The possibility of measuring intrinsic electronic correlations in graphene using a d-wave contact Josephson junction

While not widely recognized, electronic correlations might play an important role in graphene. Indeed, Pauling's resonance valence bond (RVB) theory for the pp-bonded planar organic molecules, of which graphene is the infinite extension, already established the importance of the nearest neighbor spin-singlet bond (SB) state in these materials. However, despite the recent growth of interest in graphene, there is still no quantitative estimate of the effects of Coulomb repulsion in either undoped or doped graphene. Here we use a tight-binding Bogoliubov-de Gennes (TB BdG) formalism to show that in unconventional d-wave contact graphene Josephson junctions the intrinsic SB correlations are strongly enhanced. We show on a striking effect of the SB correlations in both proximity effect and Josephson current as well as establishing a 1/(T-T_c) functional dependence for the superconducting decay length. Here T_c is the superconducting transition temperature for the intrinsic SB correlations, which depends on both the effects of Coulomb repulsion and the doping level. We therefore propose that d-wave contact graphene Josephson junctions will provide a promising experimental system for the measurement of the effective strength of intrinsic SB correlations in graphene.Comment: 4 pages, 4 figure

The effect of nearest neighbor spin-singlet correlations in conventional graphene SNS Josephson junctions

Using the self-consistent tight-binding Bogoliubov-de Gennes formalism we have studied the effect of nearest neighbor spin-singlet bond (SB) correlations on Josephson coupling and proximity effect in graphene SNS Josephson junctions with conventional s-wave superconducting contacts. Despite the s-wave superconducting state in the contacts, the SB pairing state inside the junction has d-wave symmetry and clean, sharp interface junctions resemble a 'bulk-meets-bulk' situation with very little interaction between the two different superconducting states. In fact, due to a finite-size suppression of the superconducting state, a stronger SB coupling constant than in the bulk is needed in order to achieve SB pairing in a junction. For both short clean zigzag and armchair junctions a d-wave state that has a zero Josephson coupling to the s-wave state is chosen and therefore the Josephson current decreases when a SB pairing state develops in these junctions. In more realistic junctions, with smoother doping profiles and atomic scale disorder at the interfaces, it is possible to achieve some coupling between the contact s-wave state and the SB d-wave states. In addition, by breaking the appropriate lattice symmetry at the interface in order to induce another d-wave state, a non-zero Josephson coupling can be achieved which leads to a substantial increase in the Josephson current. We also report on the LDOS of the junctions and on a lack of zero energy states at interfaces despite the unconventional order parameters, which we attribute to the near degeneracy of the two d-wave solutions and their mixing at a general interface.Comment: 13 pages, 9 figures. Typos correcte

Josephson current in graphene: the role of unconventional pairing symmetries

We investigate the Josephson current in a graphene superconductor/normal/superconductor junction, where superconductivity is induced by means of the proximity effect from external contacts. We take into account the possibility of anisotropic pairing by also including singlet nearest-neighbor interactions, and investigate how the transport properties are affected by the symmetry of the superconducting order parameter. This corresponds to an extension of the usual on-site interaction assumption, which yields an isotropic s-wave order parameter near the Dirac points. Here, we employ a full numerical solution as well as an analytical treatment, and show how the proximity effect may induce exotic types of superconducting states near the Dirac points, e.g. $p_x$- and $p_y$-wave pairing or a combination of s-wave and p+\i p-wave pairing. We find that the Josephson current exhibits a weakly-damped, oscillatory dependence on the length of the junction when the graphene sheet is strongly doped. The analytical and numerical treatments are found to agree well with each other in the s-wave case when calculating the critical current and current-phase relationship. For the scenarios with anisotropic superconducting pairing, there is a deviation between the two treatments, especially for the effective $p_x$-wave order parameter near the Dirac cones which features zero-energy states at the interfaces. This indicates that a numerical, self-consistent approach becomes necessary when treating anisotropic superconducting pairing in graphene.Comment: 15 pages, 12 figure

Self-consistent solution for proximity effect and Josephson current in ballistic graphene SNS Josephson junctions

We use a tight-binding Bogoliubov-de Gennes (BdG) formalism to self-consistently calculate the proximity effect, Josephson current, and local density of states in ballistic graphene SNS Josephson junctions. Both short and long junctions, with respect to the superconducting coherence length, are considered, as well as different doping levels of the graphene. We show that self-consistency does not notably change the current-phase relationship derived earlier for short junctions using the non-selfconsistent Dirac-BdG formalism but predict a significantly increased critical current with a stronger junction length dependence. In addition, we show that in junctions with no Fermi level mismatch between the N and S regions superconductivity persists even in the longest junctions we can investigate, indicating a diverging Ginzburg-Landau superconducting coherence length in the normal region.Comment: 8 pages, 6 figure

ATP-independent reversal of a membrane protein aggregate by a chloroplast SRP subunit

Membrane proteins impose enormous challenges to cellular protein homeostasis during their post-translational targeting, and they require chaperones to keep them soluble and translocation competent. Here we show that a novel targeting factor in the chloroplast signal recognition particle (cpSRP), cpSRP43, is a highly specific molecular chaperone that efficiently reverses the aggregation of its substrate proteins. In contrast to 'ATPases associated with various cellular activities' (AAA+) chaperones, cpSRP43 uses specific binding interactions with its substrate to mediate its 'disaggregase' activity. This disaggregase capability can allow targeting machineries to more effectively capture their protein substrates and emphasizes a close connection between protein folding and trafficking processes. Moreover, cpSRP43 provides the first example to our knowledge of an ATP-independent disaggregase and shows that efficient reversal of protein aggregation can be attained by specific binding interactions between a chaperone and its substrate

Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

Understanding biological and physical processes involving nucleic acids, such as the binding of proteins to DNA and RNA, DNA condensation, and RNA folding, requires an understanding of the ion atmosphere that surrounds nucleic acids. We have used a simple model DNA system to determine how the ion atmosphere modulates interactions between duplexes in the absence of specific metal ion-binding sites and other complicated interactions. In particular, we have tested whether the Coulomb repulsion between nucleic acids can be reversed by counterions to give a net attraction, as has been proposed recently for the rapid collapse observed early in RNA folding. The conformation of two DNA duplexes tethered by a flexible neutral linker was determined in the presence of a series of cations by small angle x-ray scattering. The small angle x-ray scattering profiles of two control molecules with distinct shapes (a continuous duplex and a mimic of the compact DNA) were in good agreement with predictions, establishing the applicability of this approach. Under low-salt conditions (20 mM Na ؉ ), the tethered duplexes are extended because of a Coulombic repulsion estimated to be 2-5 kT͞bp. Addition of high concentrations of Na ؉ (1.2 M), Mg 2؉ (0.6 M), and spermidine 3؉ (75 mM) resulted in electrostatic relaxation to a random state. These results indicate that a counterion-induced attractive force between nucleic acid duplexes is not significant under physiological conditions. An upper limit on the magnitude of the attractive potential under all tested ionic conditions is estimated. correlation ͉ DNA ͉ RNA ͉ folding ͉ electrostatics N ucleic acids play a central role in the storage, transmission, and control of genetic information. DNA and RNA associate with numerous protein and nucleic acid partners to form the complexes that participate in and regulate cellular metabolism and form catalytic components of biological machines such as the ribosome. A comprehensive understanding of these biological processes requires understanding the fundamental physical and chemical principles underlying the behaviors of the participating molecules. Nucleic acids are highly charged biopolymers, with one formal negative charge per monomeric unit. There are many examples of specific interactions of nucleic acids with ions in nucleic acidprotein complexes and in folded RNAs (1, 2). Nevertheless, the vast majority of cations associated with a nucleic acid are nonspecifically bound. These counterions condense onto DNA or RNA and form a thermally fluctuating sheath commonly referred to as the ion atmosphere (3, 4). Indeed, order-of-magnitude calculations estimate enormous repulsive energies for RNA in the absence of counterions (e.g., Ϸ10 3 kT for a folded RNA with Ϸ400 nucleotides, the size of the Tetrahymena group I intron). ʈ This repulsive energy is predominantly overcome by electrostatic interactions with the ion atmosphere (3-5). Despite the clear importance of the ion atmosphere, experimental investigation has been difficult. The dynamic nature of the ion atmosphere renders it invisible in crystallographic structures. Progress has been made in the direct ''visualization'' of ion distributions around DNA duplexes in recent neutron scattering (6) and anomalous small angle x-ray scattering (SAXS) experiments that provide constraints on the shape of the ion atmosphere (7). Nevertheless, the energetic effects of this atmosphere still remain unclear. The widely used nonlinear Poisson Boltzmann (NLPB) model can estimate the electrostatic energies for nucleic acid conformations in different ionic condition (8-12). However, this model is incomplete. It does not account for the finite sizes of ions and, of particular importance to this work, positional correlations between discrete ions beyond a mean-field approximation (13). Recent theoretical work indicates that such ion-ion correlation effects can lead to a net attraction for strongly charged polyelectrolytes in the presence of multivalent cations (13-16). This effect can be thought of as analogous to attractive London dispersion forces caused by correlations of electron clouds between two nearby molecules, with the counterions arranged to minimize repulsion between one another and to maximize attractive interactions with both polyelectrolytes. Indeed, DNA condensation has been observed in numerous studies (refs. 17 and 18 and references therein), and a counterion-correlation-attractive force is a leading candidate for explaining this phenomenon (18). More recently, Murthy and Rose (15) have proposed that a counterion-induced attractive force is responsible for parallel helical arrangements common in nucleic acid crystal structures. Furthermore, a rapid ''collapse'' early in Mg 2ϩ -promoted RNA folding has been suggested to arise from analogous attractive forces induced by Mg 2ϩ ions Precise and extensive osmotic stress measurements by Parsegian and colleagues (21-26) have yielded quantitative descriptions of screened electrostatic repulsion, hydration forces, and long-range attractive forces in dense, parallel arrays of DNA double helices with several types of counterions. However, many-body effects (24) and disrupted water structure in these highly dehydrated arrays hinder the direct application of these stress measurements to isolated nucleic acids in solution. Here, we have used a simple tethered DNA in which two DNA duplexes of defined length are connected by a neutral flexible linker (Figs. 1A and 2) to isolate the counterion-modulated interactions between two helices. The results provide estimates for repulsive forces in the presence of low concentrations of monovalent cations and an upper limit for any attractive force in the presence of multivalent cations. Materials and Methods Construction of 12-bp Tethered DNAs and 24-bp Duplex DNA. The 12-bp tethered DNAs (12 /PEG9/ 12 and12 /C3/ 12) and 24-bp duplex were assembled from chemically synthesized oligonucleotides (Qiagen, Valencia, CA, and Integrated DNA Technologies, Coralville, IA) as shown in Abbreviations: SAXS, small angle x-ray scattering; NLPB, nonlinear Poisson Boltzmann. ¶ To whom correspondence may be addressed. E-mail: [email protected] or [email protected]. ʈ The Michel-Westhof model of the native Tetrahymena ribozyme (48) and a model of unfolded ribozyme with helices maximally extended from each other were used to estimate the Coulombic repulsion energy in the absence of counterions. The energies of all pairs of phosphates were calculated according to Coulomb's law and summed to yield the total Coulomb energy of the native, compact molecule relative to the unfolded one

Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples.

Panda A, Yadav A, Yeerna H, et al. Tissue- and development-stage-specific mRNA and heterogeneous CNV signatures of human ribosomal proteins in normal and cancer samples. Nucleic acids research. 2020.We give results from a detailed analysis of human Ribosomal Protein (RP) levels in normal and cancer samples and cell lines from large mRNA, copy number variation and ribosome profiling datasets. After normalizing total RP mRNA levels per sample, we find highly consistent tissue specific RP mRNA signatures in normal and tumor samples. Multiple RP mRNA-subtypes exist in several cancers, with significant survival and genomic differences. Some RP mRNA variations among subtypes correlate with copy number loss of RP genes. In kidney cancer, RP subtypes map to molecular subtypes related to cell-of-origin. Pan-cancer analysis of TCGA data showed widespread single/double copy loss of RP genes, without significantly affecting survival. In several cancer cell lines, CRISPR-Cas9 knockout of RP genes did not affect cell viability. Matched RP ribosome profiling and mRNA data in humans and rodents stratified by tissue and development stage and were strongly correlated, showing that RP translation rates were proportional to mRNA levels. In a small dataset of human adult and fetal tissues, RP protein levels showed development stage and tissue specific heterogeneity of RP levels. Our results suggest that heterogeneous RP levels play a significant functional role in cellular physiology, in both normal and disease states. © The Author(s) 2020. Published by Oxford University Press on behalf of Nucleic Acids Research

AquaSAXS: a web server for computation and fitting of SAXS profiles with non-uniformally hydrated atomic models

Small Angle X-ray Scattering (SAXS) techniques are becoming more and more useful for structural biologists and biochemists, thanks to better access to dedicated synchrotron beamlines, better detectors and the relative easiness of sample preparation. The ability to compute the theoretical SAXS profile of a given structural model, and to compare this profile with the measured scattering intensity, yields crucial structural informations about the macromolecule under study and/or its complexes in solution. An important contribution to the profile, besides the macromolecule itself and its solvent-excluded volume, is the excess density due to the hydration layer. AquaSAXS takes advantage of recently developed methods, such as AquaSol, that give the equilibrium solvent density map around macromolecules, to compute an accurate SAXS/WAXS profile of a given structure and to compare it to the experimental one. Here, we describe the interface architecture and capabilities of the AquaSAXS web server (http://lorentz.dynstr.pasteur.fr/aquasaxs.php)

Enhanced Electron Pairing in a Lattice of Berry Phase Molecules

We show that electron hopping in a lattice of molecules possessing a Berry phase naturally leads to pairing. Our building block is a simple molecular site model inspired by C$_{60}$, but realized in closer similarity with Na$_3$. In the resulting model electron hopping must be accompanied by orbital operators, whose function is to switch on and off the Berry phase as the electron number changes. The effective hamiltonians (electron-rotor and electron-pseudospin) obtained in this way are then shown to exhibit a strong pairing phenomenon, by means of 1D linear chain case studies. This emerges naturally from numerical studies of small $N$-site rings, as well as from a BCS-like mean-field theory formulation. The pairing may be explained as resulting from the exchange of singlet pairs of orbital excitations, and is intimately connected with the extra degeneracy implied by the Berry phase when the electron number is odd. The relevance of this model to fullerides, to other molecular superconductors, as well as to present and future experiments, is discussed.Comment: 30 pages, RevTe