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At least 1,243 records · Page 69

Filtering higher-order datasets

Many complex systems often contain interactions between more than two nodes, known as higher-order interactions, which can change the structure of these systems in significant ways. Researchers often assume that all interactions paint a consistent picture of a higher-order dataset's structure. In contrast, the connection patterns of individuals or entities in empirical systems are often stratified by interaction size. Ignoring this fact can aggregate connection patterns that exist only at certain scales of interaction. To isolate these scale-dependent patterns, we present an approach for analyzing higher-order datasets by filtering interactions by their size. We apply this framework to several empirical datasets from three domains to demonstrate that data practitioners can gain valuable information from this approach.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Uncovering interpretable relationships in high-dimensional scientific data through function preserving projections

Abstract In many fields of science and engineering, we frequently encounter experiments or simulations datasets that describe the behavior of complex systems and uncovering human interpretable patterns between their inputs and outputs via exploratory data analysis is essential for building intuition and facilitating discovery. Often, we resort to 2D embeddings for examining these high-dimensional relationships (e.g. dimensionality reduction). However, most existing embedding methods treat the dimensions as coordinates for samples in a high-dimensional space, which fail to capture the potential functional relationships, and the few methods that do take function into consideration either only focus on linear patterns or produce non-linear embeddings that are hard to interpret. To address these challenges, we proposed function preserving projections (FPP), which construct 2D linear embeddings optimized to reveal interpretable yet potentially non-linear patterns between the domain and the range of a high-dimensional function. The intuition here is that humans are good at understanding potentially non-linear patterns in 2D but unable to interpret non-linear mapping from high-dimensional space to 2D. Therefore, we should restrict the projection to linear but not the pattern we are seeking. Using FPP on real-world datasets, one can obtain fundamentally new insights about high-dimensional relationships in extremely large datasets that could not be processed with existing dimension reduction methods.

97 MATHEMATICS AND COMPUTING↗

Coincident learning for unsupervised anomaly detection of scientific instruments

Abstract Anomaly detection is an important task for complex scientific experiments and other complex systems (e.g. industrial facilities, manufacturing), where failures in a sub-system can lead to lost data, poor performance, or even damage to components. While scientific facilities generate a wealth of data, labeled anomalies may be rare (or even nonexistent), and expensive to acquire. Unsupervised approaches are therefore common and typically search for anomalies either by distance or density of examples in the input feature space (or some associated low-dimensional representation). This paper presents a novel approach called coincident learning for anomaly detection (CoAD), which is specifically designed for multi-modal tasks and identifies anomalies based on coincident behavior across two different slices of the feature space. We define an unsupervised metric, F ^ β , out of analogy to the supervised classification F β statistic. CoAD uses F ^ β to train an anomaly detection algorithm on unlabeled data , based on the expectation that anomalous behavior in one feature slice is coincident with anomalous behavior in the other. The method is illustrated using a synthetic outlier data set and a MNIST-based image data set, and is compared to prior state-of-the-art on two real-world tasks: a metal milling data set and our motivating task of identifying RF station anomalies in a particle accelerator.

43 PARTICLE ACCELERATORS↗

Uncovering obscured phonon dynamics from powder inelastic neutron scattering using machine learning

The study of phonon dynamics is pivotal for understanding material properties, yet it faces challenges due to the irreversible information loss inherent in powder inelastic neutron scattering spectra and the limitations of traditional analysis methods. In this study, we present a machine learning framework designed to reveal obscured phonon dynamics from powder spectra. Using a variational autoencoder, we obtain a disentangled latent representation of spectra and successfully extract force constants for reconstructing phonon dispersions. Notably, our model demonstrates effective applicability to experimental data even when trained exclusively on physics-based simulations. The fine-tuning with experimental spectra further mitigates issues arising from domain shift. Analysis of latent space underscores the model’s versatility and generalizability, affirming its suitability for complex system applications. Furthermore, our framework’s two-stage design is promising for developing a universal pre-trained feature extractor. This approach has the potential to revolutionize neutron measurements of phonon dynamics, offering researchers a potent tool to decipher intricate spectra and gain valuable insights into the intrinsic physics of materials.

domain adaptation↗

Latent Twins

Over the past decade, scientific machine learning has transformed the development of mathematical and computational frameworks for analyzing, modeling, and predicting complex systems. From inverse problems to numerical partial differential equations (PDEs), dynamical systems, and model reduction, these advances have pushed the boundaries of what can be simulated. Yet they have often progressed in parallel, with representation learning and algorithmic solution methods evolving largely as separate pipelines. With Latent Twins, we propose a unifying mathematical framework that creates a hidden surrogate in latent space for the underlying equations. Whereas digital twins mirror physical systems in the digital world, Latent Twins mirror mathematical systems in a learned latent space governed by operators. Through this lens, classical modeling, inversion, model reduction, and operator approximation all emerge as special cases of a single principle. We establish the fundamental approximation properties of Latent Twins for both ordinary differential equations (ODEs) and PDEs and demonstrate the framework across three representative settings: (i) canonical ODEs, capturing diverse dynamical regimes; (ii) a PDE benchmark using the shallow-water equations, contrasting Latent Twin simulations with deep operator network and forecasts with a four-dimensional variational method baseline; and (iii) a challenging real-data geopotential reanalysis dataset, reconstructing and forecasting from sparse, noisy observations. Latent Twins provide a compact, interpretable surrogate for solution operators that evaluate across arbitrary time gaps in a single-shot, while remaining compatible with scientific pipelines such as assimilation, control, and uncertainty quantification. Looking forward, this framework offers scalable, theory-grounded surrogates that bridge data-driven representation learning and classical scientific modeling across disciplines.

Latent Twins↗

From Optimization to Sampling Through Gradient Flows

Optimization and sampling algorithms play a central role in science and engineering as they enable finding optimal predictions, policies, and recommendations, as well as expected and equilibrium states of complex systems. The notion of “optimality” is formalized by the choice of an objective function, while the notion of an “expected” state is specified by a probabilistic model for the distribution of states. Optimizing rugged objective functions and sampling multimodal distributions is computationally challenging, especially in high-dimensional problems. Here, for this reason, many optimization and sampling methods have been developed by researchers working in disparate fields such as Bayesian statistics, molecular dynamics, genetics, quantum chemistry, machine learning, weather forecasting, econometrics, and medical imaging.

Trillos, N. García↗

Kinetics of solid–liquid interface motion in molecular dynamics and phase-field models: crystallization of chromium and silicon

The results of molecular dynamics (MD) simulations of the crystallization process in one-component materials and solid solution alloys reveal a complex temperature dependence of the velocity of the crystal–liquid interface featuring an increase up to a maximum at 10–30% undercooling below the equilibrium melting temperature followed by a gradual decrease of the velocity at deeper levels of undercooling. At the qualitative level, such non-monotonous behaviour of the crystallization front velocity is consistent with the diffusion-controlled crystallization process described by the Wilson–Frenkel model, where the almost linear increase of the interface velocity in the vicinity of melting temperature is defined by the growth of the thermodynamic driving force for the phase transformation, while the decrease in atomic mobility with further increase of the undercooling drives the velocity through the maximum and into a gradual decrease at lower temperatures. At the quantitative level, however, the diffusional model fails to describe the results of MD simulations in the whole range of temperatures with a single set of parameters for some of the model materials. The limited ability of the existing theoretical models to adequately describe the MD results is illustrated in the present work for two materials, chromium and silicon. It is also demonstrated that the MD results can be well described by the solution following from the hodograph equation, previously found from the kinetic phase-field model (kinetic PFM) in the sharp interface limit. The ability of the hodograph equation to describe the predictions of MD simulation in the whole range of temperatures is related to the introduction of slow (phase field) and fast (gradient flow) variables into the original kinetic PFM from which the hodograph equation is obtained. The slow phase-field variable is responsible for the description of data at small undercoolings and the fast gradient flow variable accounts for local non-equilibrium effects at high undercoolings. The introduction of these two types of variables makes the solution of the hodograph equation sufficiently flexible for a reliable description of all nonlinearities of the kinetic curves predicted in MD simulations of Cr and Si. This article is part of the theme issue ‘Transport phenomena in complex systems (part 1)’.

Science & Technology - Other Topics↗

Accurate and complete genomes from metagenomes

Genomes are an integral component of the biological information about an organism; thus, the more complete the genome, the more informative it is. Historically, bacterial and archaeal genomes were reconstructed from pure (monoclonal) cultures, and the first reported sequences were manually curated to completion. However, the bottleneck imposed by the requirement for isolates precluded genomic insights for the vast majority of microbial life. Shotgun sequencing of microbial communities, referred to initially as community genomics and subsequently as genome-resolved metagenomics, can circumvent this limitation by obtaining metagenome-assembled genomes (MAGs); but gaps, local assembly errors, chimeras, and contamination by fragments from other genomes limit the value of these genomes. Here, we discuss genome curation to improve and, in some cases, achieve complete (circularized, no gaps) MAGs (CMAGs). To date, few CMAGs have been generated, although notably some are from very complex systems such as soil and sediment. Through analysis of about 7000 published complete bacterial isolate genomes, we verify the value of cumulative GC skew in combination with other metrics to establish bacterial genome sequence accuracy. The analysis of cumulative GC skew identified potential misassemblies in some reference genomes of isolated bacteria and the repeat sequences that likely gave rise to them. We discuss methods that could be implemented in bioinformatic approaches for curation to ensure that metabolic and evolutionary analyses can be based on very high-quality genomes.

59 BASIC BIOLOGICAL SCIENCES↗

Simulating Heisenberg interactions in the Ising model with strong drive fields

The time evolution of an Ising model with large driving fields over discrete time intervals is shown to be reproduced by an effective XXZ-Heisenberg model at leading order in the inverse field strength. For specific orientations of the drive field, the dynamics of the XXX-Heisenberg model is reproduced. Finally, these approximate equivalences, valid above a critical driving field strength set by dynamical phase transitions in the Ising model, are expected to enable quantum devices that natively evolve qubits according to the Ising model to simulate more complex systems.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Coherent band-edge oscillations and dynamic longitudinal-optical phonon mode splitting as evidence for polarons in perovskites

The coherence of collective modes, such as phonons and polarons, and their modulation of electronic states is long sought in complex systems, which is a crosscutting issue in photovoltaics and quantum electronics. In photovoltaic cells and lasers based on metal halide perovskites, the presence of polarons, i.e., photocarriers dressed by the macroscopic motion of charged lattice, assisted by terahertz (THz) longitudinal-optical (LO) phonons, has been intensely studied yet is still debated. This may be key for explaining the remarkable properties of the perovskite materials, e.g., defect tolerance, long charge lifetimes, and diffusion lengths. In this work we use the intense single-cycle THz pulse with peak electric field up to E THz = 1000 kV/cm to drive coherent polaronic band-edge oscillations at room temperature in CH 3 NH 3 PbI 3 (MAPbI 3 ). We reveal the oscillatory behavior is dominated by a specific quantized lattice vibration mode at $ω$ LO ~ 4 THz, which is both dipole and momentum forbidden. THz-driven coherent polaron dynamics exhibits distinguishing features: room temperature coherent oscillations at ω LO longer than 1 ps in both single crystals and thin films, mode-selective modulation of different band-edge states assisted by electron-phonon interaction, and dynamic mode splitting at low temperature due to entropy and anharmonicity of organic cations. Our results demonstrate intense THz-driven coherent band-edge modulation is a powerful probe of electron-lattice coupling phenomena and polaronic quantum control in perovskites.

36 MATERIALS SCIENCE↗

Unification of nonequilibrium molecular dynamics and the mode-resolved phonon Boltzmann equation for thermal transport simulations

Nano-size confinement induces many intriguing non-Fourier heat conduction phenomena, such as nonlinear temperature gradients, temperature jumps near the contacts, and size-dependent thermal conductivity. Over the past decades, these effects have been studied and interpreted by nonequilibrium molecular dynamics (NEMD) and phonon Boltzmann transport equation (BTE) simulations separately, but no theory that unifies these two methods has ever been established. In this work, we unify these methods using a quantitative mode-level comparison and demonstrate that they are equivalent for various thermostats. We show that different thermostats result in different non-Fourier thermal transport characteristics due to the different mode-level phonon excitations inside the thermostats, which explains the different size-dependent thermal conductivities calculated using different reservoirs, even though they give the same bulk thermal conductivity. Specifically, the Langevin thermostat behaves like a thermalizing boundary in phonon BTE and provides mode-level thermal-equilibrium phonon outlets, while the Nose-Hoover chain thermostat and velocity rescaling method behave like biased reservoirs, which provide a spatially uniform heat generation and mode-level nonequilibrium phonon outlets. These findings explain why different experimental measurement methods can yield different size-dependent thermal conductivity. They also indicate that the thermal conductivity of materials can be tuned for various applications by specifically designing thermostats. Finally, the unification of NEMD and phonon BTE will largely facilitate the study of thermal transport in complex systems in the future by, e.g., replacing computationally unaffordable first-principles NEMD simulations with computationally less expensive spectral BTE simulations.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Ultrafast light-induced shear strain probed by time-resolved x-ray diffraction: Multiferroic BiFeO 3 as a case study

Enabling the light control of complex systems on ultrashort timescales gives rise to rich physics with promising applications. Although crucial, the quantitative determination of both the longitudinal and the shear photoinduced strains still remains challenging. Here, by scrutinizing asymmetric Bragg peaks pairs (±h01) in BiFeO 3 using picosecond time-resolved x-ray diffraction experiments, we simultaneously determine the longitudinal and shear strains. Importantly, we reveal a difference in the dynamical response of the longitudinal strain with respect to the shear one due to an interplay of quasilongitudinal and quasitransverse acoustic modes, well reproduced by our model. Lastly, we show that the relative amplitude of those strains can be explained only if both thermal and nonthermal processes contribute to the acoustic phonon photogeneration process.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Model emulation and closure tests for (3+1)D relativistic heavy-ion collisions

In nuclear and particle physics, reconciling sophisticated simulations with experimental data is vital for understanding complex systems like the Quark Gluon Plasma (QGP) generated in heavy ion collisions. However, computational demands pose challenges, motivating using Gaussian Process emulators for efficient parameter extraction via Bayesian calibration. We conduct a comparative analysis of Gaussian Process emulators in heavy-ion physics to identify the most adept emulator for parameter extraction with minimal uncertainty. Furthermore, our study contributes to advancing computational techniques in heavy-ion physics, enhancing our ability to interpret experimental data and understand QGP properties.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Embedding hard physical constraints in neural network coarse-graining of three-dimensional turbulence

In recent years, deep learning approaches have shown much promise in modeling complex systems in the physical sciences. A major challenge in deep learning of partial differential equations is enforcing physical constraints and boundary conditions. In this work, we propose a general framework to directly embed the notion of an incompressible fluid into convolutional neural networks, and apply this to coarse-graining of turbulent flow. These physics-embedded neural networks leverage interpretable strategies from numerical methods and computational fluid dynamics to enforce physical laws and boundary conditions by taking advantage the mathematical properties of the underlying equations. Here, we demonstrate results on three-dimensional fully developed turbulence, showing that this technique drastically improves local conservation of mass, without sacrificing performance according to several other metrics characterizing the fluid flow.

97 MATHEMATICS AND COMPUTING↗

Discrete Time-Crystalline Order Enabled by Quantum Many-Body Scars: Entanglement Steering via Periodic Driving

The control of many-body quantum dynamics in complex systems is a key challenge in the quest to reliably produce and manipulate large-scale quantum entangled states. Recently, quench experiments in Rydberg atom arrays [Bluvstein et al. Science 371, 1355 (2021)] demonstrated that coherent revivals associated with quantum many-body scars can be stabilized by periodic driving, generating stable subharmonic responses over a wide parameter regime. We analyze a simple, related model where these phenomena originate from spatiotemporal ordering in an effective Floquet unitary, corresponding to discrete time-crystalline behavior in a prethermal regime. Unlike conventional discrete time crystals, the subharmonic response exists only for Néel-like initial states, associated with quantum scars. We predict robustness to perturbations and identify emergent timescales that could be observed in future experiments. Our results suggest a route to controlling entanglement in interacting quantum systems by combining periodic driving with many-body scars.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Raman Interferometry between Autoionizing States to Probe Ultrafast Wave-Packet Dynamics with High Spectral Resolution

Photoelectron interferometry with femtosecond and attosecond light pulses is a powerful probe of the fast electron wave-packet dynamics, albeit it has practical limitations on the energy resolution. We show that one can simultaneously obtain both high temporal and spectral resolution by stimulating Raman interferences with one light pulse and monitoring the modification of the electron yield in a separate step. Applying this spectroscopic approach to the autoionizing states of argon, we experimentally resolved its electronic composition and time evolution in exquisite detail. Theoretical calculations show remarkable agreement with the observations and shed light on the light-matter interaction parameters. Using appropriate Raman probing and delayed detection steps, this technique enables highly sensitive probing and control of electron dynamics in complex systems.

74 ATOMIC AND MOLECULAR PHYSICS↗

Coexistence of Interacting Charge Density Waves in a Layered Semiconductor

Coexisting orders are key features of strongly correlated materials and underlie many intriguing phenomena from unconventional superconductivity to topological orders. Here, we report the coexistence of two interacting charge-density-wave (CDW) orders in EuTe 4 , a layered crystal that has drawn considerable attention owing to its anomalous thermal hysteresis and a semiconducting CDW state despite the absence of perfect FS nesting. By accessing unoccupied conduction bands with time- and angle-resolved photoemission measurements, we find that mono- and bi-layers of Te in the unit cell host different CDWs that are associated with distinct energy gaps. The two gaps display dichotomous evolutions following photoexcitation, where the larger bilayer CDW gap exhibits less renormalization and faster recovery. Surprisingly, the CDW in the Te monolayer displays an additional momentum-dependent gap renormalization that cannot be captured by density-functional theory calculations. This phenomenon is attributed to interlayer interactions between the two CDW orders, which account for the semiconducting nature of the equilibrium state. Finally, our findings not only offer microscopic insights into the correlated ground state of EuTe 4 but also provide a general non-equilibrium approach to understand coexisting, layer-dependent orders in a complex system.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Plasmon coupling in topological insulator multilayers

Topological insulators (TIs) house two-dimensional Dirac plasmons on their surfaces. In TI thin films, plasmons on the top and bottom surfaces couple electrostatically, giving rise to an acoustic and an optical plasmon mode. By extension, a superlattice comprising TI layers and trivially-insulating layers could house multiple complex plasmon modes which could be used to create a new type of Dirac metamaterial. In this paper, we synthesize TI superlattices, fabricate them into stripe arrays, characterize their optical and plasmonic properties, and model the samples using transfer matrices. Furthermore, we excite plasmon modes that couple to the phonons in the superlattice, resulting in hybrid plasmon phonon polaritons. These modes are modeled using an analytical Fano resonance model and the extracted resonant positions are reproduced by transfer matrix modeling. We also excite an epsilon-near-zero mode in the top dielectric material (Bi 0.5 In 0.5 ) 2 Se 3 . Understanding the behavior of the polariton modes in this complex system will lend insight into the many-body interaction in low-dimensional systems.

36 MATERIALS SCIENCE↗