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At least 1,153 records · Page 64

Leveraging public AI tools to explore systems biology resources in mathematical modeling

Predictive mathematical modeling is an essential part of systems biology and is interconnected with information management. Systems biology information is often stored in specialized formats to facilitate data storage and analysis. These formats are not designed for easy human readability and thus require specialized software to visualize and interpret results. Therefore, comprehending modeling and underlying networks and pathways is contingent on mastering systems biology tools, which is particularly challenging for users with no or little background in data science or system biology. To address this challenge, we investigated the usage of public Artificial Intelligence (AI) tools in exploring systems biology resources in mathematical modeling. We tested public AI’s understanding of mathematics in models, related systems biology data, and the complexity of model structures. Our approach can enhance the accessibility of systems biology for non-system biologists and help them understand systems biology without a deep learning curve.

59 BASIC BIOLOGICAL SCIENCES↗

Regularization by denoising diffusion models for solving inverse PDE problems with application to full waveform inversion

Partial differential equation (PDE)-governed inverse problems are fundamental across various scientific and engineering applications; yet they face significant challenges due to nonlinearity, ill-posedness, and sensitivity to noise. Here, we introduce a computational framework, regularization by denoising using diffusion models for partial differential equations (RED-DiffEq), by integrating physics-driven inversion and data-driven learning. RED-DiffEq leverages pretrained diffusion models as a regularization mechanism for PDE-governed inverse problems. We apply RED-DiffEq to solve the full waveform inversion problem in geophysics, a challenging seismic imaging technique that seeks to reconstruct high-resolution subsurface velocity models from seismic measurement data. Our method shows enhanced accuracy and robustness compared to benchmark methods. Additionally, it exhibits strong generalization and domain decomposition capacity, enabling the inversion of more complex velocity models with larger domains than those used in training the diffusion model. Our framework can also be directly applied to diverse PDE-governed inverse problems.

Shan, Siming [Yale University, New Haven, CT (Unit↗

Room temperature crystal field splitting of curium resolved by circularly polarized luminescence spectroscopy

Coordination of Cm(III) with a chiral decadentate ligand N,N,N',N'-tetrakis[(6-carboxypyridin-2-yl)methyl]-1,2-diaminocyclohexane (tpadac) generated complexes with strong luminescence allowing for the unprecedented measurement of well-resolved Cm(III) circularly polarized luminescence spectra. Quantitative resolution of the electronic structure of the [Cm(tpadac)][K] complexes was achieved at room temperature, highlighting the strength of the combination of luminescence and circularly polarized luminescence spectroscopies to unravel the fundamental electronic structure of Cm(III). These results are a clear demonstration that these spectroscopies are powerful yet simple tools for the fundamental understanding of electronic structure, which opens the door to future investigations of other Cm(III) complexes in geometries relevant to nuclear applications, and even other 5f-elements.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Uniformity, performance, and durability of roll-to-roll-coated iridium oxide electrolyzer catalyst layers

This work investigates the use of roll-to-roll coating methods for the production of iridium oxide catalyst layers for proton exchange membrane water electrolyzers. Catalyst layers were produced using two coating methods: slot die and gravure. By varying the solids content of the catalyst ink and coating process variables loadings between 0.08 and 0.64 mg Ir cm −2 were prepared with relatively high spatial uniformity. However, at loadings below 0.2 mg Ir cm −2 microscopy reveals voids in the catalyst layer due to similar length scales of catalyst agglomerates and overall layer thickness. Electrochemical testing shows that these voids do not impact initial membrane electrode assembly performance but lead to increased performance losses after potential cycling compared to spray coated catalyst layers.

08 HYDROGEN↗

Non-ideal stoichiometry and thermochemistry of aqueous iridium oxide nanoparticles in proton-coupled electron transfer and oxygen-atom transfer

Reported here are reactions of aqueous colloidal IrO x nanoparticles (NPs) with proton-coupled electron transfer (PCET) and oxygen-atom transfer (OAT) organic reagents, determining the reaction stoichiometries and thermochemistry. IrO x NPs have attracted much attention for their high electrocatalytic activity, but understanding of their fundamental reaction chemistry is limited. This IrO x NP model system is simple, with UV-vis titrations demonstrating reversible interconversion between predominantly Ir IV and predominantly Ir III NPs. This simplicity allows studies that reveal their complex non-idealities. The NP redox chemistry has a “super-Nernstian” stoichiometry of ∼1.3H + per 1e − transferred during both PCET and OAT reactions, as measured with electrochemistry and chemical methods. Spectroelectrochemistry revealed a broad distribution of surface IrO x –H bond dissociation free energies (BDFEs), becoming weaker as more H is added. Such variation in binding strengths—a non-ideal binding isotherm—is common for surface adsorbates. For IrO x , the variation of BDFE(IrO–H)s is fit well to a Frumkin isotherm with a width of 6.5 kcal mol −1 . For OAT from the reactive oxygen atoms of IrO x NPs, bracketing experiments gave 93 ± 24 kcal mol −1 for the average BDFE(O x Ir–O), with a predicted spread much larger than that for the BDFE(IrO–H). Taken together, the results show the importance of non-ideal stoichiometry and thermochemistry for IrO x NPs, and they open a path to more complete models to understand catalytic redox reactions at such surfaces.

Iridium Oxide Nanoparticles (NPs)↗

Isomers and band assignments in the cryogenic vibrational spectrum of the binary complex between water and protonated formic acid using two color, IR–IR photobleaching and H/D isotopic substitution

Protonated formic acid (PFA) is purported to be the active species in the catalytic activation of condensation reactions at the acidic interface of microdroplets. Here, we investigate the fundamental interaction between PFA and water with cryogenic ion vibrational spectroscopy of the binary PFA–H 2 O complexes generated via electrospray ionization followed by buffer gas cooling to about 20 K. The patterns displayed by the isomer-specific IR spectra of D 2 -tagged PFA–H 2 O indicate that two distinct, non-interconverting rotamers are present at low temperatures based on the cis and trans structures of the HCO 2 $H$$^{+}_{2}$ core ion. Both of these occur with the water molecule attached to the OH that is in a cis-configuration relative to the CH group (denoted E), but differ in the E vs Z (cis vs trans relative to the CH group) orientation of the spectator OH. This assignment scheme corrects a previous theoretical analysis that invoked a scenario in which structures with E- and Z-bound water molecules interconvert at low (20 K) temperatures. Isomer-specific bands arising from the OH stretches and water bending modes are deconvoluted using isotopomer-specific spectroscopy of the complexes with partial H/D exchange. The dependence of the nominal shared proton OH stretch frequency on the deuteration of the tethered water confirms strong coupling between this mode and the water bending fundamental.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

The impact of pulse width modulation on heat accumulation in AlGaN channel HEMTs

The poor thermal properties of Aluminum–Gallium Nitride (AlGaN) channel High Electron Mobility Transistors (HEMTs) on sapphire limit the device’s maximum switching frequency due to high channel temperatures. Extracting the correct thermal time constants can provide guidelines for the device’s safe frequency operation. This study experimentally quantifies the impact of pulse width and duty cycle on the transient thermal dynamics of multi-finger AlGaN channel HEMTs. In most transient thermal metrology, lock-in averaging approaches are leveraged to increase signal-to-noise ratio and measure the device’s relative temperature rise. Assuming no heat accumulation, the temperature rise is used to quantify the device’s thermal resistance under continued pulsed biasing. For devices grown on sapphire substrates, however, heat accumulation leads to elevated reference temperatures and causes the differential measurement to underestimate the peak temperature. This study demonstrates the capability of transient Gate Resistance Thermometry (tGRT) to measure the absolute temperature, which is required to precisely evaluate the device’s thermal resistance. When an absolute temperature measurement is not feasible (such as thermoreflectance imaging), a solution is proposed to derive the peak temperature under pulsed biasing based on the differential temperature under pulsing and the steady-state thermal resistance (which is typically easier to obtain). Finally, additional tGRT (without averaging) is performed to demonstrate the temperature-dependent thermal time constants required to minimize heat accumulation effects.

Field effect transistors↗

Influence of nanoscale interfaces on the dynamic deformation and spall failure of Cu–Fe alloy microstructures

Additively manufactured immiscible Cu–Fe alloys can exhibit a distribution of nanoscale interfaces due to the distribution of nanoscale clusters in the equilibrium and metastable phases. Molecular dynamics simulations investigate the role of such interfaces on the phase stability and transformation behavior during shock compression, as well as the mechanisms of damage nucleation during spall failure. The model multiphase Cu–Fe systems studied here comprise a distribution of Fe clusters in an FCC Cu matrix, as well as Cu clusters in a BCC Fe matrix. The length scales of the nanoscale clusters determine the energetics of the interfaces that can result in FCC/BCC (equilibrium) or FCC/FCC (metastable) interfaces in the Cu system matrix, and BCC/FCC (equilibrium) or BCC/BCC (metastable) interfaces in the Fe matrix. The MD simulations demonstrate that nanoscale metastable interface microstructures can induce plastic deformation and also stabilize phases or suppress phase transformations in metastable phase clusters. In contrast, equilibrium interfaces can influence phase transformation thresholds and serve as additional void nucleation sites during failure.

36 MATERIALS SCIENCE↗

Efficient and generalizable nested Fourier-DeepONet for three-dimensional geological carbon sequestration

Geological carbon sequestration (GCS) involves injecting CO2 into subsurface geological formationsfor permanent storage. Numerical simulations could guide decisions in GCS projects by predictingCO 2 migration pathways and the pressure distribution in storage formation. However, these simula-tions are often computationally expensive due to highly coupled physics and large spatial-temporalsimulation domains. Surrogate modelling with data-driven machine learning has become a promis-ing alternative to accelerate physics-based simulations. Among these, the Fourier neural operator(FNO) has been applied to three-dimensional synthetic subsurface models. Despite its good accuracyin simulating CO 2 plume migration, it requires large computational resources in training and alsolacks generalizability. Here, to further improve performance, we have developed a nested Fourier-DeepONet by combining the expressiveness of the FNO with the modularity of a deep operatornetwork (DeepONet). This new framework is twice as efficient as a nested FNO for training and has atleast 80% lower GPU memory requirement due to its flexibility to treat temporal coordinates sepa-rately. These performance improvements are achieved without compromising prediction accuracy.In addition, the generalization and extrapolation ability of nested Fourier-DeepONet beyond thetraining range has been thoroughly evaluated. Nested Fourier-DeepONet outperformed the nestedFNO for extrapolation in time with more than 50% reduced error. It also exhibited good extrapolationaccuracy beyond the training range in terms of reservoir properties, number of wells, and injectionrate.

Lee, Jonathan E. [Department of Chemical and Envir↗

Integration of ultra-low coverage whole-genome sequences for reconstructing the evolutionary history of Galapagos giant tortoises

Genomic data from contemporary and historical samples often need to be coupled for evolutionary reconstructions of multitaxon complexes. However, the genetic data recovered from historical samples may result only in ultra-low coverage whole-genome sequences (ulcWGS; <0.15× depth), leading to inaccurate evolutionary inferences given a preponderance of missing data. Using the Galapagos giant tortoise radiation as a study system (Chelonoidis spp., composed of 13 extant and four extinct lineages), we assembled a novel methodological pipeline that removes potential noise introduced by the missing data and enhances the evolutionary signal from ulcWGS samples. We leveraged existing tools for phylogenomic placement (EPA-ng), population genomic structure (smartsnp) and admixture (Admixfrog, NGSadmix) to demonstrate that the evolutionary history of samples can be uncovered with sequencing depths as low as 0.008–0.139×. Importantly, these approaches do not use genotype imputation of the ulcWGS samples, which would require extensive reference datasets. Our application to two cases of extinct lineages of Galapagos giant tortoises, with and without references from the same lineage, demonstrates the general value of the approach. We confirm where the extinct lineages from San Cristóbal and Santa Fe islands fit into the Galapagos giant tortoise radiation, and that these lineages were evolutionarily distinct entities.

ancient DNA↗

Co-designing Spectral Transformation Oracles with Hybrid Oscillator-Qubit Quantum Processors: From Algorithms to Compilation

We co-design a family of quantum eigenvalue transformation oracles that can be efficiently implemented on hybrid discrete- or continuous-variable (qubit or qumode) hardware. To illustrate the oracle’s representation-theoretic power and near-term experimental accessibility, we encode a Gaussian imaginary time-evolution spectral filter. As a result, we define a continuous linear combination of unitaries block encoding. Due to the ancillary qumode’s infinite-dimensional nature, continuous-variable qumodes constitute a powerful compilation tool for encoding continuous spectral functions without discretization errors while minimizing resource requirements. We then focus on the ubiquitous task of preparing eigenstates in quantum spin models. For completeness, we provide an end-to-end compilation which expresses high-level oracles in terms of an experimentally realizable instruction set architecture in both 1D and 2D. Finally, we examine the leading-order effects of physical errors and highlight open research directions. Our algorithms scale linearly with the spatial extent of the target system and are applicable to both near-term and large-scale quantum processors.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

New H erwig7 underlying event tune: From RHIC to LHC energies

We present parameter sets corresponding to new underlying event tunes for the H erwig7.3 Monte Carlo event generator. The existing H erwig tunes are in good agreement with LHC data, however, they are not typically designed for center-of-mass energies below $\sqrt{𝑠}$ = 300 GeV. The tunes presented in this study can describe midrapidity data collected at the nominal RHIC energy of $\sqrt{𝑠}$ = 200 GeV as well as higher center-of-mass energies utilized by experiments at the LHC and Tevatron. The base “New Haven” tune is developed by fitting minimum-bias simulations of proton-proton ($𝑝⁢𝑝$) collisions to midrapidity identified hadron and jet data from the STAR experiment. The “Nashville” tune includes a separate set of parameters developed by tuning to Tevatron proton-antiproton ($𝑝\bar{⁢𝑝}$) data at $\sqrt{𝑠}$ = 300, 900 and 1960 GeV from CDF, and LHC $𝑝⁢𝑝$ measurements from CMS at $\sqrt{𝑠}$ =7 TeV, in addition to the STAR measurements. Both new tunes demonstrate significant improvements over the recommended default tune currently included in the latest version of H erwig for minimum bias production. As such, we advocate using these tunes for future simulation studies at midrapidity by experimental collaborations at RHIC (STAR and sPHENIX) and the LHC (ALICE, ATLAS, and CMS).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Low-energy enhancement of the magnetic dipole radiation in odd-mass lanthanides

We compute the magnetic dipole (M1) $\gamma$-ray strength functions ($\gamma$SF) for the odd-mass lanthanides $^{\textrm{143-151}}$Nd and $^{\textrm{147-153}}$Sm using the shell-model Monte Carlo method in combination with the static-path approximation and the maximum-entropy method. In particular, we quantify the statistical uncertainties in the calculated M1 $\gamma$SFs and show that they are under control for the excitation energies relevant to the experiments despite a Monte Carlo sign problem that originates in the projection onto an odd number of neutrons. We identify a low-energy enhancement (LEE) in the M1 $\gamma$SFs of these odd-mass lanthanides, which was recently observed experimentally in some of them. We also find a scissors mode resonance (SR) in the strongly deformed isotopes. We observe that the decrease in the LEE strength with neutron number along an isotopic chain is compensated for by an increase in the SR strength in the deformed nuclei. Furthermore, we compare our results with recent experiments.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

Hadronic light-by-light contribution to the muon anomaly from lattice QCD with infinite volume QED at physical pion mass

The hadronic light-by-light scattering contribution to the muon anomalous magnetic moment, (g–2)⁢/2, is computed in the infinite volume QED framework with lattice QCD. We report $a^{HLbL}_μ$ = 12.47⁢(1.15)⁢(0.95) ×10 –10 where the first error is statistical and the second systematic. The result is mainly based on the 2+1 flavor Möbius domain wall fermion ensemble with inverse lattice spacing a –1 = 1.73 GeV, lattice size L = 5.5 fm, and m π = 139 MeV, generated by the RBC-UKQCD collaborations. The leading systematic error of this result comes from the lattice discretization. This result is consistent with previous determinations.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Robust nonlinear isolators based on frozen mode exceptional point degeneracies

We introduce a class of imperfection-protected nonlinear isolators designed to operate at exceptional point degeneracies (EPDs) of the Bloch modes of periodic photonic structures. These Bloch EPDs are responsible for slow light and the emergence of a scattering frozen mode regime (FMR). When a weak spectral asymmetry is introduced, the group velocity in their proximity varies sharply, boosting the directional nature of the nonlinear interactions and leading to extreme isolation.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Dichotomy of flat bands in the van der Waals ferromagnet Fe 5 ⁢GeTe 2

Quantum materials with bands of narrow bandwidth near the Fermi level represent a promising platform for exploring a diverse range of fascinating physical phenomena, as the high density of states within the small energy window often enables the emergence of many-body physics. On one hand, flat bands can arise from strong Coulomb interactions that localize atomic orbitals. On the other hand, quantum destructive interference can quench the electronic kinetic energy. Although both have a narrow bandwidth, the two types of flat bands should exhibit very distinct spectral properties arising from their distinctive origins. So far, the two types of flat bands have only been realized in very different material settings and chemical environments, preventing a direct comparison. Here, in this study, we report the observation of the two types of flat bands within the same material system—an above-room-temperature van der Waals ferromagnet, Fe 5−x GeTe 2 , distinguishable by a switchable iron site order. The contrasting nature of the flat bands is also identified by the remarkably distinctive temperature evolution of the spectral features, indicating that one arises from electron correlations in the Fe(1) site-disordered phase, while the other geometrical frustration in the Fe(1) site-ordered phase. Our results therefore provide a direct juxtaposition of the distinct formation mechanism of flat bands in quantum materials and an avenue for understanding the distinctive roles flat bands play in the presence of magnetism, topology, and lattice geometrical frustration, utilizing sublattice ordering as a key control parameter.

Wu, Han [Rice Univ., Houston, TX (United States)] ↗

Combining molecular beam epitaxy and low-energy electron microscopy with in situ magnetic susceptibility measurements within an integrated ultrahigh vacuum system

Quantum two-dimensional materials, including ultrathin superconducting films, are of great current research interest. These films are typically fabricated under ultra-high vacuum (UHV) conditions and are sensitive to the environment—prone to oxidation and contamination when exposed to the atmosphere. This hampers the study of their intrinsic properties by standard ex situ techniques. Here, we present a variable-temperature mutual inductance probe system integrated under UHV with molecular beam epitaxy (MBE) synthesis and low-energy electron microscopy, enabling nondestructive in situ characterization of superconducting thin films. The system employs a reflection-type configuration and reaches a low temperature (∼4 K) using a high-cooling-power, vibration-isolated cryocooler. In conclusion, we demonstrate the system performance by measuring the superconducting critical temperature in a copper-oxide thin film.

2D materials↗