Long-range Pairing Research Articles

The homie insulator has sub-elements with different insulating and long-range pairing properties.

Chromatin insulators are major determinants of chromosome architecture. Specific architectures induced by insulators profoundly influence nuclear processes, including how enhancers and promoters interact over long distances and between homologous chromosomes. Insulators can pair with copies of themselves in trans to facilitate homolog pairing. They can also pair with other insulators, sometimes with great specificity, inducing long-range chromosomal loops. Contrary to their canonical function of enhancer blocking, these loops can bring distant enhancers and promoters together to activate gene expression, while at the same time blocking other interactions in cis . The details of these effects depend on the choice of pairing partner, and on the orientation specificity of pairing, implicating the 3-dimensional architecture as a major functional determinant. Here we dissect the homie insulator from the Drosophila even skipped ( eve ) locus, to understand its substructure. We test pairing function in cis based on homie -carrying transgenes interacting with endogenous eve . The assay is sensitive to both pairing strength and orientation. Using this assay, we found that a Su(Hw) binding site in homie is required for efficient long-range interaction, although some activity remains without it. This binding site also contributes to the canonical insulator activities of enhancer blocking and barrier function. Based on this and other results from our functional dissection, each of the canonical insulator activities, chromosomal loop formation, enhancer blocking, and barrier activity, are partially separable. Our results show the complexity inherent in insulator functions, which can be provided by an array of different proteins with both shared and distinct properties.

Structural determinants of inverted Alu-mediated backsplicing revealed by -MaP and -JuMP.

Biogenesis of circular RNA usually involves a backsplicing reaction where the downstream donor site is ligated to the upstream acceptor site by the spliceosome. For this reaction to occur, it is hypothesized that these sites must be in proximity. Inverted repeat sequences, such as Alu elements, in the upstream and downstream introns are predicted to base-pair and represent one mechanism for inducing proximity. Here, we investigate the pre-mRNA structure of the human HIPK3 gene at exon 2, which forms a circular RNA via backsplicing. We leverage multiple chemical probing techniques, including the recently developed SHAPE- JuMP strategy, to characterize secondary and tertiary interactions in the pre- mRNA that govern backsplicing. Our data confirm that the antisense Alu elements, AluSz(-) and AluSq2(+) in the upstream and downstream introns, form a highly- paired interaction. Circularization requires formation of long-range Alu-mediated base pairs but does not require the full-length AluSq2(+). In addition to confirming long-range base pairs, our SHAPE-JuMP data identified multiple long-range interactions between non-pairing nucleotides. Genome-wide analysis of inverted repeats flanking circular RNAs confirm that their presence favors circularization, but the overall effect is modest. Together these results suggest that secondary structure considerations alone cannot fully explain backsplicing and additional interactions are key.

Bio-metal organic framework functionalized nanofibers as efficient proton-conducting for proton exchange membrane

A membrane with a low methanol permeability and high proton conductivity (σp) is essential for the effective operation of a direct methanol-based fuel cell. Herein, a bio-metal organic framework was prepared with natural α-amino acids as ligands and then combined with hydrolyzed polyacrylonitrile (PAN) nanofibers (AA-MOF@PAN). The resulting nanocomposite membranes were subsequently integrated into a Nafion matrix (AA-MOF@PAN/Nafion). The –NH2 groups on AA-MOF@PAN interact with –SO3H groups on Nafion, forming long-range acid-base pairs along the interface between the matrix and nanofibers. This interaction creates abundant proton-conducting sites for proton exchange membrane. Notably, the AA-MOF@PAN-4h/Nafion membrane demonstrated an exceptional proton conductivity (σp) of 0.25 S cm−1 and a higher power density of 117.61 mW cm−2 compared to the recast Nafion membrane. This study offers valuable insights into the three-dimensional ordered design of a natural α-amino acids as a proton transfer sites and highlighting their potential applications in proton exchange membranes.

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.

Competition of long-range interactions and noise at a ramped quench dynamical quantum phase transition: The case of the long-range pairing Kitaev chain

The nonequilibrium dynamics of long-range pairing Kitaev model with noiseless/noisy linear time dependent chemical potential, is investigated in the framework of dynamical quantum phase transitions (DQPTs). We have shown that for the ramp crossing a single quantum critical point, while the short-range pairing Kitaev model displays a single critical time scale, the long-range pairing induces a region with three DQPTs time scales. We have found that the region with three DQPTs time scales shrinks in the presence of the noise. In addition, we have uncovered that for a quench crossing two critical points, the critical sweep velocity above which the DQPTs disappear enhances by the long-range pairing exponent while decreases in the presence of the noise. On the basis of numerical simulations, we have shown that noise diminishes the long-range pairing inductions. Published by the American Physical Society 2024

Discovery and Quantification of Long-Range RNA Base Pairs in Coronavirus Genomes with SEARCH-MaP and SEISMIC-RNA.

RNA molecules perform a diversity of essential functions for which their linear sequences must fold into higher-order structures. Techniques including crystallography and cryogenic electron microscopy have revealed 3D structures of ribosomal, transfer, and other well-structured RNAs; while chemical probing with sequencing facilitates secondary structure modeling of any RNAs of interest, even within cells. Ongoing efforts continue increasing the accuracy, resolution, and ability to distinguish coexisting alternative structures. However, no method can discover and quantify alternative structures with base pairs spanning arbitrarily long distances - an obstacle for studying viral, messenger, and long noncoding RNAs, which may form long-range base pairs. Here, we introduce the method of Structure Ensemble Ablation by Reverse Complement Hybridization with Mutational Profiling (SEARCH-MaP) and software for Structure Ensemble Inference by Sequencing, Mutation Identification, and Clustering of RNA (SEISMIC-RNA). We use SEARCH-MaP and SEISMIC-RNA to discover that the frameshift stimulating element of SARS coronavirus 2 base-pairs with another element 1 kilobase downstream in nearly half of RNA molecules, and that this structure competes with a pseudoknot that stimulates ribosomal frameshifting. Moreover, we identify long-range base pairs involving the frameshift stimulating element in other coronaviruses including SARS coronavirus 1 and transmissible gastroenteritis virus, and model the full genomic secondary structure of the latter. These findings suggest that long-range base pairs are common in coronaviruses and may regulate ribosomal frameshifting, which is essential for viral RNA synthesis. We anticipate that SEARCH-MaP will enable solving many RNA structure ensembles that have eluded characterization, thereby enhancing our general understanding of RNA structures and their functions. SEISMIC-RNA, software for analyzing mutational profiling data at any scale, could power future studies on RNA structure and is available on GitHub and the Python Package Index.

Long-range Cooper pair splitting by chiral Majorana edge states

Long-range Cooper pair splitting by chiral Majorana edge states

Electron-electron attraction via Coulomb correlations and possible superconductivity in a 1D electron liquid on a rigid neutralizing background

Conditions at which a quasi-one-dimensional (1D) electron system can be considered as a quantum liquid of impenetrable charged particles are theoretically analyzed. In the presence of an inert, neutralizing background, a motion of impenetrable electrons is shown to expose a positive charge, resulting in an effective mutual attraction of infinite range. As a result, all electrons are involved in the long-range pairing. A model of spinless fermions with infinitesimal attraction of infinite range is proposed to describe the excitation spectrum and the superconducting gap in low-density 1D electron channels. In contrast with the conventional theory, the energy gap does not contain exponentially small factors. It depends mostly on the Coulombic parameters of the system, which guides practical aspects of high-temperature superconductivity.

Long-range Pairing in Monolayer NbSe2 Facilitates the Emergence of Topological Superconducting States

Abstract NbSe2, which simultaneously exhibits superconductivity and spin-orbit coupling, is anticipated to pave the way for topological superconductivity and unconventional electron pairing. In this paper, we systematically study topological superconducting (TSC) phases in monolayer NbSe2 through mixing on-site s-wave pairing (ps) with long-range pairing (psA1) based on a tight-binding model. We observe rich phases with both fixed and sensitive Chern numbers (CNs) depending on the chemical potential (μ) and out-of-plane magnetic field (Vz). As psA1 increases, the TSC phase manifests matching and mismatching features according to whether there is a bulk-boundary correspondence (BBC). Strikingly, the introduction of long-range pairing significantly reduces the critical Vz to form TSC phases compared with the pure s-wave paring. Moreover, the TSC phase can be modulated even at Vz=0 under appropriate μ and psA1, which is identified by the robust topological edge states (TESs) of ribbons. Additionally, the long-range pairing influences the hybridization of bulk and edge states, resulting in a matching/mismatching BBC with localized/oscillating TESs on the ribbon. Our finding is helpful for realization of TSC states in experiment, as well as designing and regulating TSC materials.

Genomic surveillance of SARS-CoV-2 using long-range PCR primers.

Whole Genome Sequencing (WGS) of the SARS-CoV-2 virus is crucial in the surveillance of the COVID-19 pandemic. Several primer schemes have been developed to sequence nearly all of the ~30,000 nucleotide SARS-CoV-2 genome, using a multiplex PCR approach to amplify cDNA copies of the viral genomic RNA. Midnight primers and ARTIC V4.1 primers are the most popular primer schemes that can amplify segments of SARS-CoV-2 (400 bp and 1200 bp, respectively) tiled across the viral RNA genome. Mutations within primer binding sites and primer-primer interactions can result in amplicon dropouts and coverage bias, yielding low-quality genomes with 'Ns' inserted in the missing amplicon regions, causing inaccurate lineage assignments, and making it challenging to monitor lineage-specific mutations in Variants of Concern (VoCs). In this study we used a set of seven long-range PCR primer pairs to sequence clinical isolates of SARS-CoV-2 on Oxford Nanopore sequencer. These long-range primers generate seven amplicons approximately 4500 bp that covered whole genome of SARS-CoV-2. One of these regions includes the full-length S-gene by using a set of flanking primers. We also evaluated the performance of these long-range primers with Midnight primers by sequencing 94 clinical isolates in a Nanopore flow cell. Using a small set of long-range primers to sequence SARS-CoV-2 genomes reduces the possibility of amplicon dropout and coverage bias. The key finding of this study is that long range primers can be used in single-molecule sequencing of RNA viruses in surveillance of emerging variants. We also show that by designing primers flanking the S-gene, we can obtain reliable identification of SARS-CoV-2 variants.

Regulation of translation by ribosomal RNA pseudouridylation.

Pseudouridine is enriched in ribosomal, spliceosomal, transfer, and messenger RNA and thus integral to the central dogma. The chemical basis for how pseudouridine affects the molecular apparatus such as ribosome, however, remains elusive owing to the lack of structures without this natural modification. Here, we studied the translation of a hypopseudouridylated ribosome initiated by the internal ribosome entry site (IRES) elements. We analyzed eight cryo-electron microscopy structures of the ribosome bound with the Taura syndrome virus IRES in multiple functional states. We found widespread loss of pseudouridine-mediated interactions through water and long-range base pairings. In the presence of the translocase, eukaryotic elongation factor 2, and guanosine 5'-triphosphate hydrolysis, the hypopseudouridylated ribosome favors a rare unconducive conformation for decoding that is partially recouped in the ribosome population that remains modified at the P-site uridine. The structural principles learned establish the link between functional defects and modification loss and are likely applicable to other pseudouridine-associated processes.

Direct observation of nonlocal fermion pairing in an attractive Fermi-Hubbard gas

The Hubbard model of attractively interacting fermions provides a paradigmatic setting for fermion pairing. It features a crossover between Bose-Einstein condensation of tightly bound pairs and Bardeen-Cooper-Schrieffer superfluidity of long-range Cooper pairs, and a “pseudo-gap” region where pairs form above the superfluid critical temperature. We directly observe the nonlocal nature of fermion pairing in a Hubbard lattice gas, using spin- and density-resolved imaging of ∼ 1000 fermionic potassium-40 atoms under a bilayer microscope. Complete fermion pairing is revealed by the vanishing of global spin fluctuations with increasing attraction. In the strongly correlated regime, the fermion pair size is found to be on the order of the average interparticle spacing. Our study informs theories of pseudo-gap behavior in strongly correlated fermion systems.

Structure formation by electrostatic interactions in strongly coupled medium.

The formation of correlated structures is of importance in many diverse contexts such as strongly coupled plasmas, soft matter, and even biological mediums. In all these contexts the dynamics are mainly governed by electrostatic interactions and result in the formation of a variety of structures. In this study, the process of formation of structures is investigated with the help of molecular dynamics (MD) simulations in two and three dimensions. The overall medium has been modeled with an equal number of positive and negatively charged particles interacting via long-range pair Coulomb potential. A repulsive short-range Lennard-Jones (LJ) potential is added to take care of the blowing up of attractive Coulomb interaction between unlike charges. In the strongly coupled regime, a variety of classical bound states form. However, complete crystallization of the system, as typically observed in the context of one-component strongly coupled plasmas, does not occur. The influence of localized perturbation in the system has also been studied. The formation of a crystalline pattern of shielding clouds around this disturbance is observed. The spatial properties of the shielding structure have been analyzed using the radial distribution function and Voronoi diagram. The process of accumulation of oppositely charged particles around the disturbance triggers a lot of dynamic activity in the bulk of the medium. As a result of this, close encounters are possible even between those particles/clusters which were initially and/or at some point of time widely separated. This leads to the formation of a larger number of bigger clusters. There are, however, also instances when bound pairs break up and the electrons from bound pairs contribute to the shielding cloud, whereas ions bounce back into the bulk. A detailed discussion of these features has been provided in the manuscript.

Long-Range Hot Charge Transfer Exciton Dissociation in an Organic/2D Semiconductor Hybrid Excitonic Heterostructure.

Whether and how an electron-hole pair at the donor-acceptor interface separates from their mutual Coulombic interaction has been a long-standing question for both fundamental interests and optoelectronic applications. This question is particularly interesting but yet to be unraveled in the emerging mixed-dimensional organic/2D semiconductor excitonic heterostructures where the Coulomb interaction is poorly screened. Here, by tracking the characteristic electroabsorption (Stark effect) signal from separated charges using transient absorption spectroscopy, we directly follow the electron-hole pair separation process in a model organic/2D heterostructure, vanadium oxide phthalocyanine/monolayer MoS2. After sub-100 fs photoinduced interfacial electron transfer, we observe a barrier-less long-range electron-hole pair separation to free carriers within 1 ps by hot charge transfer exciton dissociation. Further experiment reveals the key role of the charge delocalization in organic layers sustained by the local crystallinity, while the inherent in-plane delocalization of the 2D semiconductor has a negligible contribution to charge pair separation. This study reconciles the seemingly contradicting charge transfer exciton emission and dissociation process and is important to the future development of efficient organic/2D semiconductor optoelectronic devices.

Logarithmic, fractal and volume-law entanglement in a Kitaev chain with long-range hopping and pairing

Thanks to their prominent collective character, long-range interactions promote information spreading and generate forms of entanglement scaling, which cannot be observed in traditional systems with local interactions. In this work, we study the asymptotic behavior of the entanglement entropy for Kitaev chains with long-range hopping and pairing couplings decaying with a power law of the distance. We provide a fully-fledged analytical and numerical characterization of the asymptotic growth of the ground state entanglement in the large subsystem size limit, finding that the truly non-local nature of the model leads to an extremely rich phenomenology. Most significantly, in the strong long-range regime, we discovered that the system ground state may have a logarithmic, fractal, or volume-law entanglement scaling, depending on the value of the chemical potential and on the strength of the power law decay.

Structural defects of hypopseudouridylated ribosome observed during IRES-mediated translation initiation.

Pseudouridine is an abundant chemical modification found on major functional RNA molecules. Loss of pseudouridine is linked to diseases such as the X-linked dyskeratosis congenita (X-DC). While there is rich biophysical data on pseudouridine in model RNA molecules that show its stabilization role, little is known on its roles in intact functional RNA such as those within ribosome. To fill this gap, we studied structures of yeast ribosome isolated from cells that lack ribosome pseudouridine synthesis capability. We performed cryoEM structural analysis of hypopseudouridylated ribosome during initiation by the Taura syndrome virus (TSV) IRES, as the IRES-mediated translation has been found to be severely impaired in X-DC patient cells or by ribosome isolated from them. We found that though the overall fold of hypopseudouridylated ribosome remains similar to native ribosome, high resolution features reveal significant loss of pseudouridine-mediated interactions through water and long-range base pairings. Strikingly, when bound with TSV IRES and in presence of the elongation factor, eEF2, and GTP hydrolysis, the hypopseudouridylated ribosome favors an unconducive conformation for decoding linked to the loss of heavily pseudouridylated helix H69 and a hypermodified P site uridine, consistent with its reduced rate and fidelity of translation. Our data suggest that loss of pseudouridine in key ribosome sites alters the evolutionarily tuned ribosome motions required for IRES-mediated translation.

Densities and momentum distributions in A≤12 nuclei from chiral effective field theory interactions

This study presents calculations of one- and two-body densities in both coordinate and momentum space for various nuclei up to ${}^{12}$C, using the phenomenological AV18+UX and various Norfolk $N\phantom{\rule{0}{0ex}}N$ + $N\phantom{\rule{0}{0ex}}N\phantom{\rule{0}{0ex}}N$ $\ensuremath{\chi}$EFT interactions. It features new calculations of the pair density as a function of both pair separation and center-of-mass, as well as the two-body momentum distribution for short- and long-range pairs differentiated by a pair separation boundary. The full set of results are available online for general use by the nuclear physics community and are intended to provide useful insights into the short-range structure of nuclei and various reaction processes.

Signatures of the long-range phase transition in topological Josephson junctions

The extended Kitaev models spark a recent surge of interest due to its unprecedented topological phase with fractional invariants. In this extended model of topological superconductors, long-range pairing interactions can induce a pair of subgap massive edge modes (MEMs), posing novel challenges to the unambiguous detection of Majorana bound states (MBSs) sustained by the same model in the short-range limit. Here we investigate the effect of a power-law decayed long-range pairing on the dc and ac Josephson currents between two Majorana nanowires. By varying the magnetic field and long-range pairing, the nanowires can be driven into different phases hosting MEMs, MBSs, or trivial Andreev bound states (ABSs), which considerably modulate the Josephson current. For weakly linked Josephson junctions, we show that the MEMs emerging in the long-range phases can induce a zigzag profile in the dc current-phase relation featured by two sign reversals deviating from the point where the superconducting phase difference $\ensuremath{\phi}=\ensuremath{\pi}$. In contrast, the Josephson current indicates a sharp sign reversal at $\ensuremath{\phi}=\ensuremath{\pi}$ in the short-range phase that hosts MBSs, while a smooth sinelike dc Josephson current appears in the presence of ABSs. In the nonequilibrium junction biased by a voltage, we identify a $4\ensuremath{\pi}$ ac Josephson current in the short-range phases, indicating a MBSs-mediated tunneling process dominating the supercurrents. Differently, when the system enters MEMs-hosted long-range phases, the ordinary ac Josephson current with $2\ensuremath{\pi}$ periodicity can be restored. In addition, we find the ac Josephson current induced by MEMs is significantly suppressed under the strong long-range pairing interactions. These signatures can serve as probes to discriminate MBSs from MEMs and ABSs.

Correlations, long-range entanglement, and dynamics in long-range Kitaev chains

Long-range interactions exhibit surprising features which have been less explored so far. Here, studying a one-dimensional fermionic chain with long-range hopping and pairing, we discuss some general features associated to the presence of long-range entanglement. In particular, after determining the algebraic decays of the correlation functions, we prove that a long-range quantum mutual information exists if the exponent of the decay is not larger than one. Moreover, we show that the time evolution triggered by a quantum quench between short-range and long-range regions, can be characterized by dynamical quantum phase transitions without crossing any phase boundary. We show, also, that the adiabatic dynamics is dictated by the divergence of a topological length scale at the quantum critical point, clarifying the violation of the Kibble-Zurek mechanism for long-range systems.

Local Central Limit Theorem for Long-Range Two-Body Potentials at Sufficiently High Temperatures

Dobrushin and Tirozzi [14] showed that, for a Gibbs measure with the finite-range potential, the Local Central Limit Theorem is implied by the Integral Central Limit Theorem. Campanino, Capocaccia, and Tirozzi [7] extended this result for a family of Gibbs measures for long-range pair potentials satisfying certain conditions. We are able to show for a family of Gibbs measures for long-range pair potentials not satisfying the conditions given in [7], that at sufficiently high temperatures, if the Integral Central Limit Theorem holds for a given sequence of Gibbs measures, then the Local Central Limit Theorem also holds for the same sequence. We also extend [7] when the state space is general, provided that it is equipped with a finite measure.