A Combined First Principles and Kinetic Monte Carlo study of Polyoxometalate based Molecular Memory Devices

In this paper, we combine Density Functional Theory with Kinetic Monte Carlo methodology to study the fundamental transport properties of a type of polyoxometalate (POM) and its behaviour in a potential flash memory device. DFT simulations on POM molecular junctions helps us demonstrate the link between underlying electronic structure of the molecule and its transport properties. Furthermore, we show how various electrode-molecule contact configurations determine the electron transport through the POM. Also, our work reveals that the orientation of the molecule to the electrodes plays a key role in the transport properties of the junction. With Kinetic Monte Carlo we extend this investigation by simulating the retention time of a POM-based flash memory device. Our results show that a POM based flash memory could potentially show multi-bit storage and retain charge for up to 10 years

Electronic transport in polycrystalline graphene

Most materials in available macroscopic quantities are polycrystalline. Graphene, a recently discovered two-dimensional form of carbon with strong potential for replacing silicon in future electronics, is no exception. There is growing evidence of the polycrystalline nature of graphene samples obtained using various techniques. Grain boundaries, intrinsic topological defects of polycrystalline materials, are expected to dramatically alter the electronic transport in graphene. Here, we develop a theory of charge carrier transmission through grain boundaries composed of a periodic array of dislocations in graphene based on the momentum conservation principle. Depending on the grain boundary structure we find two distinct transport behaviours - either high transparency, or perfect reflection of charge carriers over remarkably large energy ranges. First-principles quantum transport calculations are used to verify and further investigate this striking behaviour. Our study sheds light on the transport properties of large-area graphene samples. Furthermore, purposeful engineering of periodic grain boundaries with tunable transport gaps would allow for controlling charge currents without the need of introducing bulk band gaps in otherwise semimetallic graphene. The proposed approach can be regarded as a means towards building practical graphene electronics.Comment: accepted in Nature Material

Ge quantum dot arrays grown by ultrahigh vacuum molecular beam epitaxy on the Si(001) surface: nucleation, morphology and CMOS compatibility

Issues of morphology, nucleation and growth of Ge cluster arrays deposited by ultrahigh vacuum molecular beam epitaxy on the Si(001) surface are considered. Difference in nucleation of quantum dots during Ge deposition at low (<600 deg C) and high (>600 deg. C) temperatures is studied by high resolution scanning tunneling microscopy. The atomic models of growth of both species of Ge huts---pyramids and wedges---are proposed. The growth cycle of Ge QD arrays at low temperatures is explored. A problem of lowering of the array formation temperature is discussed with the focus on CMOS compatibility of the entire process; a special attention is paid upon approaches to reduction of treatment temperature during the Si(001) surface pre-growth cleaning, which is at once a key and the highest-temperature phase of the Ge/Si(001) quantum dot dense array formation process. The temperature of the Si clean surface preparation, the final high-temperature step of which is, as a rule, carried out directly in the MBE chamber just before the structure deposition, determines the compatibility of formation process of Ge-QD-array based devices with the CMOS manufacturing cycle. Silicon surface hydrogenation at the final stage of its wet chemical etching during the preliminary cleaning is proposed as a possible way of efficient reduction of the Si wafer pre-growth annealing temperature.Comment: 30 pages, 11 figure

MIRRAGGE – Minimum Information Required for Reproducible AGGregation Experiments

Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.This work was supported by (i) the European Regional Development Fund (ERDF) through the COMPETE 2020—Operacional Programme for Competitiveness and Internationalisation (POCI), Portugal 2020, and by Portuguese funds through FCT—Fundação para a Ciência e a Tecnologia (FCT/MCTES) in the framework of grants POCI-01-0145-FEDER-031173, POCI-01-0145-FEDER-007274, POCI-01-0145-FEDER-031323 (“Institute for Research and Innovation in Health Sciences”), UID/Multi/04046/2013 (BioISI) and PTDC/NEUNMC/2138/2014 (to CMG). SV was funded by the Spanish Ministry of Economy and Competitiveness (BIO2016-78310-R) and by ICREA (ICREA-Academia 2015). ZG and ZB were funded by Slovak research agentures VEGA 02/0145/17, 02/0030/18 and APVV-18-0284. RS was funded by VEGA 02/0163/19. DEO was funded by the Lundbeck Foundation (grant no. R276-2018-671) and the Independent Research Foundation Denmark | Natural Sciences (grant no. 8021-00208B). AP research was supported by UK Dementia Research Institute (RE1 3556) and by ARUK (ARUK-PG2019B-020)

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments

The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1.87-1.94 Mbp), that shared 98.7-98.8% average nucleotide identities between themselves and 'G-plasma' and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions

Large Anomalous Hall effect in a silicon-based magnetic semiconductor

Magnetic semiconductors are attracting high interest because of their potential use for spintronics, a new technology which merges electronics and manipulation of conduction electron spins. (GaMn)As and (GaMn)N have recently emerged as the most popular materials for this new technology. While Curie temperatures are rising towards room temperature, these materials can only be fabricated in thin film form, are heavily defective, and are not obviously compatible with Si. We show here that it is productive to consider transition metal monosilicides as potential alternatives. In particular, we report the discovery that the bulk metallic magnets derived from doping the narrow gap insulator FeSi with Co share the very high anomalous Hall conductance of (GaMn)As, while displaying Curie temperatures as high as 53 K. Our work opens up a new arena for spintronics, involving a bulk material based only on transition metals and Si, and which we have proven to display a variety of large magnetic field effects on easily measured electrical properties.Comment: 19 pages with 5 figure

Superfluidity of Bose-Einstein Condensate in An Optical Lattice: Landau-Zener Tunneling and Dynamical Instability

Superflow of Bose-Einstein condensate in an optical lattice is represented by a Bloch wave, a plane wave with periodic modulation of the amplitude. We review the theoretical results on the interaction effects in the energy dispersion of the Bloch waves and in the linear stability of such waves. For sufficiently strong repulsion between the atoms, the lowest Bloch band develops a loop at the edge of the Brillouin zone, with the dramatic consequence of a finite probability of Landau-Zener tunneling even in the limit of a vanishing external force. Superfluidity can exist in the central region of the Brillouin zone in the presence of a repulsive interaction, beyond which Landau instability takes place where the system can lower its energy by making transition into states with smaller Bloch wavenumbers. In the outer part of the region of Landau instability, the Bloch waves are also dynamically unstable in the sense that a small initial deviation grows exponentially in time. In the inner region of Landau instability, a Bloch wave is dynamically stable in the absence of persistent external perturbations. Experimental implications of our findings will be discussed.Comment: A new section on tight-binding approximation is added with a new figur

Using detergent to enhance detection sensitivity of African trypanosomes in human CSF and blood by Loop-Mediated Isothermal Amplification (LAMP)

&lt;p&gt;&lt;b&gt;Background:&lt;/b&gt; The loop-mediated isothermal amplification (LAMP) assay, with its advantages of simplicity, rapidity and cost effectiveness, has evolved as one of the most sensitive and specific methods for the detection of a broad range of pathogenic microorganisms including African trypanosomes. While many LAMP-based assays are sufficiently sensitive to detect DNA well below the amount present in a single parasite, the detection limit of the assay is restricted by the number of parasites present in the volume of sample assayed; i.e. 1 per µL or 103 per mL. We hypothesized that clinical sensitivities that mimic analytical limits based on parasite DNA could be approached or even obtained by simply adding detergent to the samples prior to LAMP assay.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Methodology/Principal Findings:&lt;/b&gt; For proof of principle we used two different LAMP assays capable of detecting 0.1 fg genomic DNA (0.001 parasite). The assay was tested on dilution series of intact bloodstream form Trypanosoma brucei rhodesiense in human cerebrospinal fluid (CSF) or blood with or without the addition of the detergent Triton X-100 and 60 min incubation at ambient temperature. With human CSF and in the absence of detergent, the LAMP detection limit for live intact parasites using 1 µL of CSF as the source of template was at best 103 parasites/mL. Remarkably, detergent enhanced LAMP assay reaches sensitivity about 100 to 1000-fold lower; i.e. 10 to 1 parasite/mL. Similar detergent-mediated increases in LAMP assay analytical sensitivity were also found using DNA extracted from filter paper cards containing blood pretreated with detergent before card spotting or blood samples spotted on detergent pretreated cards.&lt;/p&gt; &lt;p&gt;&lt;b&gt;Conclusions/Significance:&lt;/b&gt; This simple procedure for the enhanced detection of live African trypanosomes in biological fluids by LAMP paves the way for the adaptation of LAMP for the economical and sensitive diagnosis of other protozoan parasites and microorganisms that cause diseases that plague the developing world.&lt;/p&gt

Higher-order renormalization of graphene many-body theory

We study the many-body theory of graphene Dirac quasiparticles interacting via the long-range Coulomb potential, taking as a starting point the ladder approximation to different vertex functions. We test in this way the low-energy behavior of the electron system beyond the simple logarithmic dependence of electronic correlators on the high-energy cutoff, which is characteristic of the large-N approximation. We show that the graphene many-body theory is perfectly renormalizable in the ladder approximation, as all higher powers in the cutoff dependence can be absorbed into the redefinition of a finite number of parameters (namely, the Fermi velocity and the weight of the fields) that remain free of infrared divergences even at the charge neutrality point. We illustrate this fact in the case of the vertex for the current density, where a complete cancellation between the cutoff dependences of vertex and electron self-energy corrections becomes crucial for the preservation of the gauge invariance of the theory. The other potentially divergent vertex corresponds to the staggered (sublattice odd) charge density, which is made cutoff independent by a redefinition in the scale of the density operator. This allows to compute a well-defined, scale invariant anomalous dimension to all orders in the ladder series, which becomes singular at a value of the interaction strength marking the onset of chiral symmetry breaking (and gap opening) in the Dirac field theory. The critical coupling we obtain in this way matches with great accuracy the value found with a quite different method, based on the resolution of the gap equation, thus reassuring the predictability of our renormalization approach.Comment: 27 pages, 7 figures, references adde

Morphology and Nanomechanics of Sensory Neurons Growth Cones following Peripheral Nerve Injury

A prior peripheral nerve injury in vivo, promotes a rapid elongated mode of sensory neurons neurite regrowth in vitro. This in vitro model of conditioned axotomy allows analysis of the cellular and molecular mechanisms leading to an improved neurite re-growth. Our differential interference contrast microscopy and immunocytochemistry results show that conditioned axotomy, induced by sciatic nerve injury, did not increase somatic size of adult lumbar sensory neurons from mice dorsal root ganglia sensory neurons but promoted the appearance of larger neurites and growth cones. Using atomic force microscopy on live neurons, we investigated whether membrane mechanical properties of growth cones of axotomized neurons were modified following sciatic nerve injury. Our data revealed that neurons having a regenerative growth were characterized by softer growth cones, compared to control neurons. The increase of the growth cone membrane elasticity suggests a modification in the ratio and the inner framework of the main structural proteins