 6%) and stability. These parameters demonstrate that the proposed immunosensor has the potential to be used as an analytical platform for the detection of early-stage cancer biomarkers in clinical applications E.E. is grateful for a fellowship from the Scientific and Technological Research Council of Turkey (TUBITAK). A.C. and A.S. thank MINECO for their research grant (Juan de la Cierva.Incorporacion/no. IJCI-2016-31113, Juan de la Cierva. Formacion/no. FJC2018-036777-I, respectively). We thank Dr. Judith Langer for support in the interpretation of SERS results. This work was supported by the European Union's Horizon 2020 research and innovation program under Grant Agreements 785219 and 881603 Graphene Flagship. L.M.L.-M. acknowledges funding from the European Research Council (ERC-AdG-2017#787510). M.P., as the recipient of the AXA Bionanotechnology Chair, is grateful to the AXA Research Fund for financial support. This work was performed under the Maria de Maeztu Units of Excellence Program from the Spanish State Research Agency.grant no. MDM-20170720

Density functional theory (DFT) with semiempirical dispersion corrections (DFT-D2) has been used to calculate the binding energy of a CO2 molecule on the calcite {10.4} surface for different positions and orientations. This generated potential energy landscape was then used to parametrize a classical force field. From this, we used metadynamics (MTD) to derive free energy profiles at 300 and 350 K for CO2 binding to calcite, CO2 binding with Ca2+, and pairing of two CO2 molecules, all for aqueous conditions. We subsequently performed classical molecular dynamics (MD) simulations of CO2 and water on the {10.4} surface at pressures and temperatures relevant for CO2 geological storage. Density profiles show characteristic structured water layering at the calcite surface and two distinct phases of water and CO2. We have also calculated the densities of the CO2-rich and water-rich phases and thereby determined the mutual solubilities. For all the pressures and temperatures in the studied range, CO2 was unable ...

SUMMARY We attempted to transfect six recently characterized virus species to protoplasts of Penicillium janczewskii and Chryphonectria parasitica. None of the recovered P. janczewskii colonies was positive for the transfected viruses, but Penicillium aurantiogriseum partiti-like virus 1 (PaPLV1) was detected in three distinct regenerated C. parasitica colonies. We screened the phenotype of the infected strains in up to 45 different conditions combining different media, salinity and temperatures: our results show that the infected strains grow slower than the virus- free in most of the tested conditions with the exception of halophilic stress in a specific nutrient combination media. We proceeded to characterize molecularly the population of distinct isolates of PaPLV1 infected C. parasitica through RNAseq: comparison to the viral population present in the original host -P. auratiogriseum- showed that two isolates accumulated non-synonymous mutations suggesting adaptation to the new host. RNAseq analyses identified a second genomic RNA segment and northern blot of RNA extracted from purified virus suspensions allowed establishing that PaPLV1 is at least bipartite in nature and that it forms isometric virions of circa 36-38 nm in diameter. In light of these new acquisitions, we discuss the taxonomic placement of PaPLV1 inside the Partitiviridae. This article is protected by copyright. All rights reserved.

Glyco-gold nanoparticles combine in a single entity the peculiar properties of gold nanoparticles with the biological activity of carbohydrates. The result is an exciting nanosystem, able to mimic the natural multivalent presentation of saccharide moieties and to exploit the peculiar optical properties of the metallic core. In this review, we present recent advances on glyco-gold nanoparticle applications in different biological fields, highlighting the key parameters which inspire the glyco nanoparticle design.

Background Small RNAs (sRNAs) are short non-coding RNA molecules (20–30 nt) that regulate gene expression at transcriptional or post-transcriptional levels in many eukaryotic organisms, through a mechanism known as RNA interference (RNAi). Recent studies have highlighted that they are also involved in cross-kingdom communication: sRNAs can move across the contact surfaces from “donor” to “receiver” organisms and, once in the host cells of the receiver, they can target specific mRNAs, leading to a modulation of host metabolic pathways and defense responses. Very little is known about RNAi mechanism and sRNAs occurrence in Arbuscular Mycorrhizal Fungi (AMF), an important component of the plant root microbiota that provide several benefits to host plants, such as improved mineral uptake and tolerance to biotic and abiotic stress. Results Taking advantage of the available genomic resources for the AMF Rhizophagus irregularis we described its putative RNAi machinery, which is characterized by a single Dicer-like (DCL) gene and an unusual expansion of Argonaute-like (AGO-like) and RNA-dependent RNA polymerase (RdRp) gene families. In silico investigations of previously published transcriptomic data and experimental assays carried out in this work provided evidence of gene expression for most of the identified sequences. Focusing on the symbiosis between R. irregularis and the model plant Medicago truncatula, we characterized the fungal sRNA population, highlighting the occurrence of an active sRNA-generating pathway and the presence of microRNA-like sequences. In silico analyses, supported by host plant degradome data, revealed that several fungal sRNAs have the potential to target M. truncatula transcripts, including some specific mRNA already shown to be modulated in roots upon AMF colonization. Conclusions The identification of RNAi-related genes, together with the characterization of the sRNAs population, suggest that R. irregularis is equipped with a functional sRNA-generating pathway. Moreover, the in silico analysis predicted 237 plant transcripts as putative targets of specific fungal sRNAs suggesting that cross-kingdom post-transcriptional gene silencing may occur during AMF colonization. Electronic supplementary material The online version of this article (10.1186/s12864-019-5561-0) contains supplementary material, which is available to authorized users.

Knowledge about the interaction between fluids and solids and the interfacial tension (IFT) that results is important for predicting behavior and properties in industrial systems and in nature, such as in rock formations before, during, and after CO2 injection for long-term storage. Many authors have studied the effect of the environmental variables on the IFT in the CO2–H2O system. However, experimental measurements above CO2 supercritical conditions are scarce and sometimes contradictory. Molecular modeling is a valuable tool for complementing experimental IFT determination, and it can help us interpret results and gain insight under conditions where experiments are difficult or impossible. Here, we report predictions for CO2–water interfacial tension performed using density functional theory (DFT) combined with the COSMO-RS implicit solvent model. We predicted the IFT dependence as a function of pressure (0–50 MPa), temperature (273–383 K), and salinity (0–5 M NaCl). The results agree well with literat...

In the biomedical applications of nanoparticles (NPs), the proper choice of surface chemistry is a crucial aspect in their design. The nature of the coating can heavily impact the interaction of NPs with biomolecules, affect the state of aggregation, and ultimately determine their biological fate. As such, protein corona formation and the aggregation behaviour of gold NPs (Au NPs) are studied here. Au NPs are prepared with four distinct surface functionalisations, namely mercaptosuccinic acid (MSA), N-4-thiobutyroil glucosamine, HS-PEG(5000) and HS-alkyl-PEG(600). Corona formation, aggregation, and the intracellular behaviour of the Au NPs are then investigated by means of Fluorescence Correlation Spectroscopy (FCS) in cell culture media and in live cells. To evaluate the state of aggregation and the formation of a protein corona, the Au NPs are incubated in cell media and the diffusion coefficient is determined via FCS. The in vitro behaviour is compared with the level of aggregation of the NPs in cells. Diffusion times of the NPs are estimated at different positions in the cell after a one hour incubation period. It is found that the majority of MSA and glucose-Au NPs are present inside the cell as slowly diffusing species with diffusion times (tau(D)) greater than 6000 mu s (hydrodynamic diameter > 250 nm). PEGylated Au NPs adsorb a small amount of protein and manifest low agglomeration both in media and in living cells. In particular, the HS-alkyl-PEG(600) coating shows an excellent correlation between lower protein adsorption, 4-fold lower compared to the MSA coated NPs, and limited intracellular aggregation. In the case of single HS-alkylPEG(600) coated NPs, it is found that typical intracellular tD values range from 500 to 1500 mu s, indicating that these particles display reduced aggregation in the intracellular environment.

The development of new molecules able to efficiently act as long-circulating computed tomography (CT) contrast agents is one of the most crucial topics in the biomedical field. In the last years, the chance to manipulate materials at the nano-size level gave new boost to this research, with the specific aim to design innovative nanoprobes. Gold nanoparticles (AuNPs) have showed unique X-rays attenuation properties which, combined with their easy surface functionalization, makes them ideal candidates for the next generation of contrast agents. In this paper, we present a rational and facile approach to synthesize engineered and water-stable AuNPs, achieving concentrated colloidal solution with high Hounsfield Units (HU). An accurate control of reagents ratio allowed us to design AuNPs with different shapes, from symmetrical to anisotropic morphology, in a convenient ‘one-pot’ fashion. Their activity as efficient and reliable CT contrast agents has been evaluated and compared. Moreover, glucosamine-functionalized gold nanoparticles have been developed ([Au] = 31.20 mg/mL; HU = 2453), in order to obtain a CT contrast agent able to combine spatial resolution with metabolic information. Copyright © 2016 John Wiley & Sons, Ltd.

Hetero-nanoparticles represent an important family of composite nanomaterials that in the past years are attracting ever-growing interest. Here, we report a new strategy for the synthesis of water dispersible cobalt ferrite nano particles (CoxFe3-xO4 NPs) decorated with ultrasmall (2-3 nm). gold nanoparticles (Au NPs). The synthetic procedure is based on the use of 2,3-meso-dimercaptosuccinic acid (DMSA), which plays a double role. First, it transfers cobalt ferrite NPs from the organic phase to aqueous media. Second, the DMSA reductive power promotes the in situ nucleation of gold NPs in proximity of the magnetic NP surface. Following this procedure, we achieved a water dispersible nanosystem (CoxFe3-xO4-DMSA-Au NPs) which combines the cobalt ferrite magnetic properties with the catalytic features of ultrasmall Au NPs. We showed that CoxFe3-xO4-DMSA-Au NPs act as an efficient nanocatalyst to reduce 4-nitrophenol to 4-aminophenol and that they can be magnetically recovered and recycled. It is noteworthy that such nanosystem is more catalytically active than Au NPs with equal size. Finally, a complete structural and chemical characterization of the hetero-NPs is provided.

Assessment of the risks and environmental impacts of carbon geosequestration requires knowledge about the wetting behavior of mineral surfaces in the presence of CO2 and the pore fluids. In this context, the interfacial tension (IFT) between CO2 and the aqueous fluid and the contact angle, θ, with the pore mineral surfaces are the two key parameters that control the capillary pressure in the pores of the candidate host rock. Knowledge of these two parameters and their dependence on the local conditions of pressure, temperature, and salinity is essential for the correct prediction of structural and residual trapping. We have performed classical molecular dynamics simulations to predict the CO2-water IFT and the CO2-water-calcite contact angle. The IFT results are consistent with previous simulations, where simple point charge water models have been shown to underestimate the water surface tension, thus affecting the simulated IFT values. When combined with the EPM2 CO2 model, the SPC/Fw water model indeed underestimates the IFT in the low-pressure region at all temperatures studied. On the other hand, at high pressure and low temperature, the IFT is overestimated by ∼5 mN/m. Literature data regarding the CO2/water/calcite contact angle on calcite are contradictory. Using our new set of force field parameters, we performed NVT simulations at 323 K and 20 MPa to calculate the contact angle of a water droplet on the calcite {10.4} surface in a CO2 atmosphere. We performed simulations for both spherical and cylindrical droplet configurations for different initial radii to study the size dependence of the water contact angle on calcite in the presence of CO2. Our results suggest that the contact angle of a cylindrical droplet, is independent of droplet size, for droplets with a radius of 50 Å or more. On the contrary, spherical droplets make a contact angle that is strongly influenced by their size. At the largest size explored in this study, both spherical and cylindrical droplets converge to the same contact angle, 38°, indicating that calcite is strongly wetted by water.

RAMS is an acronym for Reliability, Availability, Maintainability and Safety. These four properties concern the application of important methodologies for designing and managing complex technical systems. The present chapter analyses several reliability allocation techniques present in literature. Starting from well-known methodologies, two reliability allocation methods has been proposed and validated: Integrated Factors Method (I.F.M.) and Critical Flow Method (C.F.M.). We focus on the most important conventional methods to discuss their limitations to motivate the current research.

Improved energy efficiency can help reduce pollution, contribute to energy security, and help consumers save money. This paper explores energy labelling schemes as a policy instrument for promoting energy-efficient cars in Spain. Specifically, it explores consumer responses to changes in vehicle prices. We derive the demand responses for two different efficiency labelling schemes: absolute and relative. To that end, we calculate own- and cross-price elasticities of demand for cars with efficiency labels on the Spanish car market. The results show that the elasticities for more efficient cars are in general higher. However, in the specific case of sedans, the elasticities depend on assumptions about how consumers decide which car to purchase. If consumers are concerned about the absolute energy performance of cars independently of other attributes, and thus pay attention to absolute labelling, demand for more efficient cars is more elastic than demand for less efficient cars. If consumers choose the car segment first and then the energy performance, using the relative label, the opposite result is found. The results suggest that both relative and absolute labelling schemes can be useful, depending on how consumers make their decisions. It might also be possible to design a mixed system.

Star-shaped gold nanoparticles (StarAuNPs) are extremely attractive nanomaterials, characterized by localized surface plasmon resonance which could be potentially employed in a large number of applications. However, the lack of a reliable and reproducible synthetic protocols for the production of StarAuNPs is the major limitation to their spreading. For the first time, here we present a robust protocol to manufacture reproducible StarAuNPs by exploiting a fluidic approach. Star-shaped AuNPs have been synthesized by means of a seed-less protocol, employing ascorbic acid as reducing agent at room temperature. Moreover, the versatility of the bench-top microfluidic protocol has been exploited to afford hydrophilic, hydrophobic and solid-supported engineered StarAuNPs, by avoiding intermediate NP purifications.

The first page of this article is displayed as the abstract., Rohit Chikkaraddy opened the discussion of the Introductory Lecture: Regarding quantifying the chemical enhancement, you showed a systematic change in the SERS enhancement for halide substituted molecules due to charge transfer from the metal. Is the extra enhancement due to an inherent increase in the Raman cross-section of the molecule? How do you go about referencing, as the charge transfer changes the vibrational frequency? Richard Van Duyne answered: The extra enhancement is not due to an increase in the Raman cross section, as that is ratioed out in the calculation of the enhancement factor. The charge transfer (CT) process does not transfer a complete electron, it is a fractional degree of CT. Thus the change in vibrational frequency is small. DFT calculations that provide eigenvectors allow one to reference the vibrational modes of the free molecule with those of the adsorbed molecule. Sylwester Gawinkowski asked: You have shown that the enhancement factor curve is redshifted relative to the plasmon resonance band and has a maximum at about 800 nm. This means that the SERS signal should be strongest for excitations in the near infrared spectral region. Why do most SERS reports, particularly related to single molecule SERS, have the excitation in the green or red spectral range and not in the near infrared?

Jurgen Popp opened a general discussion of the paper by Roy Goodacre: What is the advantage of using SERS instead of ordinary Raman spectroscopy?

In the age of competition, no industry can survive without pondering much about reducing expenditures wherever possible. Management of inventories represents one of the most important areas in business, trade and industry. The scheduling of production lots, as well as their sizing, is an area of increasing research attention within the wider field of production planning and scheduling. In the present paper a new mathematical model to find the target stocking level which minimises the total cost of the system while satisfying the service level constraint is presented. Starting from the analysis of inventory management models in literature, a completely original model has been developed and applied to a real case in healthcare sector. The analysis of the results, arising from the case study, allowed to evaluate the effectiveness of the proposed models and to highlight the differences. Nevertheless the proposed model has characteristics of generality that allow the application in other areas.