Discrete soliton collisions in a waveguide array with saturable nonlinearity

We study the symmetric collisions of two mobile breathers/solitons in a model for coupled wave guides with a saturable nonlinearity. The saturability allows the existence of breathers with high power. Three main regimes are observed: breather fusion, breather reflection and breather creation. The last regime seems to be exclusive of systems with a saturable nonlinearity, and has been previously observed in continuous models. In some cases a ``symmetry breaking'' can be observed, which we show to be an numerical artifact.Comment: 5 pages, 7 figure

Generalized conductance sum rule in atomic break junctions

When an atomic-size break junction is mechanically stretched, the total conductance of the contact remains approximately constant over a wide range of elongations, although at the same time the transmissions of the individual channels (valence orbitals of the junction atom) undergo strong variations. We propose a microscopic explanation of this phenomenon, based on Coulomb correlation effects between electrons in valence orbitals of the junction atom. The resulting approximate conductance quantization is closely related to the Friedel sum rule.Comment: 4 pages, 1 figure, appears in Proceedings of the NATO Advanced Research Workshop ``Size dependent magnetic scattering'', Pecs, Hungary, May 28 - June 1, 200

NRL^{-/-} gene edited human embryonic stem cells generate rod-deficient retinal organoids enriched in S-cone-like photoreceptors

Organoid cultures represent a unique tool to investigate the developmental complexity of tissues like the human retina. NRL is a transcription factor required for the specification and homeostasis of mammalian rod photoreceptors. In Nrl‐deficient mice, photoreceptor precursor cells do not differentiate into rods, and instead follow a default photoreceptor specification pathway to generate S‐cone‐like cells. To investigate whether this genetic switch mechanism is conserved in humans, we used CRISPR/Cas9 gene editing to engineer an NRL‐deficient embryonic stem cell (ESC) line (NRL^{−/−}), and differentiated it into retinal organoids. Retinal organoids self‐organize and resemble embryonic optic vesicles (OVs) that recapitulate the natural histogenesis of rods and cone photoreceptors. NRL−/− OVs develop comparably to controls, and exhibit a laminated, organized retinal structure with markers of photoreceptor synaptogenesis. Using immunohistochemistry and quantitative polymerase chain reaction (qPCR), we observed that NRL^{−/−} OVs do not express NRL, or other rod photoreceptor markers directly or indirectly regulated by NRL. On the contrary, they show an abnormal number of photoreceptors positive for S‐OPSIN, which define a primordial subtype of cone, and overexpress other cone genes indicating a conserved molecular switch in mammals. This study represents the first evidence in a human in vitro ESC‐derived organoid system that NRL is required to define rod identity, and that in its absence S‐cone‐like cells develop as the default photoreceptor cell type. It shows how gene edited retinal organoids provide a useful system to investigate human photoreceptor specification, relevant for efforts to generate cells for transplantation in retinal degenerative diseases

The role of metal ions in the electron transport through azurin-based junctions

We studied the coherent electron transport through metal–protein–metal junctions based on a blue copper azurin, in which the copper ion was replaced by three different metal ions (Co, Ni and Zn). Our results show that neither the protein structure nor the transmission at the Fermi level change significantly upon metal replacement. The discrepancy with previous experimental observations suggests that the transport mechanism taking place in these types of junctions is probably not fully coherent

Determination of the absorption cross sections of higher-order iodine oxides at 355 and 532 nm

Iodine oxides (IxOy) play an important role in the atmospheric chemistry of iodine. They are initiators of new particle formation events in the coastal and polar boundary layers and act as iodine reservoirs in tropospheric ozone-depleting chemical cycles. Despite the importance of the aforementioned processes, the photochemistry of these molecules has not been studied in detail previously. Here, we report the first determination of the absorption cross sections of IxOy, x=2, 3, 5, y=1–12 at λ=355 nm by combining pulsed laser photolysis of I2∕O3 gas mixtures in air with time-resolved photo-ionization time-of-flight mass spectrometry, using NO2 actinometry for signal calibration. The oxides selected for absorption cross-section determinations are those presenting the strongest signals in the mass spectra, where signals containing four iodine atoms are absent. The method is validated by measuring the absorption cross section of IO at 355 nm, σ355nm,IO=(1.2±0.1) ×10−18 cm2, which is found to be in good agreement with the most recent literature. The results obtained are σ355nm,I2O3<5×10−19 cm2 molec.−1, σ355nm,I2O4= (3.9±1.2)×10−18 cm2 molec.−1, σ355nm,I3O6= (6.1±1.6)×10−18 cm2 molec.−1, σ355nm,I3O7= (5.3±1.4)×10−18 cm2 molec.−1, and σ355nm,I5O12= (9.8±1.0)×10−18 cm2 molec.−1. Photodepletion at λ=532 nm was only observed for OIO, which enabled determination of upper limits for the absorption cross sections of IxOy at 532 nm using OIO as an actinometer. These measurements are supplemented with ab initio calculations of electronic spectra in order to estimate atmospheric photolysis rates J(IxOy). Our results confirm a high J(IxOy) scenario where IxOy is efficiently removed during daytime, implying enhanced iodine-driven ozone depletion and hindering iodine particle formation. Possible I2O3 and I2O4 photolysis products are discussed, including IO3, which may be a precursor to iodic acid (HIO3) in the presence of HO2

Heat dissipation in atomic-scale junctions

Atomic and single-molecule junctions represent the ultimate limit to the miniaturization of electrical circuits. They are also ideal platforms to test quantum transport theories that are required to describe charge and energy transfer in novel functional nanodevices. Recent work has successfully probed electric and thermoelectric phenomena in atomic-scale junctions. However, heat dissipation and transport in atomic-scale devices remain poorly characterized due to experimental challenges. Here, using custom-fabricated scanning probes with integrated nanoscale thermocouples, we show that heat dissipation in the electrodes of molecular junctions, whose transmission characteristics are strongly dependent on energy, is asymmetric, i.e. unequal and dependent on both the bias polarity and the identity of majority charge carriers (electrons vs. holes). In contrast, atomic junctions whose transmission characteristics show weak energy dependence do not exhibit appreciable asymmetry. Our results unambiguously relate the electronic transmission characteristics of atomic-scale junctions to their heat dissipation properties establishing a framework for understanding heat dissipation in a range of mesoscopic systems where transport is elastic. We anticipate that the techniques established here will enable the study of Peltier effects at the atomic scale, a field that has been barely explored experimentally despite interesting theoretical predictions. Furthermore, the experimental advances described here are also expected to enable the study of heat transport in atomic and molecular junctions, which is an important and challenging scientific and technological goal that has remained elusive.Comment: supporting information available in the journal web site or upon reques

Visualizing landscapes of the superconducting gap in heterogeneous superconductor thin films: geometric influences on proximity effects

The proximity effect is a central feature of superconducting junctions as it underlies many important applications in devices and can be exploited in the design of new systems with novel quantum functionality. Recently, exotic proximity effects have been observed in various systems, such as superconductor-metallic nanowires and graphene-superconductor structures. However, it is still not clear how superconducting order propagates spatially in a heterogeneous superconductor system. Here we report intriguing influences of junction geometry on the proximity effect for a 2D heterogeneous superconductor system comprised of 2D superconducting islands on top of a surface metal. Depending on the local geometry, the superconducting gap induced in the surface metal region can either be confined to the boundary of the superconductor, in which the gap decays within a short distance (~ 15 nm), or can be observed nearly uniformly over a distance of many coherence lengths due to non-local proximity effects.Comment: 17 pages, 4 figure

Discrete breathers in ϕ4\phi^4 and related models

We touch upon the wide topic of discrete breather formation with a special emphasis on the the $\phi^4$ model. We start by introducing the model and discussing some of the application areas/motivational aspects of exploring time periodic, spatially localized structures, such as the discrete breathers. Our main emphasis is on the existence, and especially on the stability features of such solutions. We explore their spectral stability numerically, as well as in special limits (such as the vicinity of the so-called anti-continuum limit of vanishing coupling) analytically. We also provide and explore a simple, yet powerful stability criterion involving the sign of the derivative of the energy vs. frequency dependence of such solutions. We then turn our attention to nonlinear stability, bringing forth the importance of a topological notion, namely the Krein signature. Furthermore, we briefly touch upon linearly and nonlinearly unstable dynamics of such states. Some special aspects/extensions of such structures are only touched upon, including moving breathers and dissipative variations of the model and some possibilities for future work are highlighted

Macrocyclic colibactin induces DNA double-strand breaks via copper-mediated oxidative cleavage.

Colibactin is an assumed human gut bacterial genotoxin, whose biosynthesis is linked to the clb genomic island that has a widespread distribution in pathogenic and commensal human enterobacteria. Colibactin-producing gut microbes promote colon tumour formation and enhance the progression of colorectal cancer via cellular senescence and death induced by DNA double-strand breaks (DSBs); however, the chemical basis that contributes to the pathogenesis at the molecular level has not been fully characterized. Here, we report the discovery of colibactin-645, a macrocyclic colibactin metabolite that recapitulates the previously assumed genotoxicity and cytotoxicity. Colibactin-645 shows strong DNA DSB activity in vitro and in human cell cultures via a unique copper-mediated oxidative mechanism. We also delineate a complete biosynthetic model for colibactin-645, which highlights a unique fate of the aminomalonate-building monomer in forming the C-terminal 5-hydroxy-4-oxazolecarboxylic acid moiety through the activities of both the polyketide synthase ClbO and the amidase ClbL. This work thus provides a molecular basis for colibactin's DNA DSB activity and facilitates further mechanistic study of colibactin-related colorectal cancer incidence and prevention

What traits are carried on mobile genetic elements, and why?

Although similar to any other organism, prokaryotes can transfer genes vertically from mother cell to daughter cell, they can also exchange certain genes horizontally. Genes can move within and between genomes at fast rates because of mobile genetic elements (MGEs). Although mobile elements are fundamentally self-interested entities, and thus replicate for their own gain, they frequently carry genes beneficial for their hosts and/or the neighbours of their hosts. Many genes that are carried by mobile elements code for traits that are expressed outside of the cell. Such traits are involved in bacterial sociality, such as the production of public goods, which benefit a cell's neighbours, or the production of bacteriocins, which harm a cell's neighbours. In this study we review the patterns that are emerging in the types of genes carried by mobile elements, and discuss the evolutionary and ecological conditions under which mobile elements evolve to carry their peculiar mix of parasitic, beneficial and cooperative genes