Search

Recent years have witnessed a surge in the development of protein foundation models, significantly improving performance in protein prediction and generative tasks ranging from 3D structure prediction and protein design to conformational dynamics. However, the capabilities and limitations associated with these models remain poorly understood due to the absence of a unified evaluation framework. To fill this gap, we introduce ProteinBench, a holistic evaluation framework designed to enhance the transparency of protein foundation models. Our approach consists of three key components: (i) A taxonomic classification of tasks that broadly encompass the main challenges in the protein domain, based on the relationships between different protein modalities; (ii) A multi-metric evaluation approach that assesses performance across four key dimensions: quality, novelty, diversity, and robustness; and (iii) In-depth analyses from various user objectives, providing a holistic view of model performance. Our comprehensive evaluation of protein foundation models reveals several key findings that shed light on their current capabilities and limitations. To promote transparency and facilitate further research, we release the evaluation dataset, code, and a public leaderboard publicly for further analysis and a general modular toolkit. We intend for ProteinBench to be a living benchmark for establishing a standardized, in-depth evaluation framework for protein foundation models, driving their development and application while fostering collaboration within the field., Comment: 29 pages, 1 figure and 11 tables

Recent breakthroughs have ushered the quantum network into a new era, where quantum information can be stored, transferred, and processed across multiple nodes on a metropolitan scale. A key challenge in this new era is enhancing the capabilities of individual nodes, providing precise and robust control over multiple qubits and advanced functionality for scalable quantum networks. Here, we report on precise and complex control in a hybrid quantum node based on a diamond color center. We demonstrate hybrid coherent control by entangling three types of qubits: an electron spin as an interface qubit, a nuclear spin with long memory time, and a flying photonic qubit, with their qubit frequencies spanning three distinct regimes from the optical domain to the rf domain. By incorporating two additional memory qubits, we encode three memory qubits into a logical state using the three-qubit repetition code and entangle this logical qubit with a photonic qubit. Leveraging hybrid qubits and precise control, we repeatedly read out the error syndromes of memory qubits through the electron spin, serving as an auxiliary qubit, then apply a real-time feedback operation to correct bit-flip errors. We execute and verify active error correction for up to twelve rounds and demonstrate the improvement over the uncorrected counterpart. Our results demonstrate the feasibility of several key functionalities for next-generation quantum repeaters, paving the way towards full-fledged metropolitan-scale quantum networks for a wide range of practical applications., Comment: 8 pages, 3 figures

The 1-form symmetry, manifesting as loop-like symmetries, has gained prominence in the study of quantum phases, deepening our understanding of symmetry. However, the role of 1-form symmetries in Projected Entangled-Pair States (PEPS), two-dimensional tensor network states, remains largely underexplored. We present a novel framework for understanding 1-form symmetries within tensor networks, specifically focusing on the derivation of algebraic relations for symmetry matrices on the PEPS virtual legs. Our results reveal that 1-form symmetries impose stringent constraints on tensor network representations, leading to distinct anomalous braiding phases carried by symmetry matrices. We demonstrate how these symmetries influence the ground state and tangent space in PEPS, providing new insights into their physical implications for enhancing ground state optimization efficiency and characterizing the 1-form symmetry structure in excited states., Comment: 6 pages, 1 figure. In memory of T. M. Rice for his invaluable teaching on the physics of strongly correlated systems

The advancement of industrialization has spurred the development of innovative swarm intelligence algorithms, with Lion Swarm Optimization (LSO) notable for its robustness, parallelism, simplicity, and efficiency. While LSO excels in single-objective optimization, its multi-objective variants face challenges such as poor initialization, local optima entrapment, and so on. This study proposes Dynamic Multi-Objective Lion Swarm Optimization with Multi-strategy Fusion (MF-DMOLSO) to address these limitations. MF-DMOLSO comprises three key components: initialization, swarm position update, and external archive update. The initialization unit employs chaotic mapping for uniform population distribution. The position update unit enhances behavior patterns and step size formulas for cub lions, incorporating crowding degree sorting, Pareto non-dominated sorting, and Levy flight to improve convergence speed and global search capabilities. Reference points guide convergence in higher-dimensional spaces, maintaining population diversity. An adaptive cold-hot start strategy generates a population responsive to environmental changes. The external archive update unit re-evaluates solutions based on non-domination and diversity to form the new population. Evaluations on benchmark functions showed MF-DMOLSO surpassed multi-objective particle swarm optimization, non-dominated sorting genetic algorithm II, and multi-objective lion swarm optimization, exceeding 90% accuracy for two-objective and 97% for three-objective problems. Compared to non-dominated sorting genetic algorithm III, MF-DMOLSO showed a 60% improvement. Applied to 6R robot trajectory planning, MF-DMOLSO optimized running time and maximum acceleration to 8.3s and 0.3pi rad/s^2, achieving a set coverage rate of 70.97% compared to 2% by multi-objective particle swarm optimization, thus improving efficiency and reducing mechanical dither.

Chirality in solid-state materials has sparked significant interest due to potential applications of topologically-protected chiral states in next-generation information technology. The electrical magneto-chiral effect (eMChE), arising from relativistic spin-orbit interactions, shows great promise for developing chiral materials and devices for electronic integration. Here we demonstrate an angle-resolved eMChE in an A-B-C-C type atomic-layer superlattice lacking time and space inversion symmetry. We observe non-superimposable enantiomers of left-handed and right-handed tilted uniaxial magnetic anisotropy as the sample rotates under static fields, with the tilting angle reaching a striking 45 degree. Magnetic force microscopy and atomistic simulations correlate the tilt to the emergence and evolution of chiral spin textures. The Dzyaloshinskii-Moriya interaction lock effect in competition with Zeeman effect is demonstrated to be responsible for the angle-resolved eMChE. Our findings open up a new horizon for engineering angle-resolved magneto-chiral anisotropy, shedding light on the development of novel angle-resolved sensing or writing techniques in chiral spintronics.

High-cadence, multiwavelength observations have continuously revealed the diversity of tidal disruption events (TDEs), thus greatly advancing our knowledge and understanding of TDEs. In this work, we conducted an intensive optical-UV and X-ray follow-up campaign of TDE AT2023lli, and found a remarkable month-long bump in its UV/optical light curve nearly two months prior to maximum brightness. The bump represents the longest separation time from the main peak among known TDEs to date. The main UV/optical outburst declines as $t^{-4.10}$, making it one of the fastest decaying optically selected TDEs. Furthermore, we detected sporadic X-ray emission 30 days after the UV/optical peak, accompanied by a reduction in the period of inactivity. It is proposed that the UV/optical bump could be caused by the self-intersection of the stream debris, whereas the primary peak is generated by the reprocessed emission of the accretion process. In addition, our results suggest that episodic X-ray radiation during the initial phase of decline may be due to the patched obscurer surrounding the accretion disk, a phenomenon associated with the inhomogeneous reprocessing process. The double TDE scenario, in which two stars are disrupted in sequence, is also a possible explanation for producing the observed early bump and main peak. We anticipate that the multicolor light curves of TDEs, especially in the very early stages, and the underlying physics can be better understood in the near future with the assistance of dedicated surveys such as the deep high-cadence survey of the 2.5-meter Wide Field Survey Telescope (WFST)., Comment: 14 pages, 8 figures,accepted for publication by ApJL

This paper introduces diffusion protein language model (DPLM), a versatile protein language model that demonstrates strong generative and predictive capabilities for protein sequences. We first pre-train scalable DPLMs from evolutionary-scale protein sequences within a generative self-supervised discrete diffusion probabilistic framework, which generalizes language modeling for proteins in a principled way. After pre-training, DPLM exhibits the ability to generate structurally plausible, novel, and diverse protein sequences for unconditional generation. We further demonstrate the proposed diffusion generative pre-training makes DPLM possess a better understanding of proteins, making it a superior representation learner, which can be fine-tuned for various predictive tasks, comparing favorably to ESM2 (Lin et al., 2022). Moreover, DPLM can be tailored for various needs, which showcases its prowess of conditional generation in several ways: (1) conditioning on partial peptide sequences, e.g., generating scaffolds for functional motifs with high success rate; (2) incorporating other modalities as conditioner, e.g., structure-conditioned generation for inverse folding; and (3) steering sequence generation towards desired properties, e.g., satisfying specified secondary structures, through a plug-and-play classifier guidance.

In the centers of galaxies, stars that orbit supermassive black hole binaries (SMBHBs) can undergo tidal disruptions due to the Lidov-Kozai mechanism. Nevertheless, most previous researches have predominantly focused on full tidal disruption events (FTDEs). In this study, we employ N-body simulations to investigate partial tidal disruption events (PTDEs) induced by intermediate-mass black holes (IMBHs) in SMBH-IMBH binaries, taking into account consideration the IMBH's mass, semi-major axis, and eccentricity of the outer orbit. Our findings indicate that, in comparison to FTDEs, the majority of tidal disruption events are actually PTDEs. Furthermore, we find that a significant number of stars experiencing partial disruption ultimately get captured by the IMBH, potentially leading to repeating flares. By comparing the period of the periodic eruptions observed in ASASSN-14ko, we find that PTDEs in a specific SMBH-IMBH binary system can align with the observed period if the SMBH has a mass of $10^7\rm{\ M_\odot}$, the IMBH has a mass smaller than approximately $10^5\rm{\ M_\odot}$, the eccentricity of the SMBH-IMBH binary exceeds approximately $0.5$, and the semi-major axis of the SMBH-IMBH binary is larger than approximately $0.001\rm{\ pc}$. Moreover, our model effectively accounts for the observed period derivative for ASASSN-14ko ($\dot{P}=-0.0026\pm 0.0006$), and our results also imply that some quasi-periodic eruptions may be attributed to PTDEs occurring around SMBH-IMBH binaries., Comment: 11 pages, 8 figures

The Event Horizon Telescope (EHT) observed in 2017 the supermassive black hole at the center of the Milky Way, Sagittarius A* (Sgr A*), at a frequency of 228.1 GHz ($\lambda$=1.3 mm). The fundamental physics tests that even a single pulsar orbiting Sgr A* would enable motivate searching for pulsars in EHT datasets. The high observing frequency means that pulsars - which typically exhibit steep emission spectra - are expected to be very faint. However, it also negates pulse scattering, an effect that could hinder pulsar detections in the Galactic Center. Additionally, magnetars or a secondary inverse Compton emission could be stronger at millimeter wavelengths than at lower frequencies. We present a search for pulsars close to Sgr A* using the data from the three most-sensitive stations in the EHT 2017 campaign: the Atacama Large Millimeter/submillimeter Array, the Large Millimeter Telescope and the IRAM 30 m Telescope. We apply three detection methods based on Fourier-domain analysis, the Fast-Folding-Algorithm and single pulse search targeting both pulsars and burst-like transient emission; using the simultaneity of the observations to confirm potential candidates. No new pulsars or significant bursts were found. Being the first pulsar search ever carried out at such high radio frequencies, we detail our analysis methods and give a detailed estimation of the sensitivity of the search. We conclude that the EHT 2017 observations are only sensitive to a small fraction ($\lesssim$2.2%) of the pulsars that may exist close to Sgr A*, motivating further searches for fainter pulsars in the region., Comment: 33 pages, 7 figures, 6 Tables. Accepted for publication in ApJ

In the inner region of the disc of an active galactic nucleus (AGN), the collision of two white dwarfs (WDs) through Jacobi capture might be inevitable, leading to a Type Ia supernova (SN Ia) explosion. This transient event, influenced by the disc gas and the gravity of the supermassive black hole (SMBH), exhibits distinct characteristics compared to normal SNe Ia. The energy of the explosion is mainly stored in the ejecta in the form of kinetic energy. Typically, the ejecta is not effectively decelerated by the AGN disc and rushes rapidly out of the AGN disc. However, under the influence of the SMBH, most of the ejecta falls back toward the AGN disc. As the fallback ejecta becomes more dispersed, it interacts with the disc gas, converting its kinetic energy into thermal energy. This results in a high-energy transient characterized by a rapid initial rise followed by a decay with $L\propto t^{-2.8}$. The time-scale of the transient ranges from hours to weeks, depending on the mass of the SMBH. This process generates high-energy radiation spanning from hard X-rays to the soft $\gamma$ range. Additionally, the subsequent damage to the disc may result in changing-look AGNs. Moreover, the falling back of SNe Ia ejecta onto the AGN disc significantly increases the metallicity of the AGN and can even generate heavy elements within the AGN discs., Comment: 12 pages, 12 pages

White dwarfs (WDs) in active galactic nucleus (AGNs) discs might migrate to the inner radii of the discs and form restricted three-body systems with two WDs moving around the central supermassive black hole (SMBH) in close orbits. These systems could be dynamical unstable, which can lead to very close encounters or direct collisions. In this work, we use N-body simulations to study the evolution of such systems with the different initial orbital separation $p$, relative orbital inclination $\Delta{i}$ and SMBH mass $M$. It is found that the close encounters of WDs mainly occur at $1.1R_{\rm H} \lesssim p \lesssim 2\sqrt{3}R_{\rm H}$, where $R_{\rm H}$ is the mutual Hill radius. For $p<1.1R_{\rm H}$, the majority of WDs move in horseshoe or tadpole orbits, and only few of them with small initial orbital phase difference undergo close encounters. For $p=3.0R_{\rm H}$, WD-WD collisions occur in most of the samples within a time of $10^5P_1$, and considerable collisions occur within a time of $t<62P_1$ for small orbital radii, where $P_1$ is the orbital period. The peak of the closest separation distribution increase and the WD-WD collision fraction decreases with an increase of the relative inclination. The closest separation distribution is similar in cases with the different SMBH mass, but the WD-WD collision fraction decreases as the mass of SMBHs increases. According to our estimation, the event rate of the cosmic WD-WD collision in AGN discs is about $300{\rm Gpc^{-3}yr^{-1}}$, roughly $1\%$ of the one of the observed type Ia supernova. The corresponding electromagnetic emission signals can be observed by large surveys of AGNs., Comment: 9 pages, 10 figures

Left-invariant Hermitian and Gauduchon connections are studied on an arbitrary Lie group $G$ equipped with an arbitrary left-invariant almost Hermitian structure $(\langle\cdot,\cdot\rangle,J)$. The space of left-invariant Hermitian connections is shown to be in one-to-one correspondence with the space $\wedge^{(1,1)}\mathfrak{g}^\ast\otimes \mathfrak{g}$ of left-invariant 2-forms of type (1,1) (with respect to $J$) with values in $\mathfrak{g}:=\mbox{Lie}(G)$. Explicit formulas are obtained for the torsion components of every Hermitian and Gauduchon connection with respect to a convenient choice of left-invariant frame on $G$. The curvature of Gauduchon connections is studied for the special case $G=H\times A$, where $H$ is an arbitrary $n$-dimensional Lie group, $A$ is an arbitrary $n$-dimensional abelian Lie group, and the almost complex structure is totally real with respect to $\mathfrak{h}:=\mbox{Lie}(H)$. When $H$ is compact, it is shown that $H\times A$ admits a left-invariant (strictly) almost Hermitian structure $(\langle\cdot,\cdot\rangle,J)$ such that the Gauduchon connection corresponding to the Strominger (or Bismut) connection in the integrable case is precisely the trivial left-invariant connection and, in addition, has totally skew-symmetric torsion. The almost Hermitian structure $(\langle\cdot,\cdot\rangle,J)$ on $H\times A$ is shown to satisfy the \textit{strong K\"{a}hler with torsion} condition. Furthermore, the affine line of Gauduchon connections on $H\times A$ with the aforementioned almost Hermitian structure is also shown to contain a (nontrivial) flat connection., Comment: 28 pages, new result added to Theorem 4.11

Recently, the bilayer perovskite nickelate La$_3$Ni$_2$O$_7$ has been reported to show evidence of high-temperature superconductivity (SC) under a moderate pressure of about 14 GPa. To investigate the superconducting mechanism, pairing symmetry, and the role of apical-oxygen deficiencies in this material, we perform a random-phase-approximation based study on a bilayer model consisting of the $d_{x^2-y^2}$ and $d_{3z^2-r^2}$ orbitals of Ni atoms in both the pristine crystal and the crystal with apical-oxygen deficiencies. Our analysis reveals an $s^{\pm}$-wave pairing symmetry driven by spin fluctuations. The crucial role of pressure lies in that it induces the emergence of the $\gamma$-pocket, which is involved in the strongest Fermi-surface nesting. We further found the emergence of local moments in the vicinity of apical-oxygen deficiencies, which significantly suppresses the $T_c$. Therefore, it is possible to significantly enhance the $T_c$ by eliminating oxygen deficiencies during the synthesis of the samples., Comment: Accepted by Phys. Rev. Lett

Superconducting pairing symmetry are crucial in understanding the microscopic superconducting mechanism of a superconductor. Here we report the observation of a twofold superconducting gap symmetry in an interfacial superconductor Bi$_{2}$Te$_{3}$/FeTe, by employing quasiparticle interference (QPI) technique in scanning tunneling microscopy and macroscopic magnetoresistance measurements. The QPI patterns corresponding to energies inside and outside the gap reveal a clear anisotropic superconducting gap. Furthermore, both the in-plane angle-dependent magnetoresistance and in-plane upper critical field exhibit a clear twofold symmetry. This twofold symmetry align with the Te-Te direction in FeTe, which weakens the possible generation by bi-collinear antiferromagnetism order. Our finding provides key information in further understanding of the topological properties in Bi$_{2}$Te$_{3}$/FeTe superconducting system and propels further theoretical interests in the paring mechanism in the system.

Molecular representation learning plays a crucial role in AI-assisted drug discovery research. Encoding 3D molecular structures through Euclidean neural networks has become the prevailing method in the geometric deep learning community. However, the equivariance constraints and message passing in Euclidean space may limit the network expressive power. In this work, we propose a Harmonic Molecular Representation learning (HMR) framework, which represents a molecule using the Laplace-Beltrami eigenfunctions of its molecular surface. HMR offers a multi-resolution representation of molecular geometric and chemical features on 2D Riemannian manifold. We also introduce a harmonic message passing method to realize efficient spectral message passing over the surface manifold for better molecular encoding. Our proposed method shows comparable predictive power to current models in small molecule property prediction, and outperforms the state-of-the-art deep learning models for ligand-binding protein pocket classification and the rigid protein docking challenge, demonstrating its versatility in molecular representation learning., Comment: 25 pages including Appendix

Interpretation of resolved polarized images of black holes by the Event Horizon Telescope (EHT) requires predictions of the polarized emission observable by an Earth-based instrument for a particular model of the black hole accretion system. Such predictions are generated by general relativistic radiative transfer (GRRT) codes, which integrate the equations of polarized radiative transfer in curved spacetime. A selection of ray-tracing GRRT codes used within the EHT collaboration is evaluated for accuracy and consistency in producing a selection of test images, demonstrating that the various methods and implementations of radiative transfer calculations are highly consistent. When imaging an analytic accretion model, we find that all codes produce images similar within a pixel-wise normalized mean squared error (NMSE) of 0.012 in the worst case. When imaging a snapshot from a cell-based magnetohydrodynamic simulation, we find all test images to be similar within NMSEs of 0.02, 0.04, 0.04, and 0.12 in Stokes I, Q, U , and V respectively. We additionally find the values of several image metrics relevant to published EHT results to be in agreement to much better precision than measurement uncertainties., Comment: Accepted for publication in ApJ

This paper demonstrates that language models are strong structure-based protein designers. We present LM-Design, a generic approach to reprogramming sequence-based protein language models (pLMs), that have learned massive sequential evolutionary knowledge from the universe of natural protein sequences, to acquire an immediate capability to design preferable protein sequences for given folds. We conduct a structural surgery on pLMs, where a lightweight structural adapter is implanted into pLMs and endows it with structural awareness. During inference, iterative refinement is performed to effectively optimize the generated protein sequences. Experiments show that LM-Design improves the state-of-the-art results by a large margin, leading to up to 4% to 12% accuracy gains in sequence recovery (e.g., 55.65%/56.63% on CATH 4.2/4.3 single-chain benchmarks, and >60% when designing protein complexes). We provide extensive and in-depth analyses, which verify that LM-Design can (1) indeed leverage both structural and sequential knowledge to accurately handle structurally non-deterministic regions, (2) benefit from scaling data and model size, and (3) generalize to other proteins (e.g., antibodies and de novo proteins), Comment: 10 pages; ver.2 update: added image credit to RFdiffusion (Watson et al., 2022) in Fig. 1F, and fixed some small presentation errors

Antibodies are vital proteins offering robust protection for the human body from pathogens. The development of general protein and antibody-specific pre-trained language models both facilitate antibody prediction tasks. However, there have been limited studies that comprehensively explore the representation capability of distinct pre-trained language models on different antibody tasks. To investigate the problem, we aim to answer several key questions in this paper, such as how pre-trained language models perform in antibody tasks with different specificity and how introducing specific biological mechanisms to the pre-training process can benefit the model. Additionally, we evaluate if the learned antibody pre-trained representations can be applied to real-world antibody problems, like drug discovery and immune process understanding. Previously, no benchmark available largely hindered the study to answer these questions. To aid in our investigation, we provide an AnTibody Understanding Evaluation (ATUE) benchmark. We comprehensively evaluate the performance of protein pre-trained language models by empirical study along with conclusions and new insights. Our ATUE and code are released at https://github.com/dqwang122/EATLM., Comment: Accepted in ICLR 2023

Antimicrobial peptides (AMPs) are promising therapeutic approaches against drug-resistant pathogens. Recently, deep generative models are used to discover new AMPs. However, previous studies mainly focus on peptide sequence attributes and do not consider crucial structure information. In this paper, we propose a latent sequence-structure model for designing AMPs (LSSAMP). LSSAMP exploits multi-scale vector quantization in the latent space to represent secondary structures (e.g. alpha helix and beta sheet). By sampling in the latent space, LSSAMP can simultaneously generate peptides with ideal sequence attributes and secondary structures. Experimental results show that the peptides generated by LSSAMP have a high probability of antimicrobial activity. Our wet laboratory experiments verified that two of the 21 candidates exhibit strong antimicrobial activity. The code is released at https://github.com/dqwang122/LSSAMP., Comment: KDD 2023

Learning from non-stationary data streams, also called Task-Free Continual Learning (TFCL) remains challenging due to the absence of explicit task information. Although recently some methods have been proposed for TFCL, they lack theoretical guarantees. Moreover, forgetting analysis during TFCL was not studied theoretically before. This paper develops a new theoretical analysis framework which provides generalization bounds based on the discrepancy distance between the visited samples and the entire information made available for training the model. This analysis gives new insights into the forgetting behaviour in classification tasks. Inspired by this theoretical model, we propose a new approach enabled by the dynamic component expansion mechanism for a mixture model, namely the Online Discrepancy Distance Learning (ODDL). ODDL estimates the discrepancy between the probabilistic representation of the current memory buffer and the already accumulated knowledge and uses it as the expansion signal to ensure a compact network architecture with optimal performance. We then propose a new sample selection approach that selectively stores the most relevant samples into the memory buffer through the discrepancy-based measure, further improving the performance. We perform several TFCL experiments with the proposed methodology, which demonstrate that the proposed approach achieves the state of the art performance., Comment: Accepted at the 36th Conference on Neural Information Processing Systems (NeurIPS 2022)

There is a very popular two-zone accretion disk model that the inner part of the non-advective Keplerian disk (Shakura-Sunyaev disk) can produce hot advection-dominated accretion flow, which can generate high energy power-law radiation and outflows/jets. However, we find that this simple model is inadequate to automatically explain many properties of the sources (such as hysteresis effect, counter-clockwise traversal in a hardness-intensity diagram, peculiar variabilities, and association/non-association of jets in a black hole $X-$ray binary) without considering additional assumptions. We also find some theoretical issues in this model, such as understanding of variation of transition region and formation of an outer disk, which has only Keplerian distribution. Based on the recent theoretical studies on advective disk structures, as well as, many observational behaviors of the accreting black holes, we conclude that there should be a third component (TC) of accretion flow parallel to the two-zone disk model, which can naturally explain all above mentioned issues. Interestingly, this modified model also provides a new scenario for the jet generation and evolution with the TC flow during high energy states, which can make the jet close to the axis. We also find out an expression of jet kinetic power., Comment: 17 pages, 7 figures, comments are welcome