bluuebunny/crossref_metadata_2025 huggingface dataset:
Potential for Biodiversity in Shared Residential Yards
Authors: Livne Havi , Gruntman Michal , Blumenfeld Lieberthal Efrat
Published: November 2024

In urban environments, attention has traditionally been paid to public open spaces. However, private open spaces constitute a significant percentage of the urban area and can thus play a significant role in enhancing biological diversity and facilitating direct interactions between humans and nature within urban settings. According to the 2018 European Union report, 46% of homeowners across Europe live in apartment buildings and yet, most studies that examine the effect of private open spaces on biodiversity focus primarily on yards of single-family housing. The objective of this study is to examine the biodiversity potential offered by shared residential yards focusing exclusively on wild plant species, with the aim of offering planning guidelines that address both the management practices of these lot spaces and their spatial arrangement and qualities. The study was conducted in the city of Givatayim, Israel, in shared residential yards. The basic units (lots and buildings on them) in the city were delineated using a novel approach through a separate characterization of lot sizes and building types, as well as their combination. This process resulted in typologies that cover all residential fabric in the city, allowing systematic sampling. In the spring of 2022, plant surveys were conducted in 56 randomly chosen yards. In these lots, potential open area was measured, and the level of non-maintenance (neglection) was also rated. 74 species of wild plants were found, representing a quarter of all wild plant species in the city. Our results show the combined positive effect of available open space and levels of non-maintenance in these yards on the richness and diversity of wild species. This study highlights the substantial area occupied by residential yards in the city and its role in maintaining biodiversity in urban environments. This study indicates the importance of considering these aspects in architectural and management policies in cities.
Inhibition of Myoglobin Oxidation by Food Grade Botanical Antioxidant Formulations
Authors: Vergara-Stange Valentina , Batista-Gonzalez Ana , Contreras Rodrigo A.
Published: November 2024

This study explores the antioxidant capabilities of green tea and acerola extracts in inhibiting myoglobin oxidation, a critical factor in preserving color stability in food products, mainly plant-based meat analogs. Extracts were analyzed for their antioxidant activity using DPPH and ORAC assays, followed by evaluations of their inhibitory effects on myoglobin oxidation at 25 °C and 35 °C. Acerola showed quick inhibitory effects even at lower concentrations and moderate temperatures, likely due to its high ascorbic acid levels. On the other hand, green tea’s effectiveness varied with temperature, with inhibition rates rising at 35 °C, probably because its polyphenolic compounds are sensitive to heat. The kinetics and thermodynamics analysis showed positive activation energy (Ea) for green tea, meaning it becomes more active as temperatures rise. In contrast, acerola’s negative Ea indicates heat reduces its efficacy. These results suggest that acerola and green tea could be natural alternatives to synthetic antioxidants, helping preserve the appearance and stability of different food products.
Comprehensive Evaluation of AlphaFold-Multimer, AlphaFold3 and ColabFold, and Scoring Functions in Predicting Protein-Peptide Complex Structures
Authors: Manshour Negin , Ren Jarett Zida , Esmaili Farzaneh , Bergstrom Erik , Xu Dong
Published: November 2024

Determining the three-dimensional structures of protein-peptide complexes is crucial for elucidating biological processes and designing peptide-based drugs. Protein-peptide docking has become essential for predicting complex structures. AlphaFold-Multimer, ColabFold and AlphaFold3 provided groundbreaking tools to enhance the protein-peptide docking accuracy. This study evaluates these three tools for predicting protein-peptide complex structures using Template-Based (TB) and Template-Free (TF) methods. AlphaFold-Multimer excels in TB predictions and performs moderately in TF scenarios in the prediction pool, but TF outperforms TB in the first-ranked models. ColabFold demonstrates versatility in both TB and TF settings. AlphaFold3 generates high-quality structures for more proteins, but the medium accuracy is not as good as AlphaFold-Multimer using a large model pool. We also assessed the performance of various scoring functions in ranking predicted protein-peptide complex structures. While the scoring function built in AlphaFold demonstrates the best performance, some other scoring functions, e.g., FoldX-Stability and HADDOCK-mdscore, provide complementary values. The findings suggest the potential for enhancing scoring functions targeting AlphaFold-based predictions by combining multiple scoring functions or using a consensus approach from many prediction models.
The Virtual Lab: AI Agents Design New SARS-CoV-2 Nanobodies with Experimental Validation
Authors: Swanson Kyle , Wu Wesley , Bulaong Nash L. , Pak John E. , Zou James
Published: November 2024

Science frequently benefits from teams of interdisciplinary researchers. However, most scientists don’t have access to experts from multiple fields. Fortunately, large language models (LLMs) have recently shown an impressive ability to aid researchers across diverse domains by answering scientific questions. Here, we expand the capabilities of LLMs for science by introducing the Virtual Lab, an AI-human research collaboration to perform sophisticated, interdisciplinary science research. The Virtual Lab consists of an LLM principal investigator agent guiding a team of LLM agents with different scientific backgrounds (e.g., a chemist agent, a computer scientist agent, a critic agent), with a human researcher providing high-level feedback. We design the Virtual Lab to conduct scientific research through a series of team meetings, where all the agents discuss a scientific agenda, and individual meetings, where an agent accomplishes a specific task. We demonstrate the power of the Virtual Lab by applying it to design nanobody binders to recent variants of SARS-CoV-2, which is a challenging, open-ended research problem that requires reasoning across diverse fields from biology to computer science. The Virtual Lab creates a novel computational nanobody design pipeline that incorporates ESM, AlphaFold-Multimer, and Rosetta and designs 92 new nanobodies. Experimental validation of those designs reveals a range of functional nanobodies with promising binding profiles across SARS-CoV-2 variants. In particular, two new nanobodies exhibit improved binding to the recent JN.1 or KP.3 variants of SARS-CoV-2 while maintaining strong binding to the ancestral viral spike protein, suggesting exciting candidates for further investigation. This demonstrates the ability of the Virtual Lab to rapidly make impactful, real-world scientific discovery.
Phosphorylation of MdWRKY70L by MdMPK6/02G mediates reactive oxygen synthesis to regulate apple fruit senescence
Authors: Wang Hui , Zhang Shuhui , Feng Yuchen , Sun Lulong , Yan Peng , Feng Yifeng , Zhao Zhengyang
Published: November 2024

Apple (Malus domestica) is a globally significant crop and a vital dietary component worldwide. During ripening, apples exhibit a longitudinal gradient, ripening first at the stalk cavity and extending toward the calyx pit. Over-ripening in the stalk cavity leads to early senescence, characterized by peel browning, which diminishes fruit quality. This study examines the natural senescence process in 6-year-old ‘Ruixue’ apples by screening transcriptome data to uncover senescence-related genes and validate their molecular functions. Our analysis of antioxidant capacity and reactive oxygen species in different peel regions revealed that malondialdehyde, hydrogen peroxide, and superoxide anion levels increased with senescence, especially in the stalk cavity. Transcriptome clustering and enrichment analyses across developmental stages revealedMdWRKY70L,MdSAG101, andMdZAT12as key regulators of peel senescence. Further invitroand invivostudies demonstrated that MdWRKY70L is phosphorylated at Ser199 by MdMPK6/02G, enhancing its stability and promoting peel senescence. These findings offer insights for developing strategies to delay fruit senescence and improve postharvest quality control.
Prothrombin prevents fatal T cell-dependent anemia during chronic virus infection of mice
Authors: Cantrell Rachel , Feldman H. Alex , Rosenfeldt Leah , Ali Ayad , Gourley Benjamin , Sprague Cassandra , Leino Daniel , Crosby Jeff , Revenko Alexey , Monia Brett , Waggoner Stephen N. , Palumbo Joseph S.
Published: November 2024

Thrombin promotes the proliferation and function of CD8+ T cells. To test if thrombin prevents exhaustion and sustains antiviral T cell activity during chronic viral infection, we depleted the thrombin-precursor prothrombin to 10% of normal levels in mice prior to infection with the clone 13 strain of lymphocytic choriomeningitis virus. Unexpectedly, prothrombin insufficiency resulted in 100% mortality after infection that was prevented by depletion of CD8+ T cells, suggesting that reduced availability of prothrombin enhances virus-induced immunopathology. Yet, the number, function, and apparent exhaustion of virus-specific T cells were measurably unaffected by prothrombin depletion. Histological analysis of the lung, heart, liver, kidney, spleen, intestine, and brain did not reveal any evidence of hemorrhage or increased tissue damage in low prothrombin mice that could explain mortality. Viral loads were also similar in infected mice regardless of prothrombin levels. Instead, infection of prothrombin-depleted mice resulted in a severe, T cell-dependent anemia associated with increased hemolysis. Thus, thrombin plays an unexpected protective role in preventing hemolytic anemia during virus infection, with potential implications for patients who are using direct thrombin inhibitors as an anticoagulant therapy.
Adaptive protein coevolution preserves telomere integrity
Authors: Lin Sung-Ya , Futeran Hannah , Levine Mia T.
Published: November 2024

Many essential conserved functions depend, paradoxically, on proteins that evolve rapidly under positive selection. How such adaptively evolving proteins promote biological innovation while preserving conserved, essential functions remains unclear. Here, we experimentally test the hypothesis that adaptive protein-protein coevolution within an essential multi-protein complex mitigates the deleterious incidental byproducts of innovation under pressure from selfish genetic elements. We swapped a single, adaptively evolving subunit of a telomere protection complex fromDrosophila yakubainto its close relative,D. melanogaster. The heterologous subunit uncovered a catastrophic interspecies incompatibility that caused lethal telomere fusions. Restoring six adaptively evolving sites on the protein-protein interaction surface, or introducing theD. yakubainteraction partner, rescued telomere integrity and viability. Ourin vivo, evolution-guided manipulations illuminate how adaptive protein-protein coevolution preserves essential functions threatened by an evolutionary pressure to innovate.
Measuring Growth, Resistance, and Recovery after Artemisinin Treatment of Plasmodium falciparum in a single semi-high-throughput Assay
Authors: Sievert Mackenzie A.C. , Singh Puspendra P. , Shoue Douglas A. , Checkley Lisa A. , Brenneman Katelyn M. , Qahash Tarrick , Cassady Zione , Kumar Sudhir , Li Xue , Nosten François H. , Anderson Timothy J.C. , Vaughan Ashley M. , Romero-Severson Jeanne , Ferdig Michael T.
Published: November 2024

Background

Artemisinin partial resistance (ART-R) has spread throughout Southeast Asia and mutations inpfKelch13, the molecular marker of resistance, are widely reported in East Africa. Effectivein vitroassays and robust phenotypes are crucial for monitoring populations for the emergence and spread of resistance. The recently developed extended Recovery Ring-stage Survival Assay used a qPCR-based readout to reduce the labor intensiveness forin vitrophenotyping of ART-R and improved correlation with the clinical phenotype of ART-R. Here, we extend and refine this assay to include measurements of parasite growth and recovery after drug exposure. Clinical isolates and progeny from two genetic crosses were used to optimize and validate the reliability of a straight-from-blood, SYBR Green-based qPCR protocol in a 96-well plate format to accurately measure phenotypes for Growth, Resistance, and Recovery.

Results

The assay determined growth between 6 h and 96 h, resistance at 120 h, and recovery from 120 h and 192 h. Growth can be accurately captured by qPCR and is shown by reproduction of previous growth phenotypes from HB3 × Dd2. Resistance measured at 120 h continually shows the most consistent phenotype for ring stage susceptibility. Recovery identifies an additional response to drug than parasites that are determined sensitive by Fold Change at 120 h. Comparison of progeny phenotypes for Growth vs Resistance showed a minor but significant correlation, whereas Growth vs Recovery and Resistance vs Recovery showed no significant correlation. Additionally, dried blood spot (DBS) samples matched Fold Change measured from liquid samples demonstrating Resistance can be easily quantified using either storage method.

Conclusions

The qPCR-based methodology provides the throughput needed to quickly measure large numbers of parasites for multiple relevant phenotypes. Growth can reveal fitness defects and illuminate relationships between proliferation rates and drug response. Recovery serves as a complementary phenotype to resistance that quantifies the ability of sensitive parasites to tolerate drug exposure. All three phenotypes offer a comprehensive assessment of parasite-drug interaction each with independent genetic determinants of main effect and overlapping secondary effects that should be further. By adapting our method to include DBS, readouts can be easily extended toex vivosurveillance applications.
Asymmetric neuromodulation in the respiratory network contributes to rhythm and pattern generation
Authors: Dhingra Rishi R. , MacFarlane Peter M. , Thomas Peter J. , Paton Julian F.R. , Dutschmann Mathias
Published: November 2024

Like other brain circuits, the brainstem respiratory network is continually modulated by neurotransmitters that activate slow metabotropic receptors. In many cases, activation of these receptors only subtly modulates the respiratory motor pattern. However, activation of some receptor types evokes the arrest of the respiratory motor pattern as can occur following the activation of µ-opioid receptors. We propose that the varied effects of neuromodulation on the respiratory motor pattern depend on the pattern of neuromodulator receptor expression and their influence on the excitability of their post-synaptic targets. Because a comprehensive characterization of these cellular properties across the respiratory network remains challenging, we test our hypothesis by combining computational modelling with ensemble electrophysiologic recording in the pre-Bötzinger complex (pre-BötC) using high-density multi-electrode arrays (MEA). Our computational model encapsulates the hypothesis that neuromodulatory transmission is organized asymmetrically across the respiratory network to promote rhythm and pattern generation. To test this hypothesis, we increased the strength of neuromodulatory connections in the model and used selective agonistsin situwhile monitoring pre-BötC ensemble activities. The model predictions of increasing slow inhibition were consistent with experiments examining the effect of systemic administration of the 5HT1aR agonist 8-OH-DPAT. Similarly, the predicted effects of increasing slow excitation in the model were experimentally confirmed in pre-BötC ensemble activities before and after systemic administration of the µ-opioid receptor agonist fentanyl. We conclude that asymmetric neuromodulation can contribute to respiratory rhythm and pattern generation and accounts for its varied effects on breathing.
U1 snRNP-Specific U1C Acts as the Gatekeeper of the Survival of Motor Neurons (SMN) Complex in snRNP Biogenesis
Authors: Ngu Duc Minh , Myti Sanat , Khan Ayesha Ali , Keita Jeannine , Moore Tessa , Andega Paul , Aziz Alaa , Raj Ritu , Park Meeyeon , Johnson-Winters Kayunta , Suh Eul hyun , Yong Jeongsik , So Byung Ran
Published: November 2024

The stability and abundance of spliceosomal snRNPs are determined by the assembly of an Sm protein ring (Sm core) on each snRNA, a process facilitated by the survival of motor neuron (SMN) complex. Whereas the SMN complex’s role as a chaperone is well-established, the mechanisms that regulate its activity remain unclear. Our study identifies U1C, a U1 snRNP-specific protein, as a key regulator of the SMN complex. U1C together with U1-70K facilitates U1 snRNP formation, rendering the SMN complex accessible for other snRNAs to assemble Sm cores. Remarkably, a prevalent cancer-associated mutation in U1 snRNA near the U1C binding site not only disrupts Sm core assembly but also sequesters the SMN complex, inhibiting canonical snRNP formation. Our findings provide mechanistic insights into how snRNP-specific proteins regulate the SMN complex and suggest that U1 snRNA mutations in numerous cancers disrupt the SMN complex, leading to perturbation in various RNA metabolism pathways.

Highlights

U1C facilitates the formation of Sm core not only on U1 snRNA but also on other snRNAs.

U1C together with U1-70K promotes U1 snRNP formation, enabling the SMN complex to recruit Gemin5/other snRNAs complex.

The divalent binding of U1C to the SMN complex is mediated by U1C’s N-terminus helix, interacting with U1-70K, and its arginine-methylated C-terminus domain, binding to the SMN protein.

Multiple U1 snRNA mutations in cancer patients defect in Sm core assembly and potentially sequester the SMN complex, thereby inhibiting canonical snRNP formation.
Public opinions from Malawian and Malawi refugee camp residents of wastewater and environmental surveillance
Authors: Jeboda Dammy , Shackelford Brandie Banner , Chigwechokha Petros , Chunga Brighton A. , Ercumen Ayse , Workman Cassandra , Hart Joy L. , Smith Ted , Holm Rochelle H.
Published: November 2024

Across low- and middle-income countries, there have been calls to expand wastewater and environmental surveillance to include non-sewered sanitation systems. Considering public opinion, understanding, and acceptance, as well as any related privacy and personal health information concerns, in this context is important. This study used an in-person survey to learn more about Malawian and Malawi refugee camp residents’ perceptions of wastewater and environmental surveillance as public health tools, and their perceptions of privacy and personal health information. A 15-question survey was conducted from May to July 2024 at three locations in northern, central, and southern Malawi, including a refugee camp (n= 536). Some respondents (n= 30) also completed a board game and a post-board game survey. The results indicated high public support for surveilling communicable diseases, deadly diseases, environmental toxicants, healthy eating, illegal drugs, mental illnesses, and prescription drugs. Respondents were less supportive of surveillance that may expose their lifestyle behaviors and alcohol use. Regarding sampling locations, the surveillance of an entire city or of camp and schools had the highest acceptance. Some opposition to surveillance in business and religious organizations was found. If their sanitation waste was to be monitored, the respondents wanted the results of the data analysis to be communicated. Our findings suggested that Malawian and Malawi camp residents supported, with little concern, ongoing wastewater and environmental surveillance for public health. Considering privacy thresholds and participant autonomy regarding public health surveillance tools among cultural relevancies is important for future policy development and investment.
Single-photon large-momentum-transfer atom interferometry scheme for Sr or Yb atoms with application to determining the fine-structure constant
Authors: Schelfhout Jesse S. , Hird Thomas M. , Hughes Kenneth M. , Foot Christopher J.
Published: November 2024

The leading experimental determinations of the fine-structure constant α currently rely on atomic photon-recoil measurements from Ramsey-Bordé atom interferometry with large-momentum transfer to provide an absolute mass measurement. We propose an experimental scheme for an intermediate-scale differential atom interferometer to measure the photon recoil of neutral atomic species with a single-photon optical clock transition. We calculate trajectories for our scheme that optimize the recoil phase while nullifying the undesired gravity-gradient phase by considering independently launching two clouds of ultracold atoms with the appropriate initial conditions. For Sr and Yb, we find an atom interferometer of height 3 m to be sufficient for an absolute mass measurement precision of Δm/m∼1×10−11 with current technology. Such a precise measurement would halve the current uncertainty in α, an uncertainty that would no longer be limited by an absolute mass measurement. The removal of this limitation would allow the current uncertainty in α to be reduced by a factor of 10 by corresponding improvements in relative mass measurements, thus paving the way for higher-precision tests of the standard model of particle physics.

Published by the American Physical Society
2024
Role of harmonic and anharmonic interactions in controlling the cooperativity of spin-crossover molecular crystals
Authors: Markin Oleksandr , Gudyma Iurii , Boukheddaden Kamel
Published: November 2024

We present a theoretical model of spin transitions in homogeneous spin-crossover (SCO) materials, based on the description of the interactions between SCO molecules by the Lennard-Jones potential in which the equilibrium distances depend on the spin states of the linked molecules. By expanding the potential to order 3 considering a homogeneous lattice spacing, we demonstrate that the present model is isomorphic with an Ising-like model combining infinite long-range “ferromagnetic-like” interactions, competing with short-range “antiferromagnetic-like” between nearest neighbors in the case of harmonic interactions. When an anharmonic contribution is included, the short-range interaction becomes dependent on the average high-spin fraction, and changes its sign along the spin transition. The thermodynamic properties of the model were first investigated analytically in mean field approximation for both harmonic and anharmonic cases, for which we clarify the conditions for obtaining gradual and first-order transitions. Moreover, we demonstrated that within this approximation, the strength of the antiferromagnetic-like interactions are insufficient to produce multistep transitions. In contrast, the resolution of the previous emerging Ising-like model by Monte Carlo simulations demonstrated the possibility of obtaining gradual, first-order and two-step transitions as a result of the antagonism between long- and short-range interactions. Overall, the obtained results demonstrate the suitability of the present theoretical model to describe cooperative SCO materials. The key message of our paper is that our model can be used to predict complex behavior of spin-crossover crystals.

Published by the American Physical Society
2024
cc¯
and
bb¯
suppression in the glasma
Authors: Pooja  , Jamal Mohammad Yousuf , Bhaduri Partha Pratim , Ruggieri Marco , Das Santosh K.
Published: November 2024

This study investigates the evolution and dissociation dynamics of cc¯ and bb¯ pairs within the preequilibrium, gluon-dominated stage of high energy nuclear collisions. An attractive potential made of a perturbative Coulomb-like term and of a confining term is used to simulate the attractive strong force in the pairs. Besides, we implement the interaction of the pairs with the evolving glasma fields by virtue of the Wong equations. The interaction with the classical color fields dominates the dynamics, causing an increase in pair separation and subsequent dissociation. The observed finite probability of dissociation for these states reveals the intricate interplay between quantum chromodynamics (QCD) dynamics and the suppression of cc¯ and bb¯ states during the preequilibrium stage. The research highlights differences between cc¯ and bb¯ pairs, revealing the role of quark flavor in the dissociation process. Dissociation spectra analysis indicates a peak shift toward higher momentum, reflecting a slight energy gain by the pairs. This investigation provides valuable insights into the complex dynamics of cc¯ and bb¯ pairs in the glasma, which may help in better interpretation of experimental results on further integration with subsequent phases of the created matter.

Published by the American Physical Society
2024
Pole structures of the
X(1840)
or
X(1835)
and the
X(1880)
Authors: Niu Peng-Yu , Zhang Zhen-Yu , Li Yi-Yao , Wang Qian , Zhao Qiang
Published: November 2024

Whether the NN¯ interaction could form a state or not is a long standing question, even before the observation of the pp¯ threshold enhancement in 2003. The recent high statistic measurement in the J/ψ→γ3(π+π−) channel would provide a good opportunity to probe the nature of the peak structures around the pp¯ threshold in various processes. By constructing the NN¯ interaction respecting chiral symmetry, we extract the pole positions by fitting the pp¯ and 3(π+π−) invariant mass distributions of the J/ψ→γpp¯ and J/ψ→γ3(π+π−) processes. The threshold enhancement in the pp¯ invariant mass distribution is from the pole on the third Riemann sheet, which more couples to the isospin triplet channel. The broader structure in the 3(π+π−) invariant mass comes from the pole on the physical Riemann sheet, which more couples to the isospin singlet channel. Furthermore, the large compositeness indicates that there should exist pp¯ resonance based on the current experimental data. In addition, we also see a clear threshold enhancement in the nn¯ channel, but not as significant as that in pp¯ channel, which is useful and compared with further experimental measurement.

Published by the American Physical Society
2024
Mixing effects on spectroscopy and partonic observables of heavy mesons with logarithmic confining potential in a light-front quark model
Authors: Pandya Bhoomika , Gurjar Bheemsehan , Chakrabarti Dipankar , Choi Ho-Meoyng , Ji Chueng-Ryong
Published: November 2024

Using the variational principle, we systematically investigate the mass spectra and wave functions of both 1S and 2S state heavy pseudoscalar (P) and vector (V) mesons within the light-front quark model. This approach incorporates a Coulomb plus logarithmic confinement potential to accurately describe the constituent quark and antiquark dynamics. Additionally, spin hyperfine interactions are introduced perturbatively to compute the masses of pseudoscalar and vector mesons. The present analyses of the 1S and 2S states require the consideration of mixing between them to account for empirical constraints. These constraints include the mass gap ΔMP>ΔMV, where ΔMP(V)=MP(V)2S−MP(V)1S and the hierarchy of the decay constants f1S>f2S. We find the optimal value of the mixing angle to be θ=18°, significantly enhancing the consistency between our spectroscopic predictions and the experimental data compiled by the Particle Data Group. Furthermore, based on the predicted mass, the newly observed resonance BJ(5840) could be assigned as a 21S0 state in the B meson family. The study also reports various pertinent observables, including twist-two distribution amplitudes, electromagnetic form factors, charge radii, ξ moments, and transition form factors that are found to be consistent with both available lattice simulations and experimental data. In addition, our predicted branching ratios for the channels of B+→τ+ντ as well as rare decays of B0 and Bs0 appear in accordance with experimental data.

Published by the American Physical Society
2024
Wave functions of multiquark hadrons from representations of the symmetry groups
Sn
Authors: Miesch Nicholas , Shuryak Edward
Published: November 2024

Construction of the wave functions of multiquark hadrons by a traditional method based on the tensor products of colors, flavors, spins (and orbital) parts becomes quite complex when quark numbers grow n=5,6…12, as it gets difficult to satisfy the requirements of Fermi statistics. Our novel approach is focused directly on representations of the permutation symmetry generators. After showing how C3 is manifested in the wave functions of (excited) baryons, we use it to construct the wave functions for a set of pentaquarks and hexaquarks (n=5,6). We also have some partial results for larger systems, with n=9 and 12, and even beyond that as far as n=24.

Published by the American Physical Society
2024
QCD with
2+1
flavors at the physical point in external chromomagnetic fields
Authors: Cea Paolo , Cosmai Leonardo
Published: November 2024

We investigate full quantum chromodynamics (QCD) with (2+1)-flavor of highly improved staggered quarks fermions at the physical point in the presence of uniform Abelian chromomagnetic background fields. Our focus is to conduct an exploratory study on the renormalized light and strange chiral condensates around the pseudocritical temperature. We find that in the confined region the gauge system is subjected to the chromomagnetic catalysis that turns into the inverse catalysis in the high-temperature regime. We further observe that the chiral condensates are subjected to the so-called thermal hysteresis. Our estimate of the deconfinement temperature indicates that the critical temperature begins to decrease in the small field region, soon after it seems to saturate and finally increase with the strength of the chromomagnetic field.

Published by the American Physical Society
2024
Out-of-equilibrium chiral magnetic effect from simulations on Euclidean lattices
Authors: Buividovich P. V.
Published: November 2024

The status of the chiral magnetic effect (CME) response in full quantum chromodynamics (QCD) has been controversial so far, with previous lattice QCD studies indicating either its strong suppression or vanishing in thermal equilibrium state. We introduce the Euclidean-time correlator of axial charge and electric current as an observable that can be used to study the finite out-of-equilibrium CME response in first-principle lattice QCD simulations with background magnetic field. This observable directly reflects the fact that in the background magnetic field, a state with nonzero axial charge features nonzero electric current. For free fermions, the axial-vector correlator only receives contributions from the lowest Landau level, and exhibits a linear dependence on both magnetic field and temperature with a universal coefficient. With an appropriate regularization, nonvanishing axial-vector correlator is compatible with the vanishing of the CME current in thermal equilibrium state with nonzero chiral chemical potential μ5. We demonstrate that the real-time counterpart of the Euclidean-time axial-vector correlator is intimately related to the real-time form of the axial anomaly equation, which strongly limits possible corrections in full QCD. We present numerical results for the Euclidean-time axial-vector correlator in SU(2) lattice gauge theory with Nf=2 light quark flavors, demonstrating reasonable agreement with free fermion result on both sides of the chiral crossover. The proposed methodology should help to answer the question whether the QCD corrections might be responsible for nonobservation of CME in heavy-ion collision experiments such as the RHIC isobar run.

Published by the American Physical Society
2024
Minimal solution to the axion isocurvature problem from nonminimal coupling
Authors: Berbig Maximilian
Published: November 2024

The main limitation for preinflationary breaking of Peccei-Quinn (PQ) symmetry is the upper bound on the Hubble rate during inflation from axion isocurvature fluctuations. This leads to a tension between high scale inflation and QCD axions with grand unified theory scale decay constants, which reduces the potential for a detection of tensor modes at next generation cosmic microwave background (CMB) experiments. We propose a mechanism that explicitly breaks PQ symmetry via nonminimal coupling to gravity, that lifts the axion mass above the Hubble scale during inflation and has negligible impact on today’s axion potential. The initially heavy axion gets trapped at an intermediate minimum during inflation given by the phase of the nonminimal coupling, before it moves to its true CP-conserving minimum after inflation. During this stage, it undergoes coherent oscillations around an adiabatically decreasing minimum, which slightly dilutes the axion energy density, while still being able to explain the observed dark matter relic abundance. This scenario can be tested by the combination of next generation CMB surveys like CMB-S4 and LiteBIRD with haloscopes such as ABRACADABRA, DMRadio, or CASPEr-Electric.

Published by the American Physical Society
2024
Majoron-driven leptogenesis in gauged
U(1)Lμ−Lτ
model
Authors: Wada Juntaro
Published: November 2024

We propose a novel leptogenesis scenario in the gauged U(1)Lμ−Lτ model. Achieving successful leptogenesis in the U(1)Lμ−Lτ symmetric phase is challenging due to the absence of a CP phase, caused by restriction from the gauge symmetry. To overcome this issue, we introduce an additional global symmetry, U(1)B−L, and a scalar field Φ responsible for breaking this symmetry. Through the kinetic misalignment mechanism, the Majoron field associated with U(1)B−L symmetry breaking has a kinetic motion in the early Universe. Subsequently, time-dependent Majoron field background induces the background CP phase dynamically, leading to successful leptogenesis in the U(1)Lμ−Lτ symmetric phase. Furthermore, Majoron itself serves as a dark matter candidate in this scenario. As one of the phenomenological applications, we consider the model that can also explain the muon g−2 anomaly.

Published by the American Physical Society
2024
Electric-magnetic duality of dyonic Kerr-Newman-NUT-AdS spacetimes
Authors: Corral Cristóbal , Olea Rodrigo
Published: November 2024

We study the (anti-)self-duality conditions under which the electric and magnetic parts of the conserved charges of the dyonic Kerr-Newman-NUT-anti-de Sitter solution become equivalent. Within a holographic framework, the stress tensor and the boundary Cotton tensor are computed from the electric/magnetic content of the Weyl tensor. The holographic stress tensor/Cotton tensor duality is recovered along the (anti-)self-dual curve in parameter space. We show that the latter not only implies a duality relation for the mass but also for the angular momentum. The partition function is computed to first order in the saddle-point approximation and a Bogomol’nyi-Prasad-Sommerfield bound is obtained. The ground state of the theory is enlarged to all the (anti-)self-dual configurations when the SO(4) and U(1) Pontryagin densities are introduced. We demonstrate this at the level of the action and variations thereof.

Published by the American Physical Society
2024
Supergeometric quantum effective action
Authors: Gattus Viola , Pilaftsis Apostolos
Published: November 2024

Supergeometric quantum field theories (SG-QFTs) are theories that go beyond the standard supersymmetric framework, since they allow for general scalar-fermion field transformations on the configuration space of a supermanifold, without requiring an equality between bosonic and fermionic degrees of freedom. After revisiting previous considerations, we extend them by calculating the one-loop effective action of minimal SG-QFTs that feature nonzero fermionic curvature in two and four spacetime dimensions. By employing an intuitive approach to the Schwinger–DeWitt heat-kernel technique and a novel field-space generalized Clifford algebra, we derive the ultraviolet structure of characteristic effective-field-theory (EFT) operators up to four spacetime derivatives that emerge at the one-loop order and are of physical interest. Upon minimizing the impact of potential ambiguities due to the so-called multiplicative anomalies, we find that the EFT interactions resulting from the one-loop supergeometric effective action are manifestly diffeomorphically invariant in configuration space. The extension of our approach to evaluating higher loops of the supergeometric quantum effective action is described. The emerging landscape of theoretical and phenomenological directions for further research of SG-QFTs is discussed.

Published by the American Physical Society
2024
Notes on peculiarities of the Schwinger-DeWitt technique: One-loop double poles, total-derivative terms, and determinant anomalies
Authors: Barvinsky A. O. , Kalugin A. E.
Published: November 2024

We discuss peculiarities of the Schwinger-DeWitt technique for quantum effective action, associated with the origin of dimensionally regularized double-pole divergences of the one-loop functional determinant for massive Proca model in a curved spacetime. These divergences have the form of the total-derivative term generated by integration by parts in the functional trace of the heat kernel for the Proca vector field operator. Because of the nonminimal structure of second-order derivatives in this operator, its vector field heat kernel has a nontrivial form, involving the convolution of the scalar d’Alembertian Green’s function with its heat kernel. Moreover, its asymptotic expansion is very different from the universal predictions of Gilkey-Seeley heat kernel theory because the Proca operator violates one of the basic assumptions of this theory—the nondegeneracy of the principal symbol of an elliptic operator. This modification of the asymptotic expansion explains the origin of double-pole total-derivative terms. Another hypostasis of such terms is in the problem of multiplicative determinant anomalies—lack of factorization of the functional determinant of a product of differential operators into the product of their individual determinants. We demonstrate that this anomaly should have the form of total-derivative terms and check this statement by calculating divergent parts of functional determinants for products of minimal and nonminimal second-order differential operators in curved spacetime.

Published by the American Physical Society
2024
Emergent spacetime and the ergodic hierarchy
Authors: Gesteau Elliott
Published: November 2024

Various diagnostics of the emergence of an arrow of time in the bulk description of a holographic theory have been proposed, including the decay of some real time correlation functions and the appearance of type III1 von Neumann algebras carrying half-sided modular inclusions. This Letter puts forward a close parallel between these diagnostics and a quantum formulation of the ergodic hierarchy of dynamical systems. Theories with an emergent spacetime appear to sit near the top of this hierarchy.

Published by the American Physical Society
2024
Interaction of complex particles: A framework for the rapid and accurate approximation of pair potentials using neural networks
Authors: Isfeldt Gusten , Lundell Fredrik , Wohlert Jakob
Published: November 2024

Motivated by the limitations of conventional coarse-grained molecular dynamics for simulation of large systems of nanoparticles and the challenges in efficiently representing general pair potentials for rigid bodies, we present a method for approximating general rigid body pair potentials based on a specialized type of deep neural network that maintains essential properties, such as conservation of energy and invariance to the chosen origins of the particles. The network uses a specialized geometric abstraction layer to convert the relative coordinates of the rigid bodies to input more suitable to a conventional artificial neural network, which is trained together with the specialized layer. This results in geometric representations of the particles optimized for the specific potential. The network can be trained directly on scalar values to fit a model without explicit gradient and then used to efficiently evaluate the force and torque on the particles resulting from the potential. The concept is demonstrated with an atomistic interaction model for carbon nanotubes and the resulting model is compared with a common type of coarse-grained model optimized for the same potential, with even very small networks comparing favourably and larger networks achieving up to two orders of magnitude lower cost. The sensitivity to noise in the training data is investigated and the model is found to strongly reject noise up to 12.5% given a dataset of 107 samples. The performance of a proof-of-concept implementation is demonstrated on a variety of hardware, showing the models viability for large-scale simulations. Furthermore, generalization to soft bodies and potentials for polydisperse systems are discussed.

Published by the American Physical Society
2024
Relative State Counting for Semiclassical Black Holes
Authors: Akers Chris , Sorce Jonathan
Published: November 2024

It has been shown that entropy differences between certain states of perturbative quantum gravity can be computed without specifying an ultraviolet completion. This is analogous to the situation in classical statistical mechanics, where entropy differences are defined but absolute entropy is not. Unlike in classical statistical mechanics, however, the entropy differences computed in perturbative quantum gravity do not have a clear physical interpretation. Here we construct a family of perturbative black hole states for which the entropy difference can be interpreted as a relative counting of states. Conceptually, this Letter begins with the algebra of mass fluctuations around a fixed black hole background, and points out that while this is a type I algebra, it is not a factor and therefore has no canonical definition of entropy. As in previous work, coupling the mass fluctuations to quantum matter embeds the mass algebra within a type II factor, in which entropy differences (but not absolute entropies) are well defined. It is then shown that for microcanonical wave functions of mass fluctuation, the type II entropy difference equals the logarithm of the dimension of the extra Hilbert space that is needed to map one microcanonical window to another using gauge-invariant unitaries. The Letter closes with comments on type II entropy difference in a more general class of states, where the von Neumann entropy difference does not have a physical interpretation, but “one-shot” entropy differences do.

Published by the American Physical Society
2024
Experimental Demonstration of Mode-Coupled and High-Brightness Self-Amplified Spontaneous Emission in an X-Ray Free-Electron Laser
Authors: Prat Eduard , Hu Wenxiang , Arrell Christopher , Calvi Marco , Dijkstal Philipp , Follath Rolf , Reiche Sven
Published: November 2024

X-ray free-electron lasers (FELs) are modern research tools with applications in multiple scientific fields. Standard x-ray FEL pulses are produced by the self-amplified spontaneous emission (SASE) mechanism. SASE-FEL pulses have high power, short duration, and excellent transverse coherence but exhibit poor temporal coherence with power and spectral profiles consisting of multiple randomly distributed spikes. Here, we present the demonstration of two modes that enhance the temporal coherence of SASE-FEL radiation: mode-coupled and high-brightness SASE. Both schemes are based on delaying the electron beam with magnetic chicanes placed between the undulator modules of the FEL facility. First, we show the generation of frequency combs with tunable peak separation via the mode-coupled SASE scheme. Second, we present a proof-of-principle demonstration of the high-brightness SASE mechanism, producing FEL pulses with a bandwidth reduction up to a factor of 3 with respect to standard SASE pulses. The demonstration was done at Athos, the soft x-ray beamline of SwissFEL, for photon energies between 500 and 600 eV. Our work will benefit current applications and may open up new research areas requiring frequency combs or narrow bandwidths.

Published by the American Physical Society
2024
Characterizing non-Markovian and coherent errors in quantum simulation
Authors: Prakash Aditya , Hebbe Madhusudhana Bharath
Published: November 2024

Quantum simulation of many-body systems, particularly using ultracold atoms and trapped ions, presents a unique form of quantum control—it is a direct implementation of a multi-qubit gate generated by the Hamiltonian. As a consequence, it also faces a unique challenge in terms of benchmarking, because the well-established gate benchmarking techniques are unsuitable for this form of quantum control. Here we show that the symmetries of the target many-body Hamiltonian can be used not only to benchmark but to characterize experimental errors in the quantum simulation. We use our results to develop protocols to characterize these errors, which can be implemented using state-of-the-art technology. We consider two forms of errors: (i) unitary errors arising out of systematic errors in the applied Hamiltonian and (ii) canonical non-Markovian errors arising out of random shot-to-shot fluctuations in the applied Hamiltonian. We show that the dynamics of the expectation value of the target Hamiltonian itself, which is ideally constant in time, can be used to characterize these errors. In the presence of errors, the expectation value of the target Hamiltonian shows a characteristic thermalization dynamics, when it satisfies the operator thermalization hypothesis (OTH). That is, an oscillation in the short time followed by relaxation to a steady-state value in the long time limit. We show that while the steady-state value can be used to characterize the coherent errors, the amplitude of the oscillations can be used to estimate the non-Markovian errors. We prove a sandwich theorem to establish a linear relation between the amplitude of the oscillations and the magnitude of the non-Markovian errors. Moreover, by varying the initial state, we show that the steady state values can be used to completely construct the generator of the coherent errors. Using these results, we develop two experimental protocols to characterize the unitary errors based on these results, one of which requires single-qubit addressing and the other one doesn't. We also develop a protocol to characterize non-Markovian errors.

Published by the American Physical Society
2024