Weak Pair Research Articles

Pairing instabilities of Dirac composite fermions

Recently, a Dirac (particle-hole symmetric) description of composite fermions in the half-filled quantum Hall system was proposed [D. T. Son, Phys. Rev. X 5, 031027 (2015)], and we study its possible consequences on BCS (Cooper) pairing of composite fermions (CF's). One of the main consequences is the existence of anisotropic states in single and bilayer systems, which was previously suggested in Ref. [J. S. Jeong and K. Park, Phys. Rev. B 91, 195119 (2015)]. We argue that in the half-filled single layer the gapped states may sustain anisotropy, because isotropic pairings may coexist with anisotropic ones. Furthermore, anisotropic pairings with addition of a particle-hole (PH) symmetry breaking mass term may evolve into rotationally symmetric states, i.e. Pfaffian states of Halperin-Lee-Read (HLR) ordinary CF's. On the basis of the Dirac formalism, we argue that in the quantum Hall bilayer at total filling one, with decreasing distance between layers weak pairing of p-wave paired CF's is gradually transformed from Dirac to ordinary, HLR-like, with concomitant decrease in the CF number. Global characterization of low-energy spectrum based on the Dirac CF's agrees well with previous calculations performed by exact diagonalization on a torus. Finally, we discuss features of Dirac formalism when applied in this context.

Temporo-parietal connectivity uniquely predicts reading change from childhood to adolescence

Previous research has shown that left posterior middle temporal gyrus (pMTG) is a core node in the semantic network, and cross-sectional studies have shown that activation in this region changes developmentally and is related to skill measured concurrently. However, it is not known how functional connectivity with this region changes developmentally, and whether functional connectivity is related to future gains in reading. We conducted a longitudinal functional magnetic resonance imaging (fMRI) study in 30 typically developing children (aged 8–15) to examine whether initial brain measures, including activation and connectivity, can predict future behavioral improvement in a semantic judgment task. Participants were scanned on entering the study (time 1, T1) and a follow-up period of 2years (time 2, T2). Character pairs were arranged in a continuous variable according to association strength (i.e. strong versus weak), and participants were asked to determine if these visually presented pairs were related in meaning. Our results demonstrated greater developmental changes from time 1 to time 2 for weaker association pairs in the left pMTG for the children (aged 8–11) as compared to the adolescents (aged 12–15). Moreover, the results showed greater developmental changes from time 1 to time 2 for weaker association pairs in connectivity between the pMTG and inferior parietal lobule (IPL) for the children as compared to the adolescents. Furthermore, a hierarchical stepwise regression model revealed that connectivity between the pMTG and IPL in weak association pairs was uniquely predictive of behavioral improvement from time 1 to time 2 for the children, but not the adolescents. Taken together, the activation results suggest relatively rapid development before adolescence of semantic representations in the pMTG. Moreover, the connectivity results of pMTG with IPL tentatively suggest that early development of semantic representations may be facilitated by enhanced engagement of phonological short-term memory.

Weak Dual Pairs and Jetlet Methods for Ideal Incompressible Fluid Models in $$n \ge 2$$ n ≥ 2 Dimensions

We review the role of dual pairs in mechanics and use them to derive particle-like solutions to regularized incompressible fluid systems. In our case we have a dual pair resulting from the action of diffeomorphisms on point particles (essentially by moving the points). We then augment our dual pair by considering the action of diffeomorphisms on Taylor series, also known as jets. The augmented weak dual pairs induce a hierarchy of particle-like solutions and conservation laws with particles carrying a copy of a jet group. We call these augmented particles jetlets. The jet groups serve as finite-dimensional models of the diffeomorphism group itself, and so the jetlet particles serve as a finite-dimensional model of the self-similarity exhibited by ideal incompressible fluids. The conservation law associated to jetlet solutions is shown to be a shadow of Kelvin's circulation theorem. Finally, we study the dynamics of infinite time particle mergers. We prove that two merging particles at the zeroth level in the hierarchy yield dynamics which asymptotically approach that of a single particle in the first level in the hierarchy. This merging behavior is then verified numerically as well as the exchange of angular momentum which must occur during a near collision of two particles. The resulting particle-like solutions suggest a new class of meshless methods which work in dimensions $n \geq 2$ and which exhibit a shadow of Kelvin's circulation theorem. More broadly, this provides one of the first finite-dimensional models of self-similarity in ideal fluids.

The Dynamic Nucleotide Selection Mechanism of DNA Polymerase I at Atomic Resolution

Replicative DNA polymerases use complex induced fit mechanisms to distinguish substrates complementary to the template from mismatches with remarkable speed and accuracy. The transient conformations and their order in the mechanism underly the speed and accuracy of polymerases, yet are difficult to characterize due to the sub‐millisecond time scales of the transitions. We employed microsecond scale, all‐atom, explicit waters molecular dynamics to characterize and visualize the conformational changes that occur when DNA polymerase I, large fragment, from Bacillus stearothermophilus encounters a complementary dCTP or a mismatched dTTP opposite a template dG. The dCTP and the Mg2+ cofactor immediately formed a stable base pair with dG and induced fluctuations of the mobile fingers subdomain between the open conformation and a state intermediate between open and closed. The enzyme closed only upon the binding of a second cation to the active site, followed by a rotation of a conserved histidine towards the 3′‐OH of the growing primer strand. We speculate this is the deprotonation step that initiates catalysis. In the presence of the mismatched dTTP‐Mg2+, a weak base pair forms with dG, but quickly breaks, leading to near dissociation of the dTTP during the 3μs simulation. These simulations detail the complex polymerase mechanism and provide structural explanations for the behavior and high fidelity of dynamic DNA polymerases during nucleotide selection.Support or Funding InformationThe authors would like to acknowledge the Jeffress Trust Awards Program in Interdisciplinary Research for funding, as well as the University of Richmond for computing resources.This work also used Extreme Science Engineering Discovery Environment (XSEDE) allocations TG‐MCB140003 and TG‐MCB140073, which are supported by National Science Foundation grant number OCI‐1053575. Additional computing resources were utilized as part of the MERCURY Consortium supported by NSF grant number CHE‐1229354

Weak Index Pairs and the Conley Index for Discrete Multivalued Dynamical Systems

Motivated by the problem of reconstructing dynamics from samples, we revisit the Conley index theory for discrete multivalued dynamical systems [T. Kaczynski and M. Mrozek, Topology Appl., 65 (1995), pp. 83--96]. We introduce a new, less restrictive definition of the isolating neighborhood. It turns out that then the main tool for the construction of the index, i.e., the index pair, is no longer useful. In order to overcome this obstacle we use the concept of weak index pairs.

Approximate Solution of the Pairing Hamiltonian in the Berggren Basis

We derive the approximate solution for the pairing Hamiltonian in the Berggren ensemble of single particle states including bound, resonance and non-resonant scattering states. We show that this solution is reliable in the limit of a weak pairing interaction.

Symmetry-Adapted Perturbation Theory study on interactions between small cycloalkanes

Partitioning of interaction energy reveals factors involved in the build-up of supramolecular structures. It is known that in molecular crystals a sum of weaker forces can be as important as a single, stronger one. This study is devoted to the Symmetry-Adapted Perturbation Theory (SAPT) investigations on dimers of cyclopropane, cyclobutane, aziridine and oxirane. Angular variations of SAPT terms are discussed. For saturated cycloalkanes the dispersion term is found decisive for the dimer formation. Weak lone pair interactions in case of oxirane and aziridine have significant impact on the structure of dimers, and will decide on the structure of larger motifs.

Interference effects for H → W W → ℓ ν q q ¯ ′ $$ H\to W\;W\to \ell \nu q{\overline{q}}^{\prime } $$ and H → Z Z → ℓ ℓ ¯ q q ¯ $$ H\to ZZ\to \ell \overline{\ell}q\overline{q} $$ searches in gluon fusion at the LHC

Signal-background interference effects are studied for H → W W and H → ZZ searches in gluon fusion at the LHC. More specifically, the interference in the channels with semileptonic weak boson pair decay is analysed for light and heavy Higgs masses with minimal and realistic experimental selection cuts. In the semileptonic decay modes, the interference is affected by tree-level background contributions enhanced by 1/e 2 relative to the gluon-fusion continuum background in the fully leptonic decay modes. We find that for both light and heavy Higgs masses the interference with the loop-induced weak-boson pair background dominates over the interference with the tree-level weak-boson plus jets background for a range of selection cuts. We therefore conclude that higher-order background contributions can induce leading interference effects. With appropriate background suppression cuts the interference can be reduced to the 10% level for heavy Higgs masses, and to the per mille level for the light SM Higgs.

Interplay of magnetic order, pairing, and phase separation in a one-dimensional spin-fermion model

We consider a lattice model of itinerant electrons coupled to an array of localized classical Heisenberg spins. The nature of the ground state ordered magnetic phases that result from the indirect spin-spin coupling mediated by the electrons is determined as a function of density and the spin-fermion coupling $J$. At a fixed chemical potential, spiral phases exist only up to values of $J$ which are less than roughly half the electronic bandwidth. At a fixed electron density and near half filling, the system phase separates into a half-filled antiferromagnetic phase and a spiral phase. The ferromagnetic phases are shown to be fully polarized, while the spiral phases have equal admixture of up and down spins. Phase separation survives in the presence of weak pairing field $\Delta$ but disappears when $\Delta$ exceeds a critical value $\Delta_c$. If pairing fields are large enough, an additional spiral state arises at strong coupling $J$. The relevance of this study, especially the phase separation, to artificially engineered systems of adjacent itinerant electrons and localized spins is discussed. In particular, we propose a method which might allow for the braiding of Majorana fermions by changing the density and moving their location as they are pulled along by a phase separation boundary.

Strong, Neutral, or Weak: Exploring the Impostor Score Distribution

The strong, neutral, or weak (SNoW) face impostor pairs problem is intended to explore the causes and impact of impostor face pairs that are inherently strong (easily recognized as nonmatches) or weak (possible false matches). The SNoW technique develops three partitions within the impostor score distribution of a given data set. Results provide evidence that varying degrees of impostor scores impact the overall performance of a face recognition system. This paper extends our earlier work to incorporate improvements regarding outlier detection for partitioning, explores the SNoW concept for the additional modalities of fingerprint and iris, and presents methods for how to begin to reveal the causes of weak impostor pairs. We also show a clear operational difference between strong and weak comparisons as well as identify partition stability across multiple algorithms.

Communication: Improved pair approximations in local coupled-cluster methods.

In local coupled cluster treatments the electron pairs can be classified according to the magnitude of their energy contributions or distances into strong, close, weak, and distant pairs. Different approximations are introduced for the latter three classes. In this communication, an improved simplified treatment of close and weak pairs is proposed, which is based on long-range cancellations of individually slowly decaying contributions in the amplitude equations. Benchmark calculations for correlation, reaction, and activation energies demonstrate that these approximations work extremely well, while pair approximations based on local second-order Møller-Plesset theory can lead to errors that are 1-2 orders of magnitude larger.

Characterization of log del Pezzo pairs via anticanonical models

There are several variations of the definition of log del Pezzo pairs in the literature. We define their suitable smooth models, and we show that they are the same. In particular, we obtain a characterization of smooth log del Pezzo pairs in terms of anticanonical models. As applications, we classify non-rational weak log canonical del Pezzo pairs, and we prove that every surface of globally F-regular type is of Fano type.

Autonomous assembly of synthetic oligonucleotides built from an expanded DNA alphabet. Total synthesis of a gene encoding kanamycin resistance.

Background: Many synthetic biologists seek to increase the degree of autonomy in the assembly of long DNA (L-DNA) constructs from short synthetic DNA fragments, which are today quite inexpensive because of automated solid-phase synthesis. However, the low information density of DNA built from just four nucleotide “letters”, the presence of strong (G:C) and weak (A:T) nucleobase pairs, the non-canonical folded structures that compete with Watson–Crick pairing, and other features intrinsic to natural DNA, generally prevent the autonomous assembly of short single-stranded oligonucleotides greater than a dozen or so.Results: We describe a new strategy to autonomously assemble L-DNA constructs from fragments of synthetic single-stranded DNA. This strategy uses an artificially expanded genetic information system (AEGIS) that adds nucleotides to the four (G, A, C, and T) found in standard DNA by shuffling hydrogen-bonding units on the nucleobases, all while retaining the overall Watson–Crick base-pairing geometry. The added information density allows larger numbers of synthetic fragments to self-assemble without off-target hybridization, hairpin formation, and non-canonical folding interactions. The AEGIS pairs are then converted into standard pairs to produce a fully natural L-DNA product. Here, we report the autonomous assembly of a gene encoding kanamycin resistance using this strategy. Synthetic fragments were built from a six-letter alphabet having two AEGIS components, 5-methyl-2’-deoxyisocytidine and 2’-deoxyisoguanosine (respectively S and B), at their overlapping ends. Gaps in the overlapped assembly were then filled in using DNA polymerases, and the nicks were sealed by ligase. The S:B pairs in the ligated construct were then converted to T:A pairs during PCR amplification. When cloned into a plasmid, the product was shown to make Escherichia coli resistant to kanamycin. A parallel study that attempted to assemble similarly sized genes with optimally designed standard nucleotides lacking AEGIS components gave successful assemblies of up to 16 fragments, but generally failed when larger autonomous assemblies were attempted.Conclusion: AEGIS nucleotides, by increasing the information density of DNA, allow larger numbers of DNA fragments to autonomously self-assemble into large DNA constructs. This technology can therefore increase the size of DNA constructs that might be used in synthetic biology.

Existence of strong-pairing quantum Hall phase in bilayer cold-atom systems with dipolar interactions

We study bilayer fermionic cold atom systems with dipolar interactions, as well as a two-component tunable pseudopotential (TCTP) model which keeps only the zeroth and first Haldane pseudopotentials, at total Landau level filling factor 1/2. Our numerical results on the TCTP model indicates that Haldane-Rezayi state describes the critical point between strong and weak d-wave pairing quantum Hall phases. Further increasing the attractive zeroth pseudopotentials, the system transits from the strong-pairing phase to a stripe phase, and then to a cluster phase (or phase separation). The dipolar interaction can be mapped onto the TCTP model in the strong-pairing phase, if high order pseudopotentials are ignored. Our numerical results show that this is indeed the case, so the strong-pairing phase can be realized in the cold atom system.

Weak base pairing in both seed and 3' regions reduces RNAi off-targets and enhances si/shRNA designs.

The use of RNA interference is becoming routine in scientific discovery and treatment of human disease. However, its applications are hampered by unwanted effects, particularly off-targeting through miRNA-like pathways. Recent studies suggest that the efficacy of such off-targeting might be dependent on binding stability. Here, by testing shRNAs and siRNAs of various GC content in different guide strand segments with reporter assays, we establish that weak base pairing in both seed and 3′ regions is required to achieve minimal off-targeting while maintaining the intended on-target activity. The reduced off-targeting was confirmed by RNA-Seq analyses from mouse liver RNAs expressing various anti-HCV shRNAs. Finally, our protocol was validated on a large scale by analyzing results of a genome-wide shRNA screen. Compared with previously established work, the new algorithm was more effective in reducing off-targeting without jeopardizing on-target potency. These studies provide new rules that should significantly improve on siRNA/shRNA design.

Synthesis of novel polymer as solid acid-base catalyst for styrene from toluene

A novel solid acid-base catalyst Cat-NH2C2H4NH2 with aluminum and nitrogen was prepared from phenol and formaldehyde by using triblock copolymer Pluronic F127 as a template and resol as a catalyst precursor via evaporation induced organic-organic assembly method. The catalyst was characterized by Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectra (XPS). The acid-base properties of the catalyst were determined by temperature programmed desorption (TPD) using CO2 and NH3 as probe molecules. The side chain alkylation of toluene with methanol over the catalysts had been studied. The results showed that Cat-NH2C2H4NH2 has demonstrated the higher activity and selectivity than the conventional alkali exchanged zeolites. This may be because that the weak or middle acid-base pairs on the catalyst are favored to bimolecular side-chain alkylation reaction.

A combined experimental and theoretical study of the supramolecular self-assembly of Cu(II) malonate complex assisted by various weak forces and water dimer

A Cu(II) malonate complex with formula [Cu(C3H2O4)(C6H8N2)(H2O)]2·4H2O (1) [C6H8N2=2-picolylamine, C3H2O42−=malonate dianion] has been synthesized by mixing the reactants in their stoichiometric proportion and its crystal structure has been determined by single-crystal X-ray diffraction. In 1, monomeric neutral metal malonate units [Cu(C3H2O4)(C6H8N2)(H2O)] are interlinked with each other through hydrogen bonds, weak lone pair⋯π and cuprophilic interactions to generate supramolecular dimers, which in turn further associated through hydrogen bonding to form infinite 1D chains. Water dimers, through series of hydrogen bonds and weak π–stacking forces are found to be responsible for interconnection of 1D chains, which resulted in a 3D network. A density functional (DFT) study of the energetic features of several noncovalent interactions observed in the solid state have been analyzed and characterized using Bader׳s theory of “atoms-in-molecules”. We also present here Hirshfeld surface analysis to investigate the close intermolecular contacts.

Spectroscopic signature of Kondo screening on single adatoms inNa(Fe0.96Co0.03Mn0.01)As

The electronic states of surface adatoms in Na(Fe0.96Co0.03Mn0.01)As have been studied by low temperature scanning tunneling spectroscopy. The spectra recorded on the adatoms display both superconducting coherence peaks and an asymmetric resonance in a larger energy scale. The Fano-type line shape of the spectra points towards a possible Kondo effect at play. The apparent energy position of the resonance peak shifts about 5 meV to the Fermi level when measured across the critical temperature, supporting that the Bogoliubov quasiparticle is responsible for the Kondo screening in the superconducting state. The tunneling spectra do not show the subgap bound states, which is explained as the weak pair breaking effect given by the weak and broad scattering potential after the Kondo screening.

Efficient and accurate treatment of weak pairs in local CCSD(T) calculations. II. Beyond the ring approximation.

In order to arrive at linear scaling of the computational cost with molecular size, local coupled cluster methods discriminate pairs of local molecular orbitals according to the spatial separation R of the latter. Only strong pairs are treated at the full coupled cluster level, whereas for weak pairs a lower level of theory (usually Møller-Plesset perturbation theory of second order, MP2) is used. Yet an MP2 treatment of weak pairs is inadequate in certain situations (for example, for describing π-stacking), which calls for an improved but still inexpensive method for dealing with the weak pairs. In a previous contribution, we proposed as a substituent for MP2 the LrCCD3 method, which is based on ring coupled cluster doubles (ring-CCD) and includes all third-order diagrams with energy contributions decaying not quicker than R(-6). In the present work, we explore a still more accurate method, which is based on the same principles. It turned out to be essential to abandon the restriction to ring-CCD, i.e., to include further CCD diagrams beyond the ring approximation. The occurring intermediates turn out to be formally very similar to LMP2 density matrices, such that an efficient evaluation of these non-ring CCD diagrams is possible. Furthermore, a computationally cheap a posteriori estimate for the fourth-order singles contribution to the weak pair energy, which also exhibits a decay behavior of R(-6), is introduced. The resulting method, denoted as LCCD[S]-R(-6), indeed provides a substantial improvement in accuracy over the previous LrCCD3 method at a relatively modest additional computational cost.

Clar theory extended for polyacenes and beyond.

An extension of Clar's classical sextet ideas is presented to allow resonance-based weak-pairing long bonds. As the prototypic illustration, the theory is developed in the context of polyacenes, where this extension is needed to properly understand what goes on in this sort of polymer, whose radicality increases with chain length. A quantification of these novel Clar-sextic ideas is made, and detailed computational results are reported for the polyacenes even to the limit of arbitrary long chains. Resonance energies, bond lengths, and local (ring) aromaticity indices are addressed. It is emphasized that weak pairing is not at all unique to the polyacenes, but also applies whenever there are suitable boundaries (say of the "zig-zag" type) on general grapheneic structures--thereby readily explaining novel features of different boundaries.