Long-range Region Research Articles

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.

Modeling of Structure H Carbon Dioxide Clathrate Hydrates: Guest-Lattice Energies, Crystal Structure, and Pressure Dependencies.

We performed first-principles computations to investigate the complex interplay of molecular interaction energies in determining the lattice structure and stability of CO2@sH clathrate hydrates. Density functional theory computations using periodic boundary conditions were employed to characterize energetics and the key structural properties of the sH clathrate crystal under pressure, such as equilibrium lattice volume and bulk modulus. The performance of exchange–correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. Structural relaxations of the fully CO2-filled and empty sH unit cells yield crystal structure and lattice energies, while their compressibility parameters were derived by including the pressure dependencies. The present quantum chemistry computations suggest anisotropy in the compressibility of the sH clathrate hydrates, with the crystal being less compressible along the a-axis direction than along the c-axis one, in distinction from nearly isotropic sI and sII structures. The detailed results presented here give insight into the complex nature of the underlying guest–host interactions, checking earlier assumptions, providing critical tests, and improving estimates. Such entries may eventually lead to better predictions of thermodynamic properties and formation conditions, with a direct impact on emerging hydrate-based technologies.

Subtype and cell type specific expression of lncRNAs provide insight into breast cancer

Long non-coding RNAs (lncRNAs) are involved in breast cancer pathogenesis through chromatin remodeling, transcriptional and post-transcriptional gene regulation. We report robust associations between lncRNA expression and breast cancer clinicopathological features in two population-based cohorts: SCAN-B and TCGA. Using co-expression analysis of lncRNAs with protein coding genes, we discovered three distinct clusters of lncRNAs. In silico cell type deconvolution coupled with single-cell RNA-seq analyses revealed that these three clusters were driven by cell type specific expression of lncRNAs. In one cluster lncRNAs were expressed by cancer cells and were mostly associated with the estrogen signaling pathways. In the two other clusters, lncRNAs were expressed either by immune cells or fibroblasts of the tumor microenvironment. To further investigate the cis-regulatory regions driving lncRNA expression in breast cancer, we identified subtype-specific transcription factor (TF) occupancy at lncRNA promoters. We also integrated lncRNA expression with DNA methylation data to identify long-range regulatory regions for lncRNA which were validated using ChiA-Pet-Pol2 loops. lncRNAs play an important role in shaping the gene regulatory landscape in breast cancer. We provide a detailed subtype and cell type-specific expression of lncRNA, which improves the understanding of underlying transcriptional regulation in breast cancer.

3D chromatin remodelling in the germ line modulates genome evolutionary plasticity

Chromosome folding has profound impacts on gene regulation, whose evolutionary consequences are far from being understood. Here we explore the relationship between 3D chromatin remodelling in mouse germ cells and evolutionary changes in genome structure. Using a comprehensive integrative computational analysis, we (i) reconstruct seven ancestral rodent genomes analysing whole-genome sequences of 14 species representatives of the major phylogroups, (ii) detect lineage-specific chromosome rearrangements and (iii) identify the dynamics of the structural and epigenetic properties of evolutionary breakpoint regions (EBRs) throughout mouse spermatogenesis. Our results show that EBRs are devoid of programmed meiotic DNA double-strand breaks (DSBs) and meiotic cohesins in primary spermatocytes, but are associated in post-meiotic cells with sites of DNA damage and functional long-range interaction regions that recapitulate ancestral chromosomal configurations. Overall, we propose a model that integrates evolutionary genome reshuffling with DNA damage response mechanisms and the dynamic spatial genome organisation of germ cells.

Wave Packet Approach to Adiabatic and Nonadiabatic Dynamics of Cold Inelastic Scatterings.

Due to the extremely large de Broglie wavelength of cold molecules, cold inelastic scattering is always characterized by the time-independent close-coupling (TICC) method. However, the TICC method is difficult to apply to collisions of large molecular systems. Here, we present a new strategy for characterizing cold inelastic scattering using wave packet (WP) method. In order to deal with the long de Broglie wavelength of cold molecules, the total wave function is divided into interaction, asymptotic and long-range regions (IALR). The three regions use different numbers of ro-vibrational basis functions, especially the long-range region, which uses only one function corresponding to the initial ro-vibrational state. Thus, a very large grid range can be used to characterize long de Broglie wavelengths in scattering coordinates. Due to its better numerical scaling law, the IALR-WP method has great potential in studying the inelastic scatterings of larger collision systems at cold and ultracold regimes.

Radar Occupancy Prediction With Lidar Supervision While Preserving Long-Range Sensing and Penetrating Capabilities

Radar shows great potential for autonomous driving by accomplishing long-range sensing under diverse weather conditions. But radar is also a particularly challenging sensing modality due to the radar noises. Recent works have made enormous progress in classifying free and occupiedspaces in radar images by leveraging lidar supervision. However, there are still several unsolved issues. Firstly, the sensing distance of the results is limited by the sensing range of lidar. Secondly, the performance of the results is degenerated by lidar due to the physical sensing discrepancies between the two sensors. For example, some objects visible to lidar are invisible to radar, and some objects occluded in lidar scans are visible in radar images. These sensing differences cause false positive and degeneration of radar penetrating capability, respectively. In this letter, we propose training data preprocessing and polar sliding window inference to solve the issues. The data preprocessing aims to reduce the effect caused by radar-invisible measurements in lidar scans. The polar sliding window inference aims to solve the limited sensing range issue by applying a near-range trained network to the long-range region. Instead of using common Cartesian representation, we propose to use polar representation to reduce the shape dissimilarity between long-range and near-range data. We find that extending a near-range trained network to long-range region inference in the polar space has 4.2 times better IoU than in Cartesian space. Besides, the polar sliding window inference can preserve the radar penetrating capability by changing the viewpoint of the inference region.

Functional Similarities of Protein-Coding Genes in Topologically Associating Domains and Spatially-Proximate Genomic Regions.

Topologically associating domains (TADs) are the structural and functional units of the genome. However, the functions of protein-coding genes existing in the same or different TADs have not been fully investigated. We compared the functional similarities of protein-coding genes existing in the same TAD and between different TADs, and also in the same gap region (the region between two consecutive TADs) and between different gap regions. We found that the protein-coding genes from the same TAD or gap region are more likely to share similar protein functions, and this trend is more obvious with TADs than the gap regions. We further created two types of gene–gene spatial interaction networks: the first type is based on Hi-C contacts, whereas the second type is based on both Hi-C contacts and the relationship of being in the same TAD. A graph auto-encoder was applied to learn the network topology, reconstruct the two types of networks, and predict the functions of the central genes/nodes based on the functions of the neighboring genes/nodes. It was found that better performance was achieved with the second type of network. Furthermore, we detected long-range spatially-interactive regions based on Hi-C contacts and calculated the functional similarities of the gene pairs from these regions.

Investigating Japanese encephalitis virus long-range terminal region interactions

Family Flaviviridae is composed of pathogenic viruses such as Dengue, West Nile, Zika, and Japanese encephalitis virus (JEV). Flaviviruses contain a single-stranded, positive-sense RNA genome that undergoes long-distance 5'-3' interaction of their terminal regions (TRs) resulting in genomic cyclization. This cyclization is hypothesized to be conserved across the various members of this family and is necessary for viral replication. However, the exact biochemical and biophysical basis underlying the 5'-3' TRs interaction has yet to be elucidated.

Quantum Wave Packet Treatment of Cold Nonadiabatic Reactive Scattering at the State-To-State Level.

Cold and ultracold collisions are dominated by quantum effects, such as resonances, tunneling, and nonadiabatic transitions between different electronic states. Due to the extremely long de Broglie wavelength in such processes, quantum reactive scattering is most conveniently characterized using the time-independent close-coupling (TICC) methods. However, the TICC approach is difficult for systems with a large number of channels because of its steep numerical scaling laws. Here, a recently proposed quantum wave packet (WP) approach for solving adiabatic reactive scattering problems at low collision energies is extended to include nonadiabatic transitions. To impose the outgoing boundary conditions, the total scattering wavefunction is split into three parts, the interaction, the asymptotic, and the long-range regions. Each region is associated with a different set of basis functions, which could be optimized separately. In this way, an extremely long grid can be used to accommodate the characteristic long de Broglie wavelengths in the scattering coordinate. The better numerical scaling laws of the WP approach have the potential for handling larger nonadiabatic reactive systems at low temperatures in the future.

A Comparative Study of Potential Energy Curves Analytical Representations for CO, N2, P2, and ScF in Their Ground Electronic States

In this study, a detailed comparative analysis of four different potential energy functions is elaborated. These potential energy functions namely are Morse, Deng-Fan, Varshni, and Lennard-Jones. Furthermore, a mathematical representation for long-range region is elucidated. As a study case, four diatomic molecules (CO, N2, P2, and ScF) in their electronic ground states were chosen. Subsequently, the corresponding dissociation energy as well as some spectroscopic parameters were calculated accordingly.

Filming ultrafast roaming-mediated isomerization of bismuth triiodide in solution

Roaming reaction, defined as a reaction yielding products via reorientational motion in the long-range region (3 – 8 Å) of the potential, is a relatively recently proposed reaction pathway and is now regarded as a universal mechanism that can explain the unimolecular dissociation and isomerization of various molecules. The structural movements of the partially dissociated fragments originating from the frustrated bond fission at the onset of roaming, however, have been explored mostly via theoretical simulations and rarely observed experimentally. Here, we report an investigation of the structural dynamics during a roaming-mediated isomerization reaction of bismuth triiodide (BiI3) in acetonitrile solution using femtosecond time-resolved x-ray liquidography. Structural analysis of the data visualizes the atomic movements during the roaming-mediated isomerization process including the opening of the Bi-Ib-Ic angle and the closing of Ia-Bi-Ib-Ic dihedral angle, each by ~40°, as well as the shortening of the Ib···Ic distance, following the frustrated bond fission.

Aromaticity in Phenyl Decorated closo-Monocarboranes. Planar-Spherical Aggregates Involving 7-12-Vertex Cages.

The characterized phenyl decorated closo-monocarboranes with variable sizes from 7- to 12-vertex cages, [Ph-closo-CBnHn]-, n = 6-11, allow us to address the role of the varying size and shape of the carborane cage in dual planar-spherical aromatic species. Our results show the formation of adjacent shielding cone characteristics enabled from both planar and spherical aromatic fragments, despite the different structures of the closo-monocarboranes. Under a field perpendicular to the phenyl ring, both shielding cones are enabled, which overlap at long-range regions, in contrast to other orientations leading to a short-range response from the planar aromatic fragment. Thus, a two- or one-aromatic circuit is enabled selectively within the same molecular unit, by controlling the orientation of the external field. Along with the series, a variable extension of the shielding cone from the carborane cage is observed, which is larger for the -CB11H11 case, decreasing toward -CB6H6, denoting a similar extension from both the planar and spherical aromatic regions at the [4-Ph-closo-4-CB8H8]- (4) counterpart. The analysis of such multiple aromatic structures shows that, despite the different sizes and shapes of the closo cages, a similar aromatic behavior remains. In addition, the anisotropy of the induced magnetic field is given graphically, denoting a larger anisotropy for the planar aromatic moiety owing to its two-dimensional structure, which is suggested to discriminate between planar and spherical aromatic fragments within the same molecule.

Dense Haze Removal by Nonlinear Transformation

Images captured in hazy or foggy weather conditions, suffer from various problems, such as limited visibility, low contrast, color distortions. These images are used in many computer vision applications, such as video surveillance, transportation, remote sensing. The elimination of the haze effect from these images is essential to ensure the perfect working of these applications. The degradation of a captured image is expressed by the physical model of hazy image formation. The physical model requires the estimation of transmission to restore a haze-free image, which is one of the most important parameters of single image dehazing (SID). Due to the ill-posed nature of SID, lots of priors/assumptions have been used. However, traditional methods fail when these priors do not hold, especially for varying haze concentrations, which lead to many issues such as incomplete haze removal or over enhancement in long-range regions. In this paper, a single image dehazing method based on a superpixel and nonlinear transformation is proposed. The proposed method transforms the minimum filtering on superpixels of a hazy image into the minimum filtering on superpixels of a haze-free image using nonlinear transformation. The nonlinear transformation prevents over enhancement in the long-range regions, while the superpixels reduce the halo artifacts in the dehazed image. The experimental results on challenging real hazy images, dense-hazy images, and synthetic images have proved that a combination of nonlinear transformation and superpixels provide the strength to the proposed method. The obtained dehazed results are evaluated qualitatively and quantitatively and it is found that the proposed method has tremendous performance as compared to state-of-the-art dehazing approaches.

Graph analysis of proton conduction pathways in scandium-doped barium zirconate.

Understanding the relationship between the acceptor dopant size and proton conductivity in barium zirconate, BaZrO3, is important for maximizing efficiency in this promising fuel cell material. While proton conduction pathways with larger YZr ' and smaller AlZr ' defects have been explored, proton pathways with ScZr ', a defect of comparable size to the replaced ion, have not been investigated using centrality measures, periodic pathway searches, and kinetic Monte Carlo (KMC). Centrality measures in BaSc0.125Zr0.875O3 highlight a trapping region by ScZr ' and scattered high centrality regions on undoped planes. Connected long-range high centrality regions are found mainly in undoped planes for BaAl0.125Zr0.875O3 and in the dopant planes for BaY0.125Zr0.875O3. The best long-range proton conduction periodic pathways in AlZr ' and ScZr ' systems travel between dopant planes, while those for yttrium-doped BaZrO3 remained on dopant planes. KMC trajectories at 1000 K show long-range proton conduction barriers of 0.86 eV, 0.52 eV, and 0.25 eV for AlZr ', ScZr ', and YZr ' systems, respectively. Long-range periodic conduction highway limiting barrier averages correlate well with the connectivity of the most central regions in each system but ignore diffusion around the dopant and through other high centrality regions. BaSc0.125Zr0.875O3 shows an intermediate overall conduction barrier limited by trapping, which earlier experiments and simulations suggest that it can be mitigated with increased oxygen vacancy concentration.

A multi-center quadrature scheme for the molecular continuum

A common way to evaluate electronic integrals for polyatomic molecules is to use Becke’s partitioning scheme (Becke and Chem, 1988) in conjunction with overlapping grids centered at each atomic site. The Becke scheme was designed for integrands that fall off rapidly at large distances, such as those approximating bound electronic states. When applied to states in the electronic continuum, however, Becke scheme exhibits slow convergence and it is highly redundant. Here, we present a modified version of Becke scheme that is applicable to functions of the electronic continuum, such as those involved in molecular photoionization and electron–molecule scattering, and which ensures convergence and efficiency comparable to those realized in the calculation of bound states. In this modified scheme, the atomic weights already present in Becke’s partition are smoothly switched off within a range of few bond lengths from their respective nuclei, and complemented by an asymptotically unitary weight. The atomic integrals are evaluated on small spherical grids, centered on each atom, with size commensurate to the support of the corresponding atomic weight. The residual integral of the interstitial and long-range region is evaluated with a central master grid. The accuracy of the method is demonstrated by evaluating integrals involving integrands containing Gaussian Type Orbitals and Yukawa potentials, on the atomic sites, as well as spherical Bessel functions centered on the master grid. These functions are representative of those encountered in realistic electron-scattering and photoionization calculations in polyatomic molecules.

Computational density-functional approaches on finite-size and guest-lattice effects in CO2@sII clathrate hydrate.

We performed first-principles computations to investigate guest-host/host-host effects on the encapsulation of the CO2 molecule in sII clathrate hydrates from finite-size clusters up to periodic 3D crystal lattice systems. Structural and energetic properties were first computed for the individual and first-neighbors clathrate-like sII cages, where highly accurate ab initio quantum chemical methods are available nowadays, allowing in this way the assessment of the density functional (DFT) theoretical approaches employed. The performance of exchange-correlation functionals together with recently developed dispersion-corrected schemes was evaluated in describing interactions in both short-range and long-range regions of the potential. On this basis, structural relaxations of the CO2-filled and empty sII unit cells yield lattice and compressibility parameters comparable to experimental and previous theoretical values available for sII hydrates. According to these data, the CO2 enclathration in the sII clathrate cages is a stabilizing process, either by considering both guest-host and host-host interactions in the complete unit cell or only the guest-water energies for the individual clathrate-like sII cages. CO2@sII clathrates are predicted to be stable whatever the dispersion correction applied and in the case of single cage occupancy are found to be more stable than the CO2@sI structures. Our results reveal that DFT approaches could provide a good reasonable description of the underlying interactions, enabling the investigation of formation and transformation processes as a function of temperature and pressure.

Various effects induced by local synchronization in neural networks

In the cerebral cortex, the large-scale synchronous firing of neurons can cause epilepsy, during which spiral waves can spontaneously occur. The relationship between the synchronous firing of a large number of neurons and the spontaneous generation of spiral waves is still unclear. In this paper, a two-dimensional neuronal network with the long-range coupling regions generated by adding long-range horizontal connections is constructed. The Morris-Lecar neuron model is used to study the propagation of waves in the two-dimensional neuronal network with the rectangular long-range coupling regions. Numerical simulation results show that the plan and target waves whose propagation directions are both parallel to that of the long-range coupling can lead the neurons to be excited synchronously in the long-range coupling region. This synchronous firing is accompanied by delayed firing of some neurons and premature firing of others. When the width of the long-range coupling region exceeds the critical width, all the neurons in the long-range coupling region delay firing. When the width of the long-range coupling region exceeds a maximum conduction width, the waves will not pass through the long-range coupling region. When the size of the rectangular region of the long-range coupling is selected appropriately, the synchronous excitation of neurons can cause network to present the backfiring effect and to have the selectivity of wave propagation direction. Furthermore, the selectivity of wave propagation direction is very sensitive to whether the neuron is in the stationary state and also to the change of coupling strength, so that the high frequency plane wave train can partially pass through the long-range coupling region whose width exceeds the maximum conduction width. So we can control whether the wave can pass through the long-range coupling region of a certain width by giving the neurons in the long-range coupling region a tiny perturbation. When one or two long-range coupling regions are constructed in the neural network and the size of the long-range coupling regions is selected appropriately, the self-sustaining plane wave, spiral wave and target wave can appear spontaneously in the network when the wave passes through the long-range coupling regions. The physical mechanisms behind those phenomena are also analyzed.

Identification of Long-Range Transport Pathways and Potential Source Regions of PM2.5 and PM10 at Akedala Station, Central Asia

Cluster analyses, potential source contribution function (PSCF) and concentration-weight trajectory (CWT) were used to identify the main transport pathways and potential source regions with hourly PM2.5 and PM10 concentrations in different seasons from January 2017 to December 2019 at Akedala Station, located in northwest China (Central Asia). The annual mean concentrations of PM2.5 and PM10 were 11.63 ± 9.31 and 19.99 ± 14.39 µg/m3, respectively. The air pollution was most polluted in winter, and the dominant part of PM10 (between 54 to 76%) constituted PM2.5 aerosols in Akedala. Particulate pollution in Akedala can be traced back to eastern Kazakhstan, northern Xinjiang, and western Mongolia. The cluster analyses showed that the Akedala atmosphere was mainly affected by air masses transported from the northwest. The PM2.5 and PM10 mainly came with air masses from the central and eastern regions of Kazakhstan, which are characterized by highly industrialized and semi-arid desert areas. In addition, the analyses of the pressure profile of back-trajectories showed that air mass distribution were mainly distributed above 840 hPa. This indicates that PM2.5 and PM10 concentrations were strongly affected by high altitude air masses. According to the results of the PSCF and CWT methods, the main potential source areas of PM2.5 were very similar to those of PM10. In winter and autumn, the main potential source areas with high weighted PSCF values were located in the eastern regions of Kazakhstan, northern Xinjiang, and western Mongolia. These areas contributed the highest PM2.5 concentrations from 25 to 40 µg/m3 and PM10 concentrations from 30 to 60 µg/m3 in these seasons. In spring and summer, the potential source areas with the high weighted PSCF values were distributed in eastern Kazakhstan, northern Xinjiang, the border between northeast Kazakhstan, and southern Russia. These areas contributed the highest PM2.5 concentrations from 10 to 20 µg/m3 and PM10 concentrations from 20 to 60 µg/m3 in these seasons.

Using functional genomics to advance the understanding of psoriatic arthritis.

Psoriatic arthritis (PsA) is a complex disease where susceptibility is determined by genetic and environmental risk factors. Clinically, PsA involves inflammation of the joints and the skin, and, if left untreated, results in irreversible joint damage. There is currently no cure and the few treatments available to alleviate symptoms do not work in all patients. Over the past decade, genome-wide association studies (GWAS) have uncovered a large number of disease-associated loci but translating these findings into functional mechanisms and novel targets for therapeutic use is not straightforward. Most variants have been predicted to affect primarily long-range regulatory regions such as enhancers. There is now compelling evidence to support the use of chromatin conformation analysis methods to discover novel genes that can be affected by disease-associated variants. Here, we will review the studies published in the field that have given us a novel understanding of gene regulation in the context of functional genomics and how this relates to the study of PsA and its underlying disease mechanism.

Structure, hydration, and proton conductivity in 50% La and Nd doped CeO2 – La2Ce2O7 and Nd2Ce2O7 – and their solid solutions

We have measured water uptake and hydration enthalpy in 50% La and Nd doped CeO2, also to be taken as compositions in the series La2−xNdxCe2O7 (x = 0.0, 0.5, 1.0 and 2.0) using combined thermogravimetry (TG) and differential scanning calorimetry (DSC), TG-DSC. The TG-DSC data unambiguously yield standard molar hydration enthalpies of ~−74 kJ/mol independent of water uptake. The interpretation of the TG results, however, does not fit a classical model of hydration of all oxygen vacancies. Instead, the hydration appears to be limited to a small fraction of the free vacancies. Hydration further decreases as the Nd content (x) and long-range order increases and regions of disorder decrease. We propose a new model explaining why hydration occurs only in a small fraction of the nominally free vacancies: The higher basicity of La/Nd compared to Ce promotes protonation at oxide ion sites with high coordination to La/Nd, and the observed water uptake and modelling suggests that mainly oxide ions fully coordinated to 4 La/Nd neighbours become protonated. The statistical variation of coordination around oxygen sites in a disordered fluorite oxide creates a limited number of such oxide ions sites which results in limited hydration. The model matches well the experimental results and DFT calculations of proton trapping at the fully La-coordinated sites for 50% La-doped CeO2, and also rationalizes conductivity data.