cometadata/datacite-rtg-text-other-reclassification-records huggingface dataset:
Dual-color Q-switched mode-locking in an Erbium-doped fiber laser
Creators: name: Lv, Chenyue
name: Lu, Baole
name: Bai, Jintao
Publisher: name: arXiv
Year: 2024
Subjects: subject: Optics (physics.optics)
subject: FOS: Physical sciences

description: Q-switched mode-locking (QML) has been widely observed in various lasers, but its generation mechanism in passive mode-locking remains unclear. In this paper, we build up a dual-color QML Erbium-doped fiber laser and find a bound-state-like envelope on the optical spectrum for the first time. Theoretically, the formation mechanism of QML is numerically investigated using the coupled Ginzburg-Landau equations. In addition, we demonstrated the existence of two QML pulse evolution patterns with gain or polarization state variations in simulation. Our results deepen the understanding of QML pulses in mode-locked fiber lasers and provide a foundation for studying mode-locking nonlinear evolutionary paths.
Relativistic Corrections to the CBF Effective Nuclear Hamiltonian
Creators: name: Sabatucci, Andrea
name: Benhar, Omar
name: Lovato, Alessandro
Publisher: name: arXiv
Year: 2024
Subjects: subject: Nuclear Theory (nucl-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: We discuss the inclusion of relativistic boost corrections into the CBF effective nuclear Hamiltonian, derived from a realistic model of two- and three-nucleon interactions using the formalism of correlated basis functions and the cluster expansion technique. Different procedures to take into account the effects of boost interactions are compared on the basis of the ability to reproduce the nuclear matter equation of state obtained from accurate many-body calculations. The results of our study show that the repulsive contribution of the boost interaction significantly depends on the underlying model of the non relativistic potential. On the other hand, the dominant relativistic correction turns out to be the corresponding reduction of the strength of repulsive three-nucleon interactions, leading to a significant softening of the equation of state at supranuclear densities.
description: Few changes to match the version published in Phys. Rev. C
Large Language Model-empowered multimodal strain sensory system for shape recognition, monitoring, and human interaction of tensegrity
Creators: name: Mao, Zebing
name: Kobayashi, Ryota
name: Nabae, Hiroyuki
name: Suzumori, Koichi
Publisher: name: arXiv
Year: 2024
Subjects: subject: Robotics (cs.RO)
subject: Computation and Language (cs.CL)
subject: FOS: Computer and information sciences

description: A tensegrity-based system is a promising approach for dynamic exploration of uneven and unpredictable environments, particularly, space exploration. However, implementing such systems presents challenges in terms of intelligent aspects: state recognition, wireless monitoring, human interaction, and smart analyzing and advising function. Here, we introduce a 6-strut tensegrity integrate with 24 multimodal strain sensors by leveraging both deep learning model and large language models to realize smart tensegrity. Using conductive flexible tendons assisted by long short-term memory model, the tensegrity achieves the self-shape reconstruction without extern sensors. Through integrating the flask server and gpt-3.5-turbo model, the tensegrity autonomously enables to send data to iPhone for wireless monitoring and provides data analysis, explanation, prediction, and suggestions to human for decision making. Finally, human interaction system of the tensegrity helps human obtain necessary information of tensegrity from the aspect of human language. Overall, this intelligent tensegrity-based system with self-sensing tendons showcases potential for future exploration, making it a versatile tool for real-world applications.
SEDMamba: Enhancing Selective State Space Modelling with Bottleneck Mechanism and Fine-to-Coarse Temporal Fusion for Efficient Error Detection in Robot-Assisted Surgery
Creators: name: Xu, Jialang
name: Sirajudeen, Nazir
name: Boal, Matthew
name: Francis, Nader
name: Stoyanov, Danail
name: Mazomenos, Evangelos
Publisher: name: arXiv
Year: 2024
Subjects: subject: Computer Vision and Pattern Recognition (cs.CV)
subject: Artificial Intelligence (cs.AI)
subject: FOS: Computer and information sciences

description: Automated detection of surgical errors can improve robotic-assisted surgery. Despite promising progress, existing methods still face challenges in capturing rich temporal context to establish long-term dependencies while maintaining computational efficiency. In this paper, we propose a novel hierarchical model named SEDMamba, which incorporates the selective state space model (SSM) into surgical error detection, facilitating efficient long sequence modelling with linear complexity. SEDMamba enhances selective SSM with a bottleneck mechanism and fine-to-coarse temporal fusion (FCTF) to detect and temporally localize surgical errors in long videos. The bottleneck mechanism compresses and restores features within their spatial dimension, thereby reducing computational complexity. FCTF utilizes multiple dilated 1D convolutional layers to merge temporal information across diverse scale ranges, accommodating errors of varying duration. Our work also contributes the first-of-its-kind, frame-level, in-vivo surgical error dataset to support error detection in real surgical cases. Specifically, we deploy the clinically validated observational clinical human reliability assessment tool (OCHRA) to annotate the errors during suturing tasks in an open-source radical prostatectomy dataset (SAR-RARP50). Experimental results demonstrate that our SEDMamba outperforms state-of-the-art methods with at least 1.82% AUC and 3.80% AP performance gains with significantly reduced computational complexity. The corresponding error annotations, code and models are released at https://github.com/wzjialang/SEDMamba.
description: Accepted by IEEE RA-L
New asymptotically (Anti)-de Sitter black holes in (super)gravity
Creators: name: Armas, Jay
name: Nicosia, Gianbattista-Piero
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: We use the duality between gravitational dynamics and fluids living on dynamical surfaces carrying multiple charges, known as the blackfold approach, to perturbativaly construct new asymptotically global (Anti)-de Sitter multi-spinning, non-extremal, multi-charged black holes in theories of higher-dimensional gravity minimally coupled to a dilaton and higher-form gauge fields in spacetime dimensions $D\ge5$, and new asymptotically AdS$_{l}\times S^{m}$ black holes in type IIB and eleven-dimensional supergravity. These solutions include the generalisation of the Kerr-Newman solution to (A)dS carrying either electric or string charge, generalisations of black rings to higher-dimensions with $\mathbb{S}^p\times \mathbb{S}^{n+1}$ horizon topology, static de Sitter solutions carrying arbitrary $q$-brane charge, as well as various asymptotically AdS$_{l}\times S^{m}$ multi-charged and multi-spinning black hole solutions, some of which correspond to novel thermal states in $\mathcal{N}=4$ Super-Yang-Mills theory.
description: 53 pages including appendices, edited lexical typos to match JHEP version
High Order Accurate Hermite Schemes on Curvilinear Grids with Compatibility Boundary Conditions
Creators: name: Loya, Allen Alvarez
name: Appelö, Daniel
name: Henshaw, William D.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Numerical Analysis (math.NA)
subject: FOS: Mathematics

description: High order accurate Hermite methods for the wave equation on curvilinear domains are presented. Boundaries are treated using centered compatibility conditions rather than more standard one-sided approximations. Both first-order-in-time (FOT) and second-order-in-time (SOT) Hermite schemes are developed. Hermite methods use the solution and multiple derivatives as unknowns and achieve space-time orders of accuracy $2m-1$ (FOT) and $2m$ (SOT) for methods using $(m+1)^d$ degree of freedom per node in $d$ dimensions. The compatibility boundary conditions (CBCs) are based on taking time derivatives of the boundary conditions and using the governing equations to replace the time derivatives with spatial derivatives. These resulting constraint equations augment the Hermite scheme on the boundary. The solvability of the equations resulting from the compatibility conditions are analyzed. Numerical examples demonstrate the accuracy and stability of the new schemes in two dimensions.
Unveiling secondary particle generation in a SONTRAC detector through GEANT4 simulations
Creators: name: Topuz, Ahmet Ilker
Publisher: name: arXiv
Year: 2024
Subjects: subject: Instrumentation and Detectors (physics.ins-det)
subject: FOS: Physical sciences

description: SOlar Neutron TRACking (SONTRAC) is a detector concept based on a bundle of plastic scintillators by aiming at tracking the solar neutrons through the generation of the secondary particles such as protons from the (n, np) and (n, p) processes. In this study, in addition to the particle population, the energy spectra of the secondary particles including protons, gamma rays, electrons, alphas, and ions that are produced either due to the interaction between the fast neutrons and a SONTRAC detector or through the interplay between the secondary particles and the detector components are determined by means of GEANT4 simulations. The detector geometry in the present study consists of 34$\times$34 Kuraray Y11-200(M) fibers, and the current fiber bundle is irradiated with a planar vertical neutron beam of 0.2$\times$0.2 cm$^{2}$ by using an energy list composed of 20, 40, 60, 80, and 100 MeV where the number of incident neutrons is $10^5$. First, It is revealed that a non-negligible number of secondary protons are generated by the fast neutron bombardment; however, the population of these secondary protons is still low compared to the incident beam, i.e. in the order of $10^3$. Secondly, it is also observed that the energy spectrum of secondary protons exhibits a decreasing trend that is limited by the kinetic energy of incident neutrons. Additionally, the range of the secondary protons along with the deposited energy is computed, and it is demonstrated that a significant portion of the generated protons lose their entire energy and stop within the present SONTRAC detector. Finally, a 34$\times$34 pixel grid detector is introduced on each side of the fiber bundle to collect the optical photons produced from the energy deposition in the scintillation fibers, and the trajectory of the secondary protons on the pixel grid is shown by using a fast neutron beam of 100 MeV.
description: 11 pages, 7 figures
Scattering amplitudes in the Randall-Sundrum model with brane-localized curvature terms
Creators: name: Chivukula, R. Sekhar
name: Mohan, Kirtimaan A.
name: Sengupta, Dipan
name: Simmons, Elizabeth H.
name: Wang, Xing
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: In this paper we investigate the scattering amplitudes of spin-2 Kaluza-Klein (KK) states in Randall-Sundrum models with brane-localized curvature terms. We show that the presence of brane-localized curvature interactions modifies the properties of (4D) scalar fluctuations of the metric, resulting in scattering amplitudes of the massive spin-2 KK states which grow as ${\cal O}(s^3)$ instead of ${\cal O}(s)$. We discuss the constraints on the size of the brane-localized curvature interactions based on the consistency of the Sturm-Liouville mode systems of the spin-2 and spin-0 metric fluctuations. We connect the properties of the scattering amplitudes to the diffeomorphism invariance of the compactified KK theory with brane-localized curvature interactions. We verify that the scattering amplitudes involving brane-localized external sources (matter) are diffeomorphism-invariant, but show that those for matter localized at an arbitrary point in the bulk are not. We demonstrate that, in Feynman gauge, the spin-0 Goldstone bosons corresponding to helicity-0 states of the massive spin-2 KK bosons behave as a tower of Galileons, and that it is their interactions that produce the high-energy behavior of the scattering amplitudes. We also outline the correspondence between our results and those in the Dvali-Gabadadze-Porrati (DGP) model. In an appendix we discuss the analogous issue in extra-dimensional gauge theory, and show that the presence of a brane-localized gauge kinetic-energy term does not change the high-energy behavior of corresponding KK vector boson scattering amplitudes.
description: 36 pages, 2 figures. Minor changes, new reference added
Scale-dependent sharpening of interfacial fluctuations in shape-based models of dense cellular sheets
Creators: name: Yue, Haicen
name: Packard, Charles R.
name: Sussman, Daniel M.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Physical sciences

description: The properties of tissue interfaces -- between separate populations of cells, or between a group of cells and its environment -- has attracted intense theoretical, computational, and experimental study. Recent work on shape-based models inspired by dense epithelia have suggested a possible ``topological sharpening'' effect, by which four-fold vertices spatially coordinated along a cellular interface lead to a cusp-like restoring force acting on cells at the interface, which in turn greatly suppresses interfacial fluctuations. We revisit these interfacial fluctuations, focusing on the distinction between short length scale reduction of interfacial fluctuations and long length scale renormalized surface tension. To do this, we implement a spectrally resolved analysis of fluctuations over extremely long simulation times. This leads to more quantitative information on the topological sharpening effect, in which the degree of sharpening depends on the length scale over which it is measured. We compare our findings with a Brownian bridge model of the interface, and close by analyzing existing experimental data in support of the role of short-length-scale topological sharpening effects in real biological systems.
description: 9 pages, 7 figures
Towards physics-informed neural networks for landslide prediction
Creators: name: Dahal, Ashok
name: Lombardo, Luigi
Publisher: name: arXiv
Year: 2024
Subjects: subject: Geophysics (physics.geo-ph)
subject: Artificial Intelligence (cs.AI)
subject: Machine Learning (cs.LG)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: For decades, solutions to regional scale landslide prediction have mostly relied on data-driven models, by definition, disconnected from the physics of the failure mechanism. The success and spread of such tools came from the ability to exploit proxy variables rather than explicit geotechnical ones, as the latter are prohibitive to acquire over broad landscapes. Our work implements a Physics Informed Neural Network (PINN) approach, thereby adding to a standard data-driven architecture, an intermediate constraint to solve for the permanent deformation typical of Newmark slope stability methods. This translates into a neural network tasked with explicitly retrieving geotechnical parameters from common proxy variables and then minimize a loss function with respect to the available coseismic landside inventory. The results are very promising, because our model not only produces excellent predictive performance in the form of standard susceptibility output, but in the process, also generates maps of the expected geotechnical properties at a regional scale. Such architecture is therefore framed to tackle coseismic landslide prediction, something that, if confirmed in other studies, could open up towards PINN-based near-real-time predictions.
Constraints on freeze-in dark matter from Lyman-$α$ forest and 21-cm signal : single-field models
Creators: name: Xu, Zixuan
name: Zhou, Quan
name: Zheng, Sibo
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: We report new Lyman-$α$ and 21-cm constraints on freeze-in dark matter (FIDM) which injects energy into the intergalactic medium either through annihilation or decay to photon(s) or electron-positron pair. With respect to Lyman-$α$ we fix the baseline ionization history using low redshift data about astrophysical reionization, whereas for 21-cm signal we adopt the baseline values of 21-cm power spectrum through a standard modeling of star formation developed so far. Using the latest numerical tools, we show that (i) for sterile neutrino FIDM, current Lyman-$α$ data and future sensitivity of SKA-low (1000 hrs) on the 21-cm power spectra excludes the FIDM mass up to $1.8\times 10^{-3}$ GeV at 95$\%$ CL and $5.46\times 10^{-4}$ GeV, respectively, and (ii) for millicharged FIDM, current Lyman-$α$ data only excludes the millicharge down to $10^{-8}$ within the FIDM mass range of $10^{-3}-1$ GeV at 95$\%$ CL, suggesting that the surviving parameter space of millicharged FIDM is still intact.
description: 17 pages, 5 figures; v2: revised version with 19 pp and 8 figs; v3: to match the published version
Towards a Quality Approach to Hierarchical Color Maps
Creators: name: Mertz, Tobias
name: Kohlhammer, Jörn
Publisher: name: arXiv
Year: 2024
Subjects: subject: Human-Computer Interaction (cs.HC)
subject: FOS: Computer and information sciences
subject: H.1.2; H.5.2

description: To improve the perception of hierarchical structures in data sets, several color map generation algorithms have been proposed to take this structure into account. But the design of hierarchical color maps elicits different requirements to those of color maps for tabular data. Within this paper, we make an initial effort to put design rules from the color map literature into the context of hierarchical color maps. We investigate the impact of several design decisions and provide recommendations for various analysis scenarios. Thus, we lay the foundation for objective quality criteria to evaluate hierarchical color maps.
Whispers from the quantum core: the ringdown of semiclassical stars
Creators: name: Arrechea, Julio
name: Liberati, Stefano
name: Vellucci, Vania
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: This investigation delves into the ringdown signals produced by semiclassical stars, which are ultra-compact, regular solutions of the Einstein equations incorporating stress-energy contributions from quantum vacuum polarization. These stars exhibit an approximately Schwarzschild exterior and an interior composed of a constant-density classical fluid and a cloud of vacuum polarization. By adjusting their compactness and density, we can alter the internal structure of these stars without modifying the exterior. This adaptability enables us to examine the sensitivity of the ringdown signal to the innermost regions of the emitting object and to compare it with similar geometries that differ substantially only at the core. Our results indicate that echo signals are intrinsically linked to the presence of stable light rings and can be very sensitive to the internal structure of the emitting object. This point was previously overlooked, either due to the imposition of reflective boundary conditions at the stellar surface or due to the assumption of low curvature interior geometries. Specifically, for stellar-sized semiclassical stars, we find that the interior travel time is sufficiently prolonged to render the echoes effectively unobservable. These findings underscore the potential efficacy of ultra-compact objects as black hole mimickers and emphasize that any phenomenological constraints on such objects necessitate a detailed understanding of their specific properties and core structure.
Going beyond Landauer scattering theory to describe spatially-resolved non-local heating and cooling in quantum thermoelectrics
Creators: name: Leumer, Nico G.
name: Basko, Denis M.
name: Jalabert, Rodolfo A.
name: Weinmann, Dietmar
name: Whitney, Robert S.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: Spatially-resolved heating and cooling in nanostructures is nowadays measured with various nanoscale thermometry techniques, including scanning thermometry. Yet the most commonly used theory of nanoscale heating and thermoelectricity -- Landauer scattering theory -- is not appropriate to model such measurements. Hence, we analyze a minimal model of spatially-resolved heat transfer between electrons and phonons in simple thermoelectric nanostructures. This combines Landauer scattering formalism with a Boltzmann equation for transport, revealing the non-locality of Joule heating and Peltier cooling induced by a scatterer in a nanowire. The corresponding heating or cooling of the phonons is caused by the voltage drop at the scatterer, but is often maximal at a certain distance from the scatterer. This distance is of the order of the electron-phonon scattering length. Scanning thermal microscopy, such as SQUID-on-tip thermometers, should detect this non-locality as phonon hot spots and cold spots, spatially separated from the scatterer. We provide physical arguments explaining the thermoelectric response of the combined system of wire and scatterer, and in particular, why the resulting heating and cooling is sometimes the opposite to that predicted by the standard Landauer scattering theory.
description: Version 2: added 2 references, some other very minor improvements
Interplay of altermagnetism and pressure in hexagonal and orthorhombic MnTe
Creators: name: Devaraj, Nayana
name: Bose, Anumita
name: Narayan, Awadhesh
Publisher: name: arXiv
Year: 2024
Subjects: subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: Alternative magnetic materials or ``altermagnets", characterized by their non-relativistic, momentum-dependent spin-split states, represent a cutting-edge advancement in the field of magnetism, offering promising avenues for spintronic applications. Among these materials, hexagonal MnTe has emerged as a standout material candidate for its substantial spin-splitting. In this study, employing first-principles electronic structure calculations and spin group symmetry analysis, we delve into the interplay of altermagnetism and pressure in two main phases of MnTe. Our relativistic calculations demonstrate the presence of tunable anomalous Hall effect (AHE) in hexagonal MnTe. In addition, our results underscore the pivotal role of pressure as a tuning parameter for the alternative magnetic traits in the system. Furthermore, we identify another phase of MnTe with orthorhombic structure, namely $γ$-MnTe, hosting altermagnetic characteristics. We study, in detail, its response in AHE and spin-spliting due to magnetization and pressure variations, respectively. Our study highlights the substantial impact of pressure on the properties of alternative magnetic materials, particularly emphasizing the pronounced tuning effect observed in the hexagonal and orthorhombic MnTe.
Consistency conditions for O-plane unsmearing from second-order perturbation theory
Creators: name: Emelin, Maxim
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Theory (hep-th)
subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: Scale-separated AdS compactifications of string theory can be constructed at the two-derivative supergravity level in the presence of smeared orientifold planes. The unsmearing corrections are known to leading order in the large volume, weak coupling limit. However, first-order perturbative approximations of non-linear problems can often produce spurious solutions, which are only weeded out by additional consistency conditions imposed at higher orders. In this work, we revisit the unsmearing procedure and present consistency conditions obtained from the second order warp factor and dilaton equations. This requires proper treatment of the near-source singularities. The resulting conditions appear as integral constraints on various non-linear combinations of the first order corrections, which we argue can generally be satisfied by appropriate choice of integration constants of the leading-order solutions. This provides a non-trivial consistency check for the perturbative unsmearing procedure and supports the existence of scale-separated AdS vacua in string theory.
description: 20 pages, JHEP version, changes: references added, several typos and coefficients fixed, section 4.1: some changes to the discussion of brane intersections, added comments on higher-derivative corrections
Emergent modified gravity: Polarized Gowdy model on a torus
Creators: name: Bojowald, Martin
name: Duque, Erick I.
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: FOS: Physical sciences

description: New covariant theories of emergent modified gravity exist not only in spherically symmetric models, as previously found, but also in polarized Gowdy systems that have a local propagating degree of freedom. Several explicit versions are derived here, depending on various modification functions. These models do not have instabilities from higher time derivatives, and a large subset is compatible with gravitational waves and minimally coupled massless matter fields travelling at the same speed. Interpreted as models of loop quantum gravity, covariant Hamiltonian constraints derived from the covariance conditions found in polarized Gowdy systems are more restricted than those in spherical symmetry, requiring new forms of holonomy modifications with an anisotropy dependence that has not been considered before. Assuming homogeneous space, the models provide access to the full anisotropy parameters of modified Bianchi I dynamics, in which case different fates of the classical singularity are realized depending on the specific class of modifications.
description: 55 pages, two figures
Approximate Relational Reasoning for Higher-Order Probabilistic Programs
Creators: name: Haselwarter, Philipp G.
name: Li, Kwing Hei
name: Aguirre, Alejandro
name: Gregersen, Simon Oddershede
name: Tassarotti, Joseph
name: Birkedal, Lars
Publisher: name: arXiv
Year: 2024
Subjects: subject: Logic in Computer Science (cs.LO)
subject: Programming Languages (cs.PL)
subject: FOS: Computer and information sciences

description: Properties such as provable security and correctness for randomized programs are naturally expressed relationally as approximate equivalences. As a result, a number of relational program logics have been developed to reason about such approximate equivalences of probabilistic programs. However, existing approximate relational logics are mostly restricted to first-order programs without general state.
 In this paper we develop Approxis, a higher-order approximate relational separation logic for reasoning about approximate equivalence of programs written in an expressive ML-like language with discrete probabilistic sampling, higher-order functions, and higher-order state. The Approxis logic recasts the concept of error credits in the relational setting to reason about relational approximation, which allows for expressive notions of modularity and composition, a range of new approximate relational rules, and an internalization of a standard limiting argument for showing exact probabilistic equivalences by approximation. We also use Approxis to develop a logical relation model that quantifies over error credits, which can be used to prove exact contextual equivalence. We demonstrate the flexibility of our approach on a range of examples, including the PRP/PRF switching lemma, IND\$-CPA security of an encryption scheme, and a collection of rejection samplers. All of the results have been mechanized in the Coq proof assistant and the Iris separation logic framework.
description: Camera-ready POPL submission including additional appendix
mdCATH: A Large-Scale MD Dataset for Data-Driven Computational Biophysics
Creators: name: Mirarchi, Antonio
name: Giorgino, Toni
name: De Fabritiis, Gianni
Publisher: name: arXiv
Year: 2024
Subjects: subject: Biomolecules (q-bio.BM)
subject: FOS: Biological sciences

description: Recent advancements in protein structure determination are revolutionizing our understanding of proteins. Still, a significant gap remains in the availability of comprehensive datasets that focus on the dynamics of proteins, which are crucial for understanding protein function, folding, and interactions. To address this critical gap, we introduce mdCATH, a dataset generated through an extensive set of all-atom molecular dynamics simulations of a diverse and representative collection of protein domains. This dataset comprises all-atom systems for 5,398 domains, modeled with a state-of-the-art classical force field, and simulated in five replicates each at five temperatures from 320 K to 450 K. The mdCATH dataset records coordinates and forces every 1 ns, for over 62 ms of accumulated simulation time, effectively capturing the dynamics of the various classes of domains and providing a unique resource for proteome-wide statistical analyses of protein unfolding thermodynamics and kinetics. We outline the dataset structure and showcase its potential through four easily reproducible case studies, highlighting its capabilities in advancing protein science.
A Quantum Leaky Integrate-and-Fire Spiking Neuron and Network
Creators: name: Brand, Dean
name: Petruccione, Francesco
Publisher: name: arXiv
Year: 2024
Subjects: subject: Quantum Physics (quant-ph)
subject: Emerging Technologies (cs.ET)
subject: Neural and Evolutionary Computing (cs.NE)
subject: FOS: Physical sciences
subject: FOS: Computer and information sciences

description: Quantum machine learning is in a period of rapid development and discovery, however it still lacks the resources and diversity of computational models of its classical complement. With the growing difficulties of classical models requiring extreme hardware and power solutions, and quantum models being limited by noisy intermediate-scale quantum (NISQ) hardware, there is an emerging opportunity to solve both problems together. Here we introduce a new software model for quantum neuromorphic computing -- a quantum leaky integrate-and-fire (QLIF) neuron, implemented as a compact high-fidelity quantum circuit, requiring only 2 rotation gates and no CNOT gates. We use these neurons as building blocks in the construction of a quantum spiking neural network (QSNN), and a quantum spiking convolutional neural network (QSCNN), as the first of their kind. We apply these models to the MNIST, Fashion-MNIST, and KMNIST datasets for a full comparison with other classical and quantum models. We find that the proposed models perform competitively, with comparative accuracy, with efficient scaling and fast computation in classical simulation as well as on quantum devices.
description: 9 pages, 6 figures, 1 table
Testing the phenomenological interacting dark energy model with gamma-ray bursts and Pantheon+ type Ia supernovae
Creators: name: Nong, Xiao-Dong
name: Liang, Nan
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cosmology and Nongalactic Astrophysics (astro-ph.CO)
subject: FOS: Physical sciences

description: In this paper, we utilize recent observational data from gamma-ray bursts (GRBs) and Pantheon+ supernovae Ia (SNe Ia) sample to explore the interacting dark energy (IDE) model in a phenomenological scenario. Results from GRBs alone, SNe Ia and GRBs+SNe Ia indicate that the energy is transferred from dark energy to dark matter and the coincidence problem is alleviated. The value of $H_0$ from GRBs+SNe Ia in the IDE scenario shows agreement with the SH0ES measurement. Considering the age estimate of the quasar APM 08279+5255 at $z = 3.91$, we find that the phenomenological IDE scenario can predict a cosmic age greater than that of the $Λ$CDM model, thus the cosmic age problem can be alleviated.
description: 12 pages,3 figures. Res. Astron. Astrophys. in press. https://doi.org/10.1088/1674-4527/ad8a07
Multiphoton dressed Rydberg excitations in a microwave cavity with ultracold Rb atoms
Creators: name: Kondo, J. D. Massayuki
name: Rittenhouse, Seth T.
name: Magalhaes, Daniel Varela
name: Rokaj, Vasil
name: Mistakidis, S. I.
name: Sadeghpour, H. R.
name: Marcassa, Luis Gustavo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: We investigate magneto-optical trap loss spectroscopy of Rydberg excited $^{85}$Rb ($66\leq n \leq 68~S_{1/2}$) atoms, placed inside a tailored microwave cavity. The cavity frequency at 13.053 GHz is in resonance with the $67S_{1/2} \rightarrow 66P_{3/2}$ transition, inducing a ladder multiphoton microwave Rydberg absorption and emission. The observed spectra are modeled with an extended Jaynes-Cumming formalism that accounts for multiphoton absorption from and emission into the cavity, the loss from the trap due to Rydberg excitation, and cavity imperfection. We calculate the average photons in each spectral feature and find evidence for fractional photon emission into the cavity modes. The microwave cavity Rydberg spectroscopy in this work should inform the application and technology development of Rydberg based sensors and hybrid Rydberg atom-superconducting resonator quantum gates.
Cell shape and orientation control galvanotactic accuracy
Creators: name: Nwogbaga, Ifunanya
name: Camley, Brian A.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Cell Behavior (q-bio.CB)
subject: Soft Condensed Matter (cond-mat.soft)
subject: Biological Physics (physics.bio-ph)
subject: FOS: Biological sciences
subject: FOS: Physical sciences

description: Galvanotaxis is believed to be driven by the redistribution of transmembrane proteins and other molecules, referred to as "sensors", through electrophoresis and electroosmosis. Here, we update our previous model of the limits of galvanotaxis due to stochasticity of sensor movements to account for cell shape and orientation. Computing the Fisher information, we find that cells in principle possess more information about the electric field direction when their long axis is parallel to the field, but that for weak fields maximum-likelihood estimators of the field direction may actually have lower variability when the cell's long axis is perpendicular to the field. In an alternate possibility, we find that if cells instead estimate the field direction by taking the average of all the sensor locations as its directional cue ("vector sum"), this introduces a bias towards the short axis, an effect not present for isotropic cells. We also explore the possibility that cell elongation arises downstream of sensor redistribution. We argue that if sensors migrate to the cell's rear, the cell will expand perpendicular the field - as is more commonly observed - but if sensors migrate to the front, the cell will elongate parallel to the field.
Switching, Amplifying, and Chirping Diode Lasers with Current Pulses for High Bandwidth Quantum Technologies
Creators: name: Buser, Gianni
Publisher: name: arXiv
Year: 2024
Subjects: subject: Optics (physics.optics)
subject: Instrumentation and Detectors (physics.ins-det)
subject: Quantum Physics (quant-ph)
subject: FOS: Physical sciences

description: A series of simple and low-cost devices for switching, amplifying, and chirping diode lasers based on current modulation are presented. Direct modulation of diode laser currents is rarely sufficient to establish precise amplitude and phase control over light, as its effects on these parameters are not independent. These devices overcome this limitation by exploiting amplifier saturation and dramatically outperform commonly used external modulators in key figures of merit for quantum technological applications. Semiconductor optical amplifiers operated on either rubidium D line are recast as intensity switches and shown to achieve ON:OFF ratios $>10^6$ in as little as 50 ns. Current is switched to a 795 nm wavelength (Rb D1) tapered amplifier to produce optical pulses of few nanosecond duration and peak powers of 3 W at a similar extinction ratio. Fast rf pulses are applied directly to a laser diode to shift its emission frequency by up to 300 MHz in either direction and at a maximum chirp rate of 150 MHz/ns. Finally, the latter components are combined, yielding a system that produces watt-level optical pulses with arbitrary frequency chirps in the given range and <2% residual intensity variation, all within 65 ns upon asynchronous demand. Such systems have broad application in atomic, molecular, and optical physics, and are of particular interest to fast experiments simultaneously requiring high power and low noise, for example quantum memory experiments with atomic vapors.
description: 8 pages, 4 figures
Rydberg atom-based microwave electrometry using polarization spectroscopy
Creators: name: Gomes, Naomy Duarte
name: Pepino, Vinicius Marrara
name: Borges, Ben-Hur Viana
name: Magalhães, Daniel Varela
name: Napolitano, Reginaldo de Jesus
name: Torres, Manuel Alejandro Lefrán
name: Kondo, Jorge Douglas Massayuki
name: Marcassa, Luis Gustavo
Publisher: name: arXiv
Year: 2024
Subjects: subject: Atomic Physics (physics.atom-ph)
subject: FOS: Physical sciences

description: In this study, we investigated Rydberg atom-based microwave electrometry using polarization spectroscopy in a room-temperature vapor cell. By measuring Autler-Townes splitting in the electromagnetically induced transparency (EIT) spectrum, we determined that the minimum measurable microwave electric field is approximately five times lower than conventional EIT techniques. The results are well reproduced by a full optical Bloch equation model, which takes into account all the hyperfine levels involved. Subsequently, the EIT setup was used to characterize a custom microwave cylindrical lens, which increases the field at the focus by a factor of three, decreasing the minimum measurable microwave electric field by the same amount. Our results indicate that the combination of polarization spectroscopy and a microwave lens may enhance microwave electrometry.
Influences of $δ$B Contribution and Parallel Inertial Term of Energetic Particles on MHD-Kinetic Hybrid Simulations: A Case Study of the 1/1 Internal Kink Mode
Creators: name: Zhang, H. X.
name: Zhang, H. W.
name: Ma, Z. W.
name: Liu, C.
Publisher: name: arXiv
Year: 2024
Subjects: subject: Plasma Physics (physics.plasm-ph)
subject: FOS: Physical sciences

description: The magnetohydrodynamic-kinetic (MHD-kinetic) hybrid model [Park et. al., 1992] has been widely applied in studying energetic particles (EPs) problems in fusion plasmas for past decades. The pressure-coupling scheme or the current-coupling scheme is adopted in this model. However, two noteworthy issues arise in the model application: firstly, the coupled term introduced in the pressure-coupling scheme, $\left( \nabla \cdot \mathbf{P}_{\mathrm{h}} \right)_{\bot}$, is often simplified by $\nabla \cdot \mathbf{P}_{\mathrm{h}}$, which is equivalent to neglecting the parallel inertial term of EPs; secondly, besides the $δf $ contribution caused by changing in the EP distribution function, the magnetic field perturbation (the $δ\mathbf{B} $ contribution) generated during development of the instabilities should also be considered, but it is often ignored in existing hybrid simulations. In this paper, we derive the analytical formulations under these two coupling schemes and then numerically study the representative case of the linear stability of the m/n=1/1 internal kink mode (IKM) [Fu et. al., 2006] by using the CLT-K code. It is found that the approximated models can still yield reasonable results when EPs are isotopically distributed. But it fails completely in cases with anisotropic EP distributions. In addition, we further investigate the influence of EP's orbit width on the stability of IKM and verify the equivalence between pressure-coupling scheme and the current-coupling scheme.
description: 32 pages, 17 figures, 2 tables
Resonant excitation of eccentricity in spherical extreme-mass-ratio inspirals
Creators: name: Eleni, Areti
name: Destounis, Kyriakos
name: Apostolatos, Theocharis A.
name: Kokkotas, Kostas D.
Publisher: name: arXiv
Year: 2024
Subjects: subject: General Relativity and Quantum Cosmology (gr-qc)
subject: High Energy Astrophysical Phenomena (astro-ph.HE)
subject: High Energy Physics - Phenomenology (hep-ph)
subject: High Energy Physics - Theory (hep-th)
subject: FOS: Physical sciences

description: Gravitational radiation reaction, has been one of the fundamental issues in general relativity. Over a span of decades, this process has been analyzed in the adiabatic limit, in order to comprehend how it drives extreme-mass-ratio binaries, that are prime targets for space-borne detectors. It has been shown that spherical orbits around Schwarzschild and Kerr black holes remain spherical (zero eccentricity) under the influence of gravitational radiation reaction. Here, we show that spherical orbits in non-Kerr black holes, that still preserve most of the good qualities and symmetries of Kerr spacetime, can access certain resonances in such a way that an initially spherical inspiral acquires non-zero eccentricity and becomes non-spherical. Therefore, the crossing of resonances under radiation reaction interrupts and even inverts, up to some small radius close to plunge, the process of circularization of orbits. The strength of resonant excitation of eccentricity depends on the initial position and inclination of the integrable extreme-mass-ratio system, as well as the integrability-breaking parameter introduced in the background spacetime that amplifies further the excitation. We find that the harmonics of gravitational waves emitted from these inspirals undergo a frequency modulation as the orbit `metamorphoses' from spherical to non-spherical, due to the effect of resonant eccentricity excitation. The gain that low-amplitude harmonics experience in these oligochromatic EMRIs, due to resonances, may be detectable with future spaceborne detectors and serves as an indicator of non-Kerrness of the background spacetime.
description: 21 pages, 8 figures, Accepted for publication in PRD
A new method to clarify contribution of chiral magnetic effect in small collision system $p^{\uparrow} + A$ involving a transversely polarized proton
Creators: name: Wu, Gui-Zhen
name: Zhang, Zong-Wei
name: Gao, Chen
name: Xu, Yi
name: Deng, Wei-Tian
Publisher: name: arXiv
Year: 2024
Subjects: subject: High Energy Physics - Phenomenology (hep-ph)
subject: Nuclear Theory (nucl-th)
subject: FOS: Physical sciences

description: In this paper, we propose a new experiment method to check contribution of chiral magnetic effect (CME). With experimental data of DIS involving transversely polarized proton, we have calculated the 3-D charge density inside the polarized proton, which is found to have a significant violation to spherical symmetry. Then we have calculated the property of electromagnetic field (E-M field) generated by a single transversely polarized proton ($p^{\uparrow}$). Based on them, the E-M field generated in small collision system $p^{\uparrow}+A$ are studied. We find that the orientation of this E-M field has a significant dependence on the polarization direction of the proton, and the correlator ($Δγ$ ) has also significant dependence on the angle between reaction plane and polarization direction. As background contribution are canceled comparing two collision geometry schemes, only contribution of CME is remained.
description: 5 pages, 8 figures
Hierarchical materials with interconnected pores from capillary suspensions for bone tissue engineering
Creators: name: Nider, Souhaila
name: De Ceulaer, Femke
name: Göksel, Berfu
name: Braem, Annabel
name: Koos, Erin
Publisher: name: arXiv
Year: 2024
Subjects: subject: Soft Condensed Matter (cond-mat.soft)
subject: Materials Science (cond-mat.mtrl-sci)
subject: FOS: Physical sciences

description: The increasing demand for bone grafts due to the aging population has opened new opportunities for the manufacture of porous ceramics to assist in bone reconstruction. In our study, we investigate a new, promising method to manufacture hierarchically porous structures in a straightforward, and tuneable way. It consists of combining the novel technology of capillary suspensions, formed by mixing solid particles and two immiscible liquids, one less than 5 vol%, with freeze casting. We have successfully achieved alumina and $β$-TCP materials with both <2 $μ$m and 20-50 $μ$m as the smallest and largest pore size, respectively. The microstructure exhibits fully open pores and high levels of porosity (>60%). The capillary suspensions' rheological behaviour indicates that silica nano-suspensions as a secondary fluid creates a stronger internal particle network than sucrose for the alumina system. Conversely, the opposite was observed with the $β$-TCP system. These differences were attributed to the change in affinity between the secondary fluids and the solid loading. Our study, both systems has served to deepen the knowledge about the new area of capillary suspensions and proves their use in hierarchical porous scaffolds for bone tissue engineering.
description: SI Included
Emergence of tunable exceptional points in altermagnet-ferromagnet junctions
Creators: name: Reja, Md Afsar
name: Narayan, Awadhesh
Publisher: name: arXiv
Year: 2024
Subjects: subject: Mesoscale and Nanoscale Physics (cond-mat.mes-hall)
subject: FOS: Physical sciences

description: The existence of exceptional points (EPs) ${-}$ where both eigenvalues and eigenvectors converge ${-}$ is a key characteristic of non-Hermitian physics. A newly-discovered class of magnets ${-}$ termed as altermagnets (AMs) ${-}$ are characterized by a net zero magnetization as well as spin-split bands. In this study, we propose the emergence of non-Hermitian physics at AM-ferromagnet (FM) junctions. We discover that such a junction hosts tunable EPs. We demonstrate that the positions of these emergent EPs can be tuned using an external applied magnetic field and show that for a critical value of the applied magnetic field the EPs can annihilate. Notably, the number and position of the EPs crucially depends on the type of AM and its orientation with respect to the FM. Our work puts forth a promising platform of exploration of non-Hermitian physics in an emerging class of magnetic materials.
description: 7 pages, 6 figures