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Designing novel proteins that bind to small molecules is a long-standing challenge in computational biology, with applications in developing catalysts, biosensors, and more. Current computational methods rely on the assumption that the binding pose of the target molecule is known, which is not always feasible, as conformations of novel targets are often unknown and tend to change upon binding. In this work, we formulate proteins and molecules as unified biotokens, and present AtomFlow, a novel deep generative model under the flow-matching framework for the design of ligand-binding proteins from the 2D target molecular graph alone. Operating on representative atoms of biotokens, AtomFlow captures the flexibility of ligands and generates ligand conformations and protein backbone structures iteratively. We consider the multi-scale nature of biotokens and demonstrate that AtomFlow can be effectively trained on a subset of structures from the Protein Data Bank, by matching flow vector field using an SE(3) equivariant structure prediction network. Experimental results show that our method can generate high fidelity ligand-binding proteins and achieve performance comparable to the state-of-the-art model RFDiffusionAA, while not requiring bound ligand structures. As a general framework, AtomFlow holds the potential to be applied to various biomolecule generation tasks in the future.

We study a center-of-mass-conserving Brownian complex Sachdev-Ye-Kitaev model with long-range (power-law) interactions characterized by $1/r^\eta$. The kinetic constraint and long-range interactions conspire to yield rich hydrodynamics associated with the conserved charge, which we reveal by computing the Schwinger-Keldysh effective action. Our result shows that charge transport in this system can be subdiffusive, diffusive, or superdiffusive, with the dynamical exponent controlled by $\eta$. We further employ a doubled Hilbert space methodology to derive an effective action for the out-of-time-order correlator (OTOC), from which we obtain the phase diagram delineating regimes where the lightcone is linear or logarithmic. Our results provide a concrete example of a quantum many-body system with kinetic constraint and long-range interactions in which the emergent hydrodynamic modes and OTOC can be computed analytically., Comment: 4.5 + 10 pages, 4 figures

In this work, we conduct a three-coupled-channel analysis of the $Z_c(3900)$ structure, focusing on the $D\bar{D}^*$, $J/\psi \pi$, and $\rho \eta_c$ channels, based on the one-boson exchange model. Drawing from previous study on the exotic state $T_{cc}$, we only utilize one more parameter to construct the interactions between the channels. Our model successfully reproduces the experimental line shapes of the invariant mass distribution at $\sqrt{s} = 4.23$ and $4.26$ GeV for the three channels. Additionally, the finite-volume energy levels in our model show agreement with current LQCD conclusion. Detailed analysis suggests that the $Z_c(3900)$ peaks in the $\pi J/\psi$ and $\rho \eta_c$ distributions primarily arise from the triangle loop involving the $D_1 \bar{D} D^*$ intermediate system. In the $D\bar{D}^*$ distribution, the threshold peak is generated by the cascade decay mechanism enhanced by a triangle diagram. Moreover, we find a virtual pole located far from the threshold, indicating that $Z_c(3900)$ peaks are not associated with physical pole. We conclude that the $Z_c(3900)$ peaks are predominantly caused by the threshold cusp.

Quantum many-body scars are rare eigenstates hidden within the chaotic spectra of many-body systems, representing a weak violation of the eigenstate thermalization hypothesis (ETH). Identifying these scars, as well as other non-thermal states in complex quantum systems, remains a significant challenge. Besides exact scar states, the nature of other non-thermal states lacking simple analytical characterization remains an open question. In this study, we employ tools from quantum machine learning -- specifically, quantum convolutional neural networks (QCNNs), to explore hidden non-thermal states in chaotic many-body systems. Our simulations demonstrate that QCNNs achieve over 99% single-shot measurement accuracy in identifying all known scars. Furthermore, we successfully identify new non-thermal states in models such as the xorX model, the PXP model, and the far-coupling Su-Schrieffer-Heeger model. In the xorX model, some of these non-thermal states can be approximately described as spin-wave modes of specific quasiparticles. We further develop effective tight-binding Hamiltonians within the quasiparticle subspace to capture key features of these many-body eigenstates. Finally, we validate the performance of QCNNs on IBM quantum devices, achieving single-shot measurement accuracy exceeding 63% under real-world noise and errors, with the aid of error mitigation techniques. Our results underscore the potential of QCNNs to uncover hidden non-thermal states in quantum many-body systems., Comment: 13 pages, 17 figures

We study the intravalley spin-polarized superconductivity in rhombohedral tetralayer graphene, which has been discovered experimentally in Han $et$ $al$ arXiv:2408.15233. We construct a minimal model for the intravalley spin-polarized superconductivity, assuming a simplified anisotropic interaction that depends only on the angle between the incoming and outgoing momenta. Despite the absence of Fermi surface nesting, we show that the superconductivity appears near the Van Hove singularity with the maximal $T_c$ near a bifurcation point of the peaks in the density of states. We identify the topological $p+ip$, topological $h+ih$, and the non-topological nodal $f$-wave pairings as the possible states, which are all pair density wave orders due to the intravalley nature. Furthermore, these pair density wave orders require a finite attractive threshold for superconductivity, resulting in narrow superconducting regions, consistent with experimental findings. We discuss the possible pairing mechanisms and point out that the Kohn-Luttinger mechanism is a plausible explanation for the intravalley spin-polarized superconductivity in the rhombohedral tetralayer graphene., Comment: 7+5 pages, 3+2 figures

The increasing volume of data stored in relational databases has led to the need for efficient querying and utilization of this data in various sectors. However, writing SQL queries requires specialized knowledge, which poses a challenge for non-professional users trying to access and query databases. Text-to-SQL parsing solves this issue by converting natural language queries into SQL queries, thus making database access more accessible for non-expert users. To take advantage of the recent developments in Large Language Models (LLMs), a range of new methods have emerged, with a primary focus on prompt engineering and fine-tuning. This survey provides a comprehensive overview of LLMs in text-to-SQL tasks, discussing benchmark datasets, prompt engineering, fine-tuning methods, and future research directions. We hope this review will enable readers to gain a broader understanding of the recent advances in this field and offer some insights into its future trajectory.

Using $(27.12\pm 0.14)\times10^8$ $\psi(3686)$ decays and data samples of $e^+e^-$ collisions with $\sqrt{s}$ from 4.130 to 4.780~GeV collected with the BESIII detector, we report the first observation of the electromagnetic Dalitz transition $h_c\to e^+e^-\eta_c$ with a statistical significance of $5.4\sigma$. We measure the ratio of the branching fractions $\frac{\mathcal{B}(h_c\rightarrow e^+e^-\eta_c)}{\mathcal{B}(h_c\rightarrow \gamma \eta_c)}$ separately for the $h_c$ samples produced via $\psi(3686)\to\pi^0h_c$ and $e^+e^-\to\pi^+\pi^-h_c$. The average ratio is determined to be $(0.59\pm0.10(\text{stat.})\pm0.04(\text{syst.}))\%$, where the uncertainty includes both statistical and systematic components.

For the first time, robust superconductivity has been independently observed in twisted WSe$_2$ bilayers by two separate groups [Y. Xia et al., arXiv:2405.14784; Y. Guo et al., arXiv:2406.03418.]. In light of this, we explore the possibility of a universal superconducting pairing mechanism in twisted WSe$_2$ bilayers. Using a continuum band structure model and a phenomenological boson-mediated effective electron-electron attraction, we find that intervalley intralayer pairing predominates over interlayer pairing. Notably, despite different experimental conditions, both twisted WSe$_2$ samples exhibit a comparable effective attraction strength. This consistency suggests that the dominant pairing glue is likely independent of the twist angle and layer polarization, pointing to a universal underlying boson-induced pairing mechanism.

We investigate magic-angle twisted bilayer graphene (MATBG) with proximity-induced Ising and Rashba spin-orbit couplings (SOC) in the top layer, as recently achieved experimentally. Utilizing the Bistritzer-MacDonald model with SOCs, we reveal a rich single-particle topological phase diagram featuring topological flat bands across different twist angles and interlayer hopping energies. The evolution of Dirac cones and Chern numbers is examined to understand the topological phase transitions. We find that all phases can be achieved with an experimentally accessible SOC strength ($\sim$1 meV) in systems with angles very close to the magic angle. Furthermore, the van Hove singularity for each topological flat band splits in the presence of SOC, significantly altering the electronic properties. Additionally, we investigate the spin textures of each band in momentum space, discovering a skyrmion-like spin texture in the center of the moir\'e Brillouin zone, which is correlated with the topological phase transitions and can be tuned via the SOCs and an out-of-plane electric field. Our findings provide a comprehensive understanding of the topological flat bands, establishing a foundation for grasping the intrinsic and rich roles of SOCs in MATBG., Comment: 19 pages, 20 figures

We study an interacting composite $(1+1/n)$ Abelian helical edge state made of a regular helical liquid carrying charge $e$ and a (fractionalized) helical liquid carrying charge $e/n$. A systematic framework is developed for these composite $(1+1/n)$ Abelian helical edge states with $n=1,2,3$. For $n=2$, the composite edge state consists of a regular helical Luttinger liquid and a fractional topological insulator (the Abelian $Z_4$ topological order) edge state arising from half-filled conjugated Chern bands. The composite edge state with $n=2$ is pertinent to the recent twisted MoTe$_2$ experiment, suggesting a possible fractional topological insulator with conductance $\frac{3}{2}\frac{e^2}{h}$ per edge. Using bosonization, we construct generic phase diagrams in the presence of $weak$ Rashba spin-orbit coupling. In addition to a phase of free bosons, we find a time-reversal symmetry-breaking localized insulator, two perfect positive drag phases, a perfect negative drag phase (for $n=2,3$), a time-reversal symmetric Anderson localization (only for $n=1$), and a disorder-dominated metallic phase analogous to the $\nu=2/3$ disordered fractional quantum Hall edges (only for $n=3$). We further compute the two-terminal edge-state conductance, the primary experimental characterization for the (fractional) topological insulator. Remarkably, the negative drag phase gives rise to an unusual edge-state conductance, $(1-1/n)\frac{e^2}{h}$, not directly associated with the filling factor. We further investigate the effect of an applied in-plane magnetic field. For $n>1$, the applied magnetic field can result in a phase with edge-state conductance $\frac{1}{n}\frac{e^2}{h}$, providing another testable signature. Our work establishes a systematic understanding of the composite $(1+1/n)$ Abelian helical edge, paving the way for future experimental and theoretical studies., Comment: 22 pages and 6 figures

Algebraic boundaries of convex semi-algebraic sets are closely related to polynomial optimization problems. Building upon Rainer Sinn's work, we refine the stratification of iterated singular loci to a Whitney (a) stratification, which gives a list of candidates of varieties whose dual is an irreducible component of the algebraic boundary of the dual convex body. We also present an algorithm based on Teissier's criterion to compute Whitney (a) stratifications, which employs conormal spaces and prime decomposition.

Twin support vector machine (TSVM) is a very classical and practical classifier for pattern classification. However, the traditional TSVM has two limitations. Firstly, it uses the L_2-norm distance metric that leads to its sensitivity to outliers. Second, it needs to select the appropriate kernel function and the kernel parameters for nonlinear classification. To effectively avoid these two problems, this paper proposes a robust capped L_1-norm kernel-free quadratic surface twin support vector machine (CL_1QTSVM). The strengths of our model are briefly summarized as follows. 1) The robustness of our model is further improved by employing the capped L_1 norm distance metric. 2) Our model is a kernel-free method that avoids the time-consuming process of selecting appropriate kernel functions and kernel parameters. 3) The introduction of L_2-norm regularization term to improve the generalization ability of the model. 4) To efficiently solve the proposed model, an iterative algorithm is developed. 5) The convergence, time complexity and existence of locally optimal solutions of the developed algorithms are further discussed. Numerical experiments on numerous types of datasets validate the classification performance and robustness of the proposed model.

Recently, video object segmentation (VOS) networks typically use memory-based methods: for each query frame, the mask is predicted by space-time matching to memory frames. Despite these methods having superior performance, they suffer from two issues: 1) Challenging data can destroy the space-time coherence between adjacent video frames. 2) Pixel-level matching will lead to undesired mismatching caused by the noises or distractors. To address the aforementioned issues, we first propose to generate an auxiliary frame between adjacent frames, serving as an implicit short-temporal reference for the query one. Next, we learn a prototype for each video object and prototype-level matching can be implemented between the query and memory. The experiment demonstrated that our network outperforms the state-of-the-art method on the DAVIS 2017, achieving a J&F score of 86.4%, and attains a competitive result 85.0% on YouTube VOS 2018. In addition, our network exhibits a high inference speed of 32+ FPS., Comment: Accepted by ICME 2024. 6 pages, 10 figures

The key to device-edge co-inference paradigm is to partition models into computation-friendly and computation-intensive parts across the device and the edge, respectively. However, for Graph Neural Networks (GNNs), we find that simply partitioning without altering their structures can hardly achieve the full potential of the co-inference paradigm due to various computational-communication overheads of GNN operations over heterogeneous devices. We present GCoDE, the first automatic framework for GNN that innovatively Co-designs the architecture search and the mapping of each operation on Device-Edge hierarchies. GCoDE abstracts the device communication process into an explicit operation and fuses the search of architecture and the operations mapping in a unified space for joint-optimization. Also, the performance-awareness approach, utilized in the constraint-based search process of GCoDE, enables effective evaluation of architecture efficiency in diverse heterogeneous systems. We implement the co-inference engine and runtime dispatcher in GCoDE to enhance the deployment efficiency. Experimental results show that GCoDE can achieve up to $44.9\times$ speedup and $98.2\%$ energy reduction compared to existing approaches across various applications and system configurations., Comment: Accepted by DAC'24

We study theoretically the magic-angle twisted bilayer graphene with proximity-induced Ising and Rashba spin-orbit couplings on the top layer. Topological flat bands (with three distinct phases) are generically realized by the spin-orbit couplings. Using a mean field analysis, we find that (partial) valley polarization prevails for a wide range of doping, suppressing the usual superconductivity with a pairing between time-reversal partners. Remarkably, we uncover that observable unconventional intervalley interband phonon-mediated superconductivity (with the highest $T_c\approx 1.2$K) can coexist with strong valley imbalance due to the approximate Fermi surface nesting between two flat bands not related by time-reversal symmetry, and the dominant pairing is an intersublattice Ising pairing, corresponding to a mixture of $p$- and $d$-waves. In contrast, the intrasublattice Ising phonon-mediated superconductivity with $s$- and $f$-wave mixing emerges in the absence of valley imbalance. Our work reveals an unprecedented route of realizing unconventional superconductivity., Comment: 9+16 pages, 4+5 figures; published version

The classification of carotid artery ultrasound images is a crucial means for diagnosing carotid plaques, holding significant clinical relevance for predicting the risk of stroke. Recent research suggests that utilizing plaque segmentation as an auxiliary task for classification can enhance performance by leveraging the correlation between segmentation and classification tasks. However, this approach relies on obtaining a substantial amount of challenging-to-acquire segmentation annotations. This paper proposes a novel weakly supervised auxiliary task learning network model (WAL-Net) to explore the interdependence between carotid plaque classification and segmentation tasks. The plaque classification task is primary task, while the plaque segmentation task serves as an auxiliary task, providing valuable information to enhance the performance of the primary task. Weakly supervised learning is adopted in the auxiliary task to completely break away from the dependence on segmentation annotations. Experiments and evaluations are conducted on a dataset comprising 1270 carotid plaque ultrasound images from Wuhan University Zhongnan Hospital. Results indicate that the proposed method achieved an approximately 1.3% improvement in carotid plaque classification accuracy compared to the baseline network. Specifically, the accuracy of mixed-echoic plaques classification increased by approximately 3.3%, demonstrating the effectiveness of our approach.

The emergence of bulk carbon ferromagnetism is long-expected over years. At nanoscale, carbon ferromagnetism was detected by analyzing the magnetic edge states via scanning tunneling microscopy(STM), and its origin can be explained by local redistribution of electron wave function. In larger scale, carbon ferromagnetism can be created by deliberately producing defects in graphite, and detected by macroscopic technical magnetization. Meanwhile, it becomes crucial to determine that the detected magnetization is originated from carbon rather than from magnetic impurities. One solution is X-ray magnetic circular dichroism (XMCD). Nonetheless, a reproducible, full section of XMCD spectrum across C-1s absorption energy has not appeared yet, which should be decisive for assuring the indisputable existence of bulk carbon ferromagnetism. Besides, the lack of direct observation on the atomic structure of the ferromagnetic carbon leaves the structural origin of its ferromagnetism still in mist. In this work, for detecting bulk carbon ferromagnetism, we managed to grow all-carbon film consisting of vertically aligned graphene multi-edge (VGME), which wove into a three-dimensional hyperfine-porous network. Magnetization (M-H) curves and XMCD spectra co-confirmed bulk carbon ferromagnetism of VGME at room temperature, with the average unit magnetic momentum of ~0.0006 miuB/atom. The influence of magnetic impurities on magnetization was excluded by both absorption spectra and inductively coupled plasma mass spectrometry measurements. The spin transfer behavior also verified the long-range and robust feature of the bulk carbon ferromagnetism. Our work provides direct evidence of elementary resolved bulk carbon ferromagnetism at room temperature and clarifies its origin from pi-electrons at graphene edges.

Motivated by the recently developed classical spin model for Migdal-Eliashberg theory, we develop new numerical and analytical methods based on this spin-chain representation and apply these methods to the Bogoliuov-Tomachov-Morel-Anderson pairing potential, which incorporates the phonon-mediated attraction and Coulomb repulsion. We show that the Monte Carlo method with heat bath updates can efficiently obtain the gap functions even for the situations challenging for the iterative solvers, suggesting an unprecedented robust approach for solving the full nonlinear Migdal-Eliashberg theory. Moreover, we derive the renormalization of all the couplings by tracing out the high-frequency spins in the partition function. The derived analytical renormalization equations produce the well-known $\mu^*$ effect for the Bogoliuov-Tomachov-Morel-Anderson pairing potential and can be generalized to other superconductivity problems. We further point out that several interesting features (e.g., sign changing in the frequency-dependent gap function) can be intuitively understood using the classical spin-chain representation for Migdal-Eliasherg theory. Our results show the advantage of using the spin-chain representation for solving Migdal-Eliashberg theory and provide new ways for tackling general superconductivity problems., Comment: 13 pages, 8 figures. Published version

We investigate the doubly bottom state $T^-_{bb}$ composed of two bottom mesons with $J^P=1^+$. The potentials are obtained using the one-boson exchange model. With the heavy quark flavor symmetry, all the parameters in the model are determined by fitting the experimental data of doubly charmed state $T_{cc}^{+}$ from our previous work. Our analysis indicates that the isospin symmetry is well-preserved. We identify a deeply bound $T^-_{bb}$ state with quantum numbers $I(J^{P})=0(1^+)$, in contrast to the loosely bound $T_{cc}^{+}$. Additionally, we discover a resonant $T^-_{bb}$ state with $I(J^{P})=1(1^+)$. Furthermore, our investigation into the $\bar{B}\bar{B}^*$-$\bar{B}^*\bar{B}^*$ coupled channel effect reveals its important impact. The binding energy of the bound $I(J^{P})=0(1^+)$ states becomes deeper, while the resonant $T^-_{bb}$ state with $I(J^{P})=1(1^+)$ remains nearly unchanged., Comment: 24 pages, 7 figures, add discussions on the pole trajectory of the heavy meson pairs and a I=1 DD* resonance, accepted for publication in PRD