Biological Physics
Engineering quantum optical responses of microtubules through tryptophan-network simulations and ultraviolet spectroscopy
Lea Gassab and Travis J. A. Craddock
Microtubules host dense ultraviolet-absorbing aromatic networks, suggesting an opportunity to engineer their optical response for biotechnology. Here we assess the feasibility of tuning microtubule fluorescence by combining an excitonic radiative-coupling model with molecular-dynamics-derived microtubule-like assemblies and steady-state absorbance and fluorescence measurements in microplate geometries. Simulations quantify how positional and orientational fluctuations reshape radiative rates and
quantum yield, and predict how perturbing the tryptophan network by removing a specific site, adding an extra tryptophan at candidate binding pockets, or using mixed modification fractions can modulate emission. Experiments on porcine tubulin dimers and taxol-stabilized microtubules support these trends: polymerization enhances microtubule
quantum yield at 280 nm and yields bounded changes at 295 nm due to scattering, while added L-tryptophan reproducibly quenches microtubules at both wavelengths. Together, theory and experiment provide evidence for chemically addressable tuning of microtubule
quantum yield and motivate design rules for engineered microtubule photonics.
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Instrumentation and Detectors
Toward Neutrino and Dark Matter Detection with Ancient Minerals: TEM Study of Heavy-Ion Tracks in Olivine
Andrew Calabrese-Day, Emilie LaVoie-Ingram, Kathryn Ream et al. (+5 more)
Solar,
supernova, and atmospheric
neutrinos, and possibly weakly interacting massive particle (WIMP) dark matter, have been interacting in the Earth beneath our feet for billions of years. The ”paleo-detector” technique seeks to detect and characterize the induced crystalline defects from these events, in particular from energetic
nuclear recoils, which in some minerals can be preserved on these timescales. Such defects can manifest as
nuclear recoil tracks, on the order of a few nanometers wide and extending up to hundreds of microns in length, which can be detected with nanoscale-resolution microscopy. In order to test the feasibility of the paleo-detector technique and to study the formation and morphology of track defects in promising mineral candidates like olivine, we use ion irradiation to artificially implant tracks to effectively mimic astrophysical particle interactions. We present a study of heavy-ion track width as a function of depth, which we relate to ion energy, in an olivine
crystal irradiated with 15 MeV Au$^{+5}$ using scanning transmission electron microscopy (STEM). Unlike previous studies, which measure tracks at the surface of the irradiated sample, we instead take measurements at various target depths via focused ion-beam sectioning of the irradiated sample. No etching techniques are used to enhance the tracks. In addition, we provide a comparison to predictions from simulations using SRIM software and previous results with a variety of ion species and energies. Notably, we find that a significant change in track continuity across the energy range studied (0.4-12.9 MeV) is indicative of the transition between electronic and
nuclear stopping power dominance, consistent with the simulations' predictions. Overall, the tracks produced in olivine indicate that this mineral is an attractive candidate for paleo-detection, with robust track creation at the MeV scale.
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All authors Andrew Calabrese-Day, Emilie LaVoie-Ingram, Kathryn Ream, Hannah Ross, Joshua Spitz, Patrick Stengel, Kai Sun, Alexander Takla
Applied Physics · Cross-listed from cs.CV
Data-Driven Automated Identification of Optimal Feature-Representative Images in Infrared Thermography Using Statistical and Morphological Metrics
Harutyun Yagdjian and Martin Gurka
Infrared thermography (IRT) is a widely used non-destructive testing technique for detecting structural features such as subsurface defects. However, most IRT post-processing methods generate image sequences in which defect visibility varies strongly across time, frequency, or coefficient/index domains, making the identification of defect-representative images a critical challenge. Conventional evaluation metrics, such as the signal-to-noise ratio (SNR) or the Tanimoto criterion, often require prior knowledge of defect locations or defect-free reference regions, limiting their suitability for automated and unsupervised analysis. In this work, a data-driven methodology is proposed to identify images within IRT
datasets that are most likely to contain and represent structural features, particularly anomalies and defects, without requiring prior spatial information. The approach is based on three complementary metrics: the Homogeneity Index of Mixture (HI), which quantifies statistical heterogeneity via deviations of local intensity distributions from a global reference distribution; a Representative Elementary Area (REA), derived from a Minkowski-functional adaptation of the Representative Elementary Volume concept to two-dimensional images; and a geometrical-topological Total Variation Energy (TVE) index, also based on two-dimensional Minkowski functionals, designed to improve sensitivity to localized anomalies. The framework is validated experimentally using pulse-heated IRT data from a carbon fiber-reinforced
polymer (CFRP) plate containing six artificial defects at depths between 0.135 mm and 0.810 mm, and is further supported by one-dimensional N-layer thermal model simulations. The results demonstrate robust and unbiased ranking of image sequences and provide a reliable basis for automated defect-oriented image selection in IRT.
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Physics Education
Instructor Framing and Incentives Shape Physics Students' Engagement and Learning Gains from an Inquiry-Based Electrostatics Tutorial on the Method of Images
Jaya Shivangani Kashyap, Robert P. Devaty and Chandralekha Singh
The method of images (MoI) is a valuable technique for solving certain electrostatic boundary value problems consisting of charge density near conductor(s). We developed and validated an inquiry-based tutorial on MoI to help students learn to identify the problems related to the concept. We implemented the inquiry-based tutorial accompanied by pretest and posttest, across three instructors' classes to evaluate student learning. We also conducted think-aloud interviews with advanced physics students, which helped us gain insights into their problem-solving strategies, evaluate their understanding developed through the tutorial and make necessary refinements to the MoI tutorial. The study identified common student difficulties, which were subsequently integrated into the inquiry-based tutorial as a guide to provide support to students. We found that advanced students have common difficulties related to physics concepts similar to those found in introductory physics courses. The performance difference in the pretest administered after lecture-based instruction and the posttest administered after working through the tutorial reflects students' ability to apply what they learned from the inquiry-based tutorial compared to traditional lecture. Another important and unanticipated finding reveals how instructor's framing about inquiry-based instructional tasks can have a significant impact on student motivation, engagement, and performance. Overall, this iterative multi-year design-based comparative research with mixed-method triangulation provides valuable insights on the challenges involved in such studies that educators and researchers alike can greatly benefit from.
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Data Analysis and Statistics
New Deep Learning Data Analysis Method for PROSPECT using GAPE: Genetic Algorithm Powered Evolution
M. Adriamirado, A. B. Balantekin, C. Bass et al. (+40 more)
We propose a genetic
algorithm powered
evolution (GAPE) method to create deep learning solutions for energy and position estimation for reactor antineutrino interactions in the Precision Reactor Oscillation and Spectrum Experiment (PROSPECT) at the highly enriched High Flux Isotope Reactor (HFIR) at Oak Ridge National Laboratory. We also apply GAPE to create classification models to distinguish signatures of inverse beta decay (IBD) interactions of reactor antineutrinos from common background types. The GAPE method can also be adopted for optimization of other types of problems that utilize machine learning (ML) models for particle physics applications. When applied in the PROSPECT context, we find that the models selected by GAPE can, in some cases, outperform the traditional models previously used for PROSPECT data analysis. In particular, when benchmarked against conventional PROSPECT
neutrino identification pathways using the same underlying information, the classifier offers the promise of improving the signal-to-background ratio by nearly 2.8 times. Performance biases uncovered during initial IBD classifier validation were primarily caused by differences in time-dependent response between background and signal training
datasets. Biases were effectively mitigated through a data-period-specific training regimen, offering a pathway towards realizing an unbiased IBD signal classifier for future reactor
neutrino datasets.
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All authors M. Adriamirado, A. B. Balantekin, C. Bass, O. Benevides Rodrigues, E. P. Bernard, N. S. Bowden, C. D. Bryan, T. Classen, A. J. Conant, N. Craft, A. Delgado, G. Deichert, M. J. Dolinski, A. Erickson, M. Fuller, A. Galindo-Uribarri, S. Ghosh, S. Gokhale, C. Grant, S. Hans, A. B. Hansell, T. E. Haugen, K. M. Heeger, B. Heffron, A. Irani, J. Koblanski, C. E. Lane, B. R. Littlejohn, A. Lozano Sanchez, J. Maricic, F. Machado, M. P. Mendenhall, A. M. Meyer, R. Milincic, P. E. Mueller, H. P. Mumm, R. Neilson, C. Roca, R. Rosero, D. Venegas-Vargas, J. Wilhelmi, M. Yeh, X. Zhang
Chemical Physics · Cross-listed from astro-ph.EP
The Fate of Frozen Carbonated Water at Europa-like Conditions
Swaroop Chandra, William T.P. Denman and Michael E. Brown
We present the results of experiments probing the retention of CO2 in crystalline water ice, frozen sodium chloride (NaCl) brines, and flash-frozen carbonated water using diffuse reflectance infrared spectroscopy. Characteristic absorptions alluding to the formation of clathrate hydrates in crystalline ices and frozen brines are observed. NaCl in frozen brines does not affect qualitatively affect the formation of clathrate hydrates. Generation and stability of clathrates in crystalline ice transiently subjected to pressure-temperature (P-T) conditions in the stability region is observed, despite conditions being unviable at the onset of freezing. Retention of CO2 in flash-frozen carbonated water is observed to be dependent on the temperature of the substrate during freezing. The state of CO2 retained in the resulting ices differs from clathrate hydrates, as inferred from the respective infrared spectra. Both mechanisms of CO2 retention are stable up to 140 K and under evacuated conditions. In the context of Europa, the P-T states traversed by the samples plausibly represent the typical conditions around endogenous CO2 if it is indeed transported from the subsurface ocean to the surface while being retained in ice/frozen brines and/or
liquid emerging on the surface. However, the absorptions of CO2 in the laboratory infrared spectra do not match those detected on the leading side of Europa by the NIRSpec instrument on board JWST. Therefore, it is unlikely that the endogenous CO2 observed at the surface of Europa is sourced directly from the ocean, unless additional processes affect the observed bands of CO2 on Europa.
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Optics · Cross-listed from nlin.PS
Homoclinic and heteroclinic solutions of the nonlinear Schrödinger equation with a complex Wadati potential
Sathyanarayanan Chandramouli, Patrick Sprenger and Mark A. Hoefer
Stationary solutions asymptoting to nonlinear plane waves of the nonlinear Schrödinger equation with a PT-symmetric, complex linear potential are characterized. The potential includes both a spatially varying gain-loss profile and a repulsive real part, generated by a Wadati potential function,that support the existence of homoclinic and heteroclinic solutions that asymptote to the same or different, respectively, nonlinear plane waves in the far field. Asymptotic analysis and numerical simulations are used to examine solution existence, bifurcations, and structure. Such solutions play an important role in resonant nonlinear wave generation of dispersive media with localized gain and loss.
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Computational Physics · Cross-listed from cs.SI
Hierarchical Community Detection in Bipartite Networks
Tania Ghosh and Kevin E. Bassler
Many bipartite networks exhibit hierarchical community structure, but existing community detection methods are not well-suited for detecting hierarchy. They also do not effectively handle weighted bipartite networks. In this work, we introduce a novel modularity-based objective function, called the generalized bipartite modularity density, Qbg, specifically designed for hierarchical community detection in bipartite systems. The framework incorporates a tunable resolution parameter that enables systematic exploration of community structure across multiple scales. It leverages resolution-limit behavior in bipartite networks as a tool to uncover hierarchical organization without projecting the network or altering its intrinsic bipartite
topology. We evaluate the method using a hierarchical synthetic bipartite
benchmark and apply it to two empirical networks. In all cases, Qbg recovers established mesoscale structure while revealing additional hierarchical and fine-scale organization beyond that detected by conventional bipartite approaches. These results establish Qbg as a flexible, interpretable, and resolution-aware framework for hierarchical community detection in bipartite networks.
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Instrumentation and Detectors · Cross-listed from astro-ph.IM
Development of the New Optical Sensor for IceCube-Gen2
Delaney Butterfield and Chris Wendt
A new digital optical module (DOM) has been developed for the proposed expansion to the IceCube detector at the South Pole, IceCube-Gen2. The "Gen2-DOM" has 4 times the integrated
photon sensitivity of the current IceCube DOMs and has built off the design features of the IceCube Upgrade modules. The Gen2-DOM has up to 18 4" photomultiplier tubes (PMTs) in a borosilicate glass pressure vessel, arranged in a uniform 4$\pi$ angular distribution. The mechanical design has been optimized to fit into a reduced borehole diameter which, in turn, will reduce drilling costs during installation. Each PMT has a dedicated readout board, designed to increase sensitivity to high-energy events aligned with the science goals of IceCube-Gen2. Internal storage enables multi-level triggering schemes with reduced overall flow of data on the long cables. Twelve prototypes of the Gen2-DOM will be deployed in the IceCube Upgrade in the 2025-2026 austral summer. This article will focus on the current status of design development and initial performance testing results.
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Medical Physics · Cross-listed from eess.IV
PSIRNet: Deep Learning-based Free-breathing Rapid Acquisition Late Enhancement Imaging
Arda Atalik, Hui Xue, Rhodri H. Davies et al. (+4 more)
Purpose: To develop and evaluate a deep learning (DL) method for free-breathing phase-sensitive inversion recovery (PSIR) late gadolinium enhancement (LGE) cardiac MRI that produces diagnostic-quality images from a single acquisition over two heartbeats, eliminating the need for 8 to 24 motion-corrected (MOCO) signal averages. Materials and Methods: Raw data comprising 800,653 slices from 55,917 patients, acquired on 1.5T and 3T scanners across multiple sites from 2016 to 2024, were used in this retrospective study. Data were split by patient: 640,000 slices (42,822 patients) for training and the remainder for validation and testing, without overlap. The training and testing data were from different institutions. PSIRNet, a physics-guided DL network with 845 million parameters, was trained end-to-end to reconstruct PSIR images with surface coil correction from a single interleaved IR/PD acquisition over two heartbeats. Reconstruction quality was evaluated using SSIM, PSNR, and NRMSE against MOCO PSIR references. Two expert cardiologists performed an independent qualitative assessment, scoring image quality on a 5-point Likert scale across bright blood, dark blood, and wideband LGE variants. Paired superiority and equivalence (margin = 0.25 Likert points) were tested using exact Wilcoxon signed-rank tests at a significance level of 0.05 using R version 4.5.2. Results: Both readers rated single-average PSIRNet reconstructions superior to MOCO PSIR for dark blood LGE (conservative P = .002); for bright blood and wideband, one reader rated it superior and the other confirmed equivalence (all P < .001). Inference required approximately 100 msec per slice versus more than 5 sec for MOCO PSIR. Conclusion: PSIRNet produces diagnostic-quality free-breathing PSIR LGE images from a single acquisition, enabling 8- to 24-fold reduction in acquisition time.
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All authors Arda Atalik, Hui Xue, Rhodri H. Davies, Thomas A. Treibel, Daniel K. Sodickson, Michael S. Hansen, Peter Kellman
Computational Physics · Cross-listed from cond-mat.mtrl-sci
Including sample shape in micromagnetics with 3D periodic boundary conditions
Frederik Laust Durhuus, Andrea Roberto Insinga and Rasmus Bjørk
Periodic boundary conditions (PBCs) for computing
magnetic fields in repeating
magnetic structures, e.g. in micromagnetic simulations, are typically imposed using the quasi periodic macrogeometry approach, where many copies of the simulated domain are introduced. This can be computationally problematic, especially if the simulated domain is incommensurate with the desired sample shape. In this work, we present a formal proof that for sufficiently large
magnetic samples, only the average magnetisation gives non-negligible shape effects. Using this insight, we develop a simple, computationally efficient modification of existing implementations which incorporates shape effects in PBC methods.
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Atmospheric and Oceanic Physics
CERBERUS: A Three-Headed Decoder for Vertical Cloud Profiles
Emily K. deJong, Nipun Gunawardena, Kevin Smalley et al. (+2 more)
Atmospheric clouds exhibit complex three-dimensional structure and microphysical details that are poorly constrained by the predominantly two-dimensional satellite observations available at global scales. This mismatch complicates data-driven learning and evaluation of cloud processes in weather and
climate models, contributing to ongoing uncertainty in atmospheric physics. We introduce CERBERUS, a probabilistic inference framework for generating vertical radar reflectivity profiles from geostationary satellite brightness temperatures, near-surface meteorological variables, and temporal context. CERBERUS employs a three-headed encoder-decoder architecture to predict a zero-inflated (ZI) vertically-resolved distribution of radar reflectivity. Trained and evaluated using ground-based Ka-band radar observations at the ARM Southern Great Plains site, CERBERUS recovers coherent structures across cloud regimes, generalizes to withheld test periods, and provides uncertainty estimates that reflect physical ambiguity, particularly in multilayer and dynamically complex clouds. These results demonstrate the value of distribution-based learning targets for bridging observational scales, introducing a path toward model-relevant synthetic observations of clouds.
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All authors Emily K. deJong, Nipun Gunawardena, Kevin Smalley, Hassan Beydoun, Peter Caldwell
Optics
Unlocking the O-Band Coherent Transmission: high-power, broadband soliton microcomb
Dmitrii Stoliarov, Nikolay G. Pavlov, Aleksandr Donodin et al. (+15 more)
The O-band (1260-1360 nm), located near the minimum chromatic dispersion of standard single-mode fiber, is an important transmission window for short-reach data-center interconnects. Its broader use is limited by the availability of scalable multi-wavelength, high-power and low-noise light sources. Here we demonstrate a high-power O-band
soliton microcomb architecture combining an 834 GHz self-injection-locked (SIL) Si3N4 microcomb spanning 1050-1650 nm with a single-stage bismuth-doped phosphosilicate fiber amplifier. The system delivers > 0 dBm per carrier for 21 O-band comb lines over a 100 nm bandwidth, exhibiting low-noise operation and a 5 dB variation in amplifier gain. We validate the amplified source in a 25-km coherent WDM transmission experiment using 32-GBd dual-polarisation 64-QAM. Comb carriers spanning the O-band are characterised under simultaneous WDM loading, yielding an aggregate GMI-estimated throughput of 7.23 Tb/s and a post-FEC throughput of 6.94 Tb/s. This approach establishes a practical route towards broadband, high-power O-band microcomb sources for multi-terabit optical interconnects.
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All authors Dmitrii Stoliarov, Nikolay G. Pavlov, Aleksandr Donodin, Daniel J. Elson, Vitaly Mikhailov, Jiawei Luo, Sergey Koptyaev, Robert Emmerich, Ruben S. Luis, Hideaki Furukawa, Colja Schubert, Ronald Freund, Yuta Wakayama, Takehiro Tsuritani, David J.DiGiovanni, John D.Jost, Maxim Karpov, Sergei K. Turitsyn
Chemical Physics
Cryogenic hydrogen embrittlement of 316plus (EN 1.4420) stainless steel at 77 K and 20 K
W. Li, A. Zafra, L. Armendariz et al. (+4 more)
This paper presents the first experimental characterisation of combined hydrogen-temperature effects in 316plus (EN 1.4420), a new austenitic stainless steel for
liquid hydrogen (LH2) storage. Uniaxial tensile tests were conducted at room temperature (RT), 77 K and 20 K on uncharged and hydrogen-precharged specimens, complemented by fractography and EBSD-based quantification of strain-induced martensite (SIM). 316plus exhibited cryogenic strengthening at 77 K and 20 K by enhanced SIM formation. Hydrogen did not influence strength at RT or 77 K and caused a modest decrease (~10%) at 20 K, keeping 316plus at the upper bound of cryogenic strength for 316L. The presence of hydrogen resulted in significant reductions in ductility at all temperatures, being most severe at 77 and 20K (~40-50%). Hydrogen suppressed SIM at 20 K, but SIM fraction did not correlate with ductility reduction. Despite the combined effect of temperature and hydrogen, 316plus retained notable ductility (reduction in area ~30%).
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All authors W. Li, A. Zafra, L. Armendariz, Z. Wang, W. Bailey, E. Martinez-Pañeda, S. Afshan
Chemical Physics
Active Learning for Generalizable Detonation Performance Prediction of Energetic Materials
R. Seaton Ullberg, Megan C. Davis, Jeremy N. Schroeder et al. (+5 more)
The discovery of new energetic materials is critical for advancing technologies from defense to private industry. However, experimental approaches remain slow and expensive while computational alternatives require accurate material property inputs that are often costly to obtain, limiting their ability to efficiently predict detonation performance across a vast chemical space. We address this challenge through an active learning strategy that integrates density functional theory calculations, thermochemical modeling, message-passing neural networks, and
Bayesian optimization. The resulting high-throughput workflow iteratively expands the training
dataset by selecting new molecules in a targeted manner that balances the exploration of broad chemical space with the exploitation of promising high-performing candidates. This approach yields the largest publicly available database of potential CHNO explosives drawn from an initial pool of more than 70 billion candidates and a generalizable surrogate model capable of accurately predicting detonation performance (R$^2$ > 0.98). Feature importance analysis on this largest-to-date
dataset reveals that oxygen balance is the dominant driver of detonation performance, complemented by contributions from local electronic structure, density, and the presence of specific functional groups. Cheminformatics analysis highlights how energetic materials with similar performance metrics tend to cluster in distinct chemical spaces offering a clearer direction for future synthesis studies. Together, the surrogate model, database, and resulting chemical insights provide a valuable foundation for high-throughput screening and targeted discovery of new energetic materials spanning diverse and previously unexplored regions of chemical space.
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All authors R. Seaton Ullberg, Megan C. Davis, Jeremy N. Schroeder, Andrew H. Salij, M. J. Cawkwell, Christopher J. Snyder, Wilton J. M. Kort-Kamp, Ivana Matanovic
Applied Physics · Cross-listed from quant-ph
Frequency resolved optical gating using parametric amplification for characterizing ultrafast temporally multimode squeezed states
Elina Sendonaris, Thomas Zacharias, Robert Gray et al. (+2 more)
Temporally multimode squeezed states have been a topic of recent interest due to their applications in
quantum communication, information processing, and sensing. Characterizing the mode shapes is crucial for effectively manipulating these states, but current mode shape and state characterization techniques necessitate constraining assumptions and complicated experimental setups. Here, we propose a characterization technique that simultaneously recovers the complex temporal mode shapes and quadrature variances of ultrafast multimode squeezed states based on frequency resolved optical gating (FROG) using an optical parametric amplifier (OPA). FROG is a promising tool for
quantum state characterization due to its flexibility of implementation and high temporal resolution. Using an OPA as the nonlinear process in FROG has the benefit of amplifying weak
quantum states to a detectable level while preserving
quantum information. Numerical simulations demonstrate the recovery of the mode shapes and levels of squeezing and anti-squeezing of ultrafast multimode squeezed states. This scheme offers a practical experimental approach to measuring arbitrary temporal mode shapes and characterizing large-scale multimode ultrafast Gaussian
quantum states.
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All authors Elina Sendonaris, Thomas Zacharias, Robert Gray, James Williams, Alireza Marandi
Atomic Physics · Cross-listed from cond-mat.quant-gas
Immiscible to miscible quenching instabilities in two-dimensional binary Bose-Einstein condensates
Lauro Tomio, S. Sabari, Arnaldo Gammal et al. (+1 more)
Immiscible to miscible quenching transitions (IMQT) in homogeneous Bose-Einstein condensate are investigated, considering rubidium isotopes $^{85}$Rb and $^{87}$Rb confined in a two-dimensional (2D) circular box, under two different initial configurations. These IMQT instabilities, triggered by sudden reductions in the two-body interspecies scattering length $a_{12}$, are explored under two distinct initialconditions, highlighting the critical role of nonlinear dynamics in their
evolution. The numerical simulations indicate that the instability dynamics are primarily driven by the production of large
vortices and the propagation of sound waves (
phonons), with sound wave excitations prevailing in the long-term
evolution. The compressible and incompressible parts of the kinetic energy spectra, in terms of the wave number $k$, are confronted with the classical Kolmogorov scaling, $k^{-5/3}$ for
turbulence, which is observed in the onset of instabilities. Before reaching the ultraviolet dissipation region at small scales, the IMQT spectra exhibit a bottleneck effect, indicating a clear departure from classical scaling behavior. In the time asymptotic miscible regime, it is observed that the vorticity and sound-wave production remain practically stable. In this regime, for both cases investigated, a linear relation is also recognized between the miscibility parameter and the initial IMQT configuration.
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All authors Lauro Tomio, S. Sabari, Arnaldo Gammal, R. K. Kumar