arXiv subjects

Cheng Peng

Publications and source records attributed to Cheng Peng.

At least 163 records · Page 9Linked to original sources

arXiv2022

Phage family classification under Caudoviricetes: a review of current tools using the latest ICTV classification framework

Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better-conserved groups and thus makes family-level classification more feasible.

q-bio.GN↗

arXiv2022

On the Nonexistence of a Strong Minimal Pair

Two nonzero recursively enumerable (r.e.) degrees $\mathbf{a}$ and $\mathbf{b}$ form a strong minimal pair if $\mathbf{a} \wedge \mathbf{b}=\mathbf{0}$ and $\mathbf{b}\vee \mathbf{x}\geq \mathbf{a}$ for any nonzero r.e. degree $\mathbf{x}\leq \mathbf{a}$. We prove that there is no strong minimal pair in the r.e. degrees. Our construction goes beyond the usual $\mathbf{0}'''$-priority arguments and we give some evidence to show that it needs $\mathbf{0}^{(4)}$-priority arguments.

math.LO↗

arXiv2022

Black holes Entangled by Radiation

We construct three models to describe the scenario where two eternal black holes are separated by a flat space, and can eventually be entangled by exchanging radiations. In the doubly holographic setup, we compute the entanglement entropy and the mutual information among the subsystems and obtain the dynamic phase structure of the entanglement. The formation of entanglement between the two black holes is delayed by the space where the radiations must travel through. Finally, if the two black holes exchange sufficient Hawking modes, the final state is characterized by a connected entanglement wedge; otherwise, the final entanglement wedge contains two separated islands. In the former case, the entanglement wedge of the two black holes forms at the time scale of the size of the flat space between them. While in both cases, unitarity of the evolution is preserved. When the sizes of two black holes are not equal, we observe a loss of entanglement between the smaller black hole and the radiation at late times. In the field theory side, we consider two Sachdev-Ye-Kitaev (SYK) clusters coupled to a Majorana chain, which resemble two black holes connected by a radiation region. We numerically compute the same entanglement measures, and obtain similar phase structures as the bulk results. In general, a time delay of the entanglement between the two SYK clusters is found in cases with a long Majorana chain. In particular, when the two SYK clusters are different in size, similar entanglement loss between the smaller SYK cluster and the Majorana chain is observed. Finally, we investigate a chain model composed of EPR clusters with particle exchanges between neighboring clusters, and reproduce the features of entanglement observed in the other models.

hep-th↗

arXiv2022

Testing the data framework for an AI algorithm in preparation for high data rate X-ray facilities

The advent of next-generation X-ray free electron lasers will be capable of delivering X-rays at a repetition rate approaching 1 MHz continuously. This will require the development of data systems to handle experiments at these type of facilities, especially for high throughput applications, such as femtosecond X-ray crystallography and X-ray photon fluctuation spectroscopy. Here, we demonstrate a framework which captures single shot X-ray data at the LCLS and implements a machine-learning algorithm to automatically extract the contrast parameter from the collected data. We measure the time required to return the results and assess the feasibility of using this framework at high data volume. We use this experiment to determine the feasibility of solutions for `live' data analysis at the MHz repetition rate.

physics.data-an↗

arXiv2022

Traces of Electron-Phonon Coupling in One-Dimensional Cuprates

The appearance of certain spectral features in one-dimensional (1D) cuprate materials has been attributed to a strong, extended attractive coupling between electrons. Here, using time-dependent density matrix renormalization group methods on a Hubbard-extended Holstein model, we show that extended electron-phonon ({\it e-ph}) coupling presents an obvious choice to produce such an attractive interaction that reproduces the observed spectral features and doping dependence seen in angle-resolved photoemission experiments: diminished $3k_F$ spectral weight, prominent spectral intensity of a holon-folding branch, and the correct holon band width. While extended {\it e-ph} coupling does not qualitatively alter the ground state of the 1D system compared to the Hubbard model, it quantitatively enhances the long-range superconducting correlations and suppresses spin correlations. Such an extended {\it e-ph} interaction may be an important missing ingredient in describing the physics of the structurally similar two-dimensional high-temperature superconducting layered cuprates, which may tip the balance between intertwined orders in favor of uniform $d$-wave superconductivity.

cond-mat.str-el↗

arXiv2022

DA-VSR: Domain Adaptable Volumetric Super-Resolution For Medical Images

Medical image super-resolution (SR) is an active research area that has many potential applications, including reducing scan time, bettering visual understanding, increasing robustness in downstream tasks, etc. However, applying deep-learning-based SR approaches for clinical applications often encounters issues of domain inconsistency, as the test data may be acquired by different machines or on different organs. In this work, we present a novel algorithm called domain adaptable volumetric super-resolution (DA-VSR) to better bridge the domain inconsistency gap. DA-VSR uses a unified feature extraction backbone and a series of network heads to improve image quality over different planes. Furthermore, DA-VSR leverages the in-plane and through-plane resolution differences on the test data to achieve a self-learned domain adaptation. As such, DA-VSR combines the advantages of a strong feature generator learned through supervised training and the ability to tune to the idiosyncrasies of the test volumes through unsupervised learning. Through experiments, we demonstrate that DA-VSR significantly improves super-resolution quality across numerous datasets of different domains, thereby taking a further step toward real clinical applications.

eess.IV↗

arXiv2022

Multi-Modal Human Authentication Using Silhouettes, Gait and RGB

Whole-body-based human authentication is a promising approach for remote biometrics scenarios. Current literature focuses on either body recognition based on RGB images or gait recognition based on body shapes and walking patterns; both have their advantages and drawbacks. In this work, we propose Dual-Modal Ensemble (DME), which combines both RGB and silhouette data to achieve more robust performances for indoor and outdoor whole-body based recognition. Within DME, we propose GaitPattern, which is inspired by the double helical gait pattern used in traditional gait analysis. The GaitPattern contributes to robust identification performance over a large range of viewing angles. Extensive experimental results on the CASIA-B dataset demonstrate that the proposed method outperforms state-of-the-art recognition systems. We also provide experimental results using the newly collected BRIAR dataset.

cs.CV↗

arXiv2022

A quantum-inspired tensor network method for constrained combinatorial optimization problems

Combinatorial optimization is of general interest for both theoretical study and real-world applications. Fast-developing quantum algorithms provide a different perspective on solving combinatorial optimization problems. In this paper, we propose a quantum-inspired tensor-network-based algorithm for general locally constrained combinatorial optimization problems. Our algorithm constructs a Hamiltonian for the problem of interest, effectively mapping it to a quantum problem, then encodes the constraints directly into a tensor network state and solves the optimal solution by evolving the system to the ground state of the Hamiltonian. We demonstrate our algorithm with the open-pit mining problem, which results in a quadratic asymptotic time complexity. Our numerical results show the effectiveness of this construction and potential applications in further studies for general combinatorial optimization problems.

cs.DS↗

arXiv2022

REGAS: REspiratory-GAted Synthesis of Views for Multi-Phase CBCT Reconstruction from a single 3D CBCT Acquisition

It is a long-standing challenge to reconstruct Cone Beam Computed Tomography (CBCT) of the lung under respiratory motion. This work takes a step further to address a challenging setting in reconstructing a multi-phase}4D lung image from just a single}3D CBCT acquisition. To this end, we introduce REpiratory-GAted Synthesis of views, or REGAS. REGAS proposes a self-supervised method to synthesize the undersampled tomographic views and mitigate aliasing artifacts in reconstructed images. This method allows a much better estimation of between-phase Deformation Vector Fields (DVFs), which are used to enhance reconstruction quality from direct observations without synthesis. To address the large memory cost of deep neural networks on high resolution 4D data, REGAS introduces a novel Ray Path Transformation (RPT) that allows for distributed, differentiable forward projections. REGAS require no additional measurements like prior scans, air-flow volume, or breathing velocity. Our extensive experiments show that REGAS significantly outperforms comparable methods in quantitative metrics and visual quality.

eess.IV↗

arXiv2022

PDRF: Progressively Deblurring Radiance Field for Fast and Robust Scene Reconstruction from Blurry Images

We present Progressively Deblurring Radiance Field (PDRF), a novel approach to efficiently reconstruct high quality radiance fields from blurry images. While current State-of-The-Art (SoTA) scene reconstruction methods achieve photo-realistic rendering results from clean source views, their performances suffer when the source views are affected by blur, which is commonly observed for images in the wild. Previous deblurring methods either do not account for 3D geometry, or are computationally intense. To addresses these issues, PDRF, a progressively deblurring scheme in radiance field modeling, accurately models blur by incorporating 3D scene context. PDRF further uses an efficient importance sampling scheme, which results in fast scene optimization. Specifically, PDRF proposes a Coarse Ray Renderer to quickly estimate voxel density and feature; a Fine Voxel Renderer is then used to achieve high quality ray tracing. We perform extensive experiments and show that PDRF is 15X faster than previous SoTA while achieving better performance on both synthetic and real scenes.

cs.CV↗

arXiv2022

Charge order and superconductivity in a minimal two-band model for infinite-layer nickelates

The recent discovery of superconductivity in infinite-layer nickelates has drawn considerable attention; however, a consensus on the fundamental building blocks and common ingredients necessary to understand and describe their ground states and emergent properties is lacking. A series of experimental and theoretical studies have suggested that an effective two-band Hubbard model with Ni 3$d_{x^2-y^2}$ and rare-earth ($R$) 5$d$ character may describe the low-energy physics. Here, we study the ground state properties of this two-band model on four-leg cylinders using the density-matrix renormalization group (DMRG) technique to better grasp whether such a simple model can embody the essential physics. A key difference compared to single-band Hubbard materials is that the system is self-doped: even at overall half-filling, the $R$-band acts as an electron reservoir, hole-doping the Ni-layer and fundamentally altering the physics expected from an undoped antiferromagnet. On the four-leg cylinder, the ground state is consistent with a Luttinger liquid, with anti-phase modulations of the charge density in the Ni- and $R$-layers having corresponding wavevectors that lock together. Light hole doping away from 1/2 filling releases the locking between the Ni and the $R$ charge modulations, as the electron density in the $R$-band decreases and eventually becomes exhausted at a hole doping concentration that depends sensitively on the effective splitting between the Ni and the $R$ orbitals. The ground state of the doped system is consistent with a Luther-Emery liquid, possessing quasi-long-range superconducting correlations in the Ni layer, similar to the single-band Hubbard model. Our results are consistent with experimental observations and may help to reveal the microscopic mechanism for pairing and other emergent properties.

cond-mat.str-el↗

arXiv2022

Emergence of Crystalline Few-body Correlations in Mass-imbalanced Fermi Polarons

Polarons can serve as an ideal platform to identify few-body correlations in tackling complex many-body problems. In this work, we reveal various crystalline few-body correlations smoothly emergent from the mass-imbalanced Fermi polarons in two dimensions. A unified variational approach up to three particle-hole excitations allows us to extract the dominant dimer, trimer or tetramer correlation in a single framework. When the fermion-impurity mass ratio is beyond certain critical value, the Fermi polaron is found to undergo a smooth crossover, instead of a sharp transition, from the polaronic to trimer and tetramer regimes as increasing the fermion-impurity attraction. The emergent trimer and tetramer correlations result in the momentum-space crystallization of particle-hole excitations featuring a stable diagonal or triangular structure, as can be directly probed through the density-density correlation of majority fermions. Our results shed light on the intriguing quantum phases in the mass-imbalanced Fermi-Fermi mixtures beyond the pairing superfluid paradigm.

cond-mat.quant-gas↗

arXiv2022

Universal tetramer and pentamer in two-dimensional fermionic mixtures

We study the emergence of universal tetramer and pentamer bound states in the two-dimensional $(N+1)$ system, which consists of $N$ identical heavy fermions interacting with a light atom. We show that the critical heavy-light mass ratio to support a ($3+1$) tetramer below the trimer threshold is $3.38$, and to support a ($4+1$) pentamer below the tetramer threshold is $5.14$. While these ground state tetramer and pentamer are both with zero total angular momentum, they exhibit very different density distributions and correlations in momentum space, due to their distinct angular momentum decompositions in the dimer-fermion frame. These universal bound states can be accessible by a number of Fermi-Fermi mixtures now realized in cold atoms laboratories, which also suggest novel few-body correlations dominant in their corresponding many-body systems.

cond-mat.quant-gas↗

arXiv2022

Disordered vector models: from higher spins to incipient strings

We present a one-parameter family of large $N$ disordered models, with and without supersymmetry, in three spacetime dimensions. They interpolate from the critical large $N$ vector model dual to a classical higher spin theory, towards a theory with a classical string dual. We analyze the spectrum and OPE data of the theories. While the supersymmetric model is always well-behaved the non-supersymmetric model is unitary only over a small parameter range. We offer some speculations on the origin of strings from the higher spins.

hep-th↗

arXiv2022

Potential energy surface and formation of superheavy nuclei with the Skyrme energy-density functional

Within the framework of Skyrme energy-density functional theory, the nucleus-nucleus potential is calculated and potential energy surface is obtained with different effective forces for accurately estimating the formation cross sections of superheavy nuclei in massive fusion reactions. The width and height of the potential pocket are influenced by the Skyrme effective forces SkM, SkM$^{\ast}$, SkP, SIII, Ska and SLy4, which correspond to the different equation of state for the isospin symmetry nuclear matter. It is found that the nucleus-nucleus potential is associated with the collision orientation and Skyrme parameters. More repulsive nuclear potential is pronounced with increasing the incompressible modulus of nuclear matter. The available data in the fusion-evaporation reaction of $^{48}$Ca+$^{238}$U are nicely reproduced with the SkM$^{\ast}$ parameter by implementing into the dinuclear system model.

nucl-th↗

arXiv2022

Enhanced superconductivity by near-neighbor attraction in the doped Hubbard model

Recent experiment has unveiled an anomalously strong electron-electron attraction in one-dimensional copper-oxide chain Ba$_{2-x}$Sr$_x$CuO$_{3+δ}$. While the near-neighbor electron attraction $V$ in the one-dimensional extended Hubbard chain has been examined recently, its effect in the Hubbard model beyond the one-dimensional chain remains unclear. We report a density-matrix renormalization group study of the extended Hubbard model on long four-leg cylinders on the square lattice. We find that the near-neighbor electron attraction $V$ can notably enhance the long-distance superconducting correlations while simultaneously suppressing the charge-density-wave correlations. Specifically, for a modestly strong electron attraction, the superconducting correlations become dominant over the CDW correlations with a Luttinger exponent $K_{sc}\sim 1$ and strong divergent superconducting susceptibility. Our results provide a promising way to realize long-range superconductivity in the doped Hubbard model in two dimensions. The relevance of our numerical results to cuprate materials is also discussed.

cond-mat.str-el↗

arXiv2022

Giant enhancement of third-harmonic generation in graphene-metal heterostructures

Nonlinear nanophotonics leverages engineered nanostructures to funnel light into small volumes and intensify nonlinear optical processes with spectral and spatial control. Due to its intrinsically large and electrically tunable nonlinear optical response, graphene is an especially promising nanomaterial for nonlinear optoelectronic applications. Here we report on exceptionally strong optical nonlinearities in graphene-insulator-metal heterostructures, demonstrating an enhancement by three orders of magnitude in the third-harmonic signal compared to bare graphene. Furthermore, by increasing the graphene Fermi energy through an external gate voltage, we find that graphene plasmons mediate the optical nonlinearity and modify the third-harmonic signal. Our findings show that graphene-insulator-metal is a promising heterostructure for optically-controlled and electrically-tunable nano-optoelectronic components.

cond-mat.mes-hall↗

arXiv2022

Matrix Entanglement

In gauge/gravity duality, matrix degrees of freedom on the gauge theory side play important roles for the emergent geometry. In this paper, we discuss how the entanglement on the gravity side can be described as the entanglement between matrix degrees of freedom. Our approach, which we call 'matrix entanglement', is different from 'target-space entanglement' proposed and discussed recently by several groups. We consider several classes of quantum states to which our approach can play important roles. When applied to fuzzy sphere, matrix entanglement can be used to define the usual spatial entanglement in two-brane or five-brane world-volume theory nonperturbatively in a regularized setup. Another application is to a small black hole in AdS5*S5 that can evaporate without being attached to a heat bath, for which our approach suggests a gauge theory origin of the Page curve. The confined degrees of freedom in the partially-deconfined states play the important roles.

hep-th↗