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At least 1,009 records · Page 56

Cartesian message passing neural networks for directional properties: Fast and transferable atomic multipoles

The message passing neural network (MPNN) framework is a promising tool for modeling atomic properties but is, until recently, incompatible with directional properties, such as Cartesian tensors. We propose a modified Cartesian MPNN (CMPNN) suitable for predicting atom-centered multipoles, an essential component of ab initio force fields. The efficacy of this model is demonstrated on a newly developed dataset consisting of 46 623 chemical structures and corresponding high-quality atomic multipoles, which was deposited into the publicly available Molecular Sciences Software Institute QCArchive server. We show that the CMPNN accurately predicts atom-centered charges, dipoles, and quadrupoles and that errors in the predicted atomic multipoles have a negligible effect on multipole–multipole electrostatic energies. The CMPNN is accurate enough to model conformational dependencies of a molecule’s electronic structure. This opens up the possibility of recomputing atomic multipoles on the fly throughout a simulation in which they might exhibit strong conformational dependence.

Glick, Zachary L. (ORCID:0000000309002849)↗

Progress with applications of three-ion ICRF scenarios for fusion research: A review

The viability of magnetic confinement fusion as an energy source depends on achieving the high ion temperatures required for D-T fusion. Among the available techniques, plasma heating with waves in the ion cyclotron range of frequencies (ICRF) is a prominent method for bulk ion heating in fusion plasmas. Furthermore, a detailed understanding of the non-linear physics of alpha heating and the complex impact of MeV-range fast ions on plasma dynamics becomes progressively more important. This paper provides a comprehensive overview of recent developments with the three-ion ICRF scenarios on Alcator C-Mod, ASDEX Upgrade and JET tokamaks. The results demonstrate the flexibility of these novel scenarios for heating bulk ions in D-T ≈ 50%-50% plasmas and efficient generation of MeV-range fast ions in multi-ion species plasmas. In conclusion, several key results relevant for ITER and future fusion reactors are highlighted.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Expanded Phylogenetic Diversity and Metabolic Flexibility of Mercury-Methylating Microorganisms

Methylmercury is a potent bioaccumulating neurotoxin that is produced by specific microorganisms that methylate inorganic mercury. Methylmercury production in diverse anaerobic bacteria and archaea was recently linked to the hgcAB genes. However, the full phylogenetic and metabolic diversity of mercury-methylating microorganisms has not been fully unraveled due to the limited number of cultured experimentally verified methylators and the limitations of primer-based molecular methods. Here, we describe the phylogenetic diversity and metabolic flexibility of putative mercury-methylating microorganisms by hgcAB identification in publicly available isolate genomes and metagenome-assembled genomes (MAGs) as well as novel freshwater MAGs. We demonstrate that putative mercury methylators are much more phylogenetically diverse than previously known and that hgcAB distribution among genomes is most likely due to several independent horizontal gene transfer events. The microorganisms we identified possess diverse metabolic capabilities spanning carbon fixation, sulfate reduction, nitrogen fixation, and metal resistance pathways. We identified 111 putative mercury methylators in a set of previously published permafrost metatranscriptomes and demonstrated that different methylating taxa may contribute to hgcA expression at different depths. Overall, we provide a framework for illuminating the microbial basis of mercury methylation using genome-resolved metagenomics and metatranscriptomics to identify putative methylators based upon hgcAB presence and describe their putative functions in the environment.

59 BASIC BIOLOGICAL SCIENCES↗

Diverging drivers of fungal diversity: seasonal effects shape aboveground communities, while geographical patterns govern belowground communities in rubber tree ecosystems

Understanding the spatiotemporal dynamics of microbial communities is essential for predicting their ecological roles and interactions with host plants. In a recent study, Wei and colleagues (Microbiol Spectr 13:e02097-24, 2024) investigated fungal diversity across multiple plant and soil compartments in rubber trees over two seasons and two geographically distinct regions in China. Their findings revealed that alpha diversity was primarily influenced by seasonal changes and physicochemical factors, while beta diversity exhibited a strong geographical pattern, shaped by leaf phosphorus and soil available potassium. These results highlight the role of environmental drivers in shaping within-community diversity, while other factors contribute to the differences between fungal communities across the soil–plant continuum. By distinguishing the effects of temporal and spatial factors, this study provides detailed insights into plant-associated microbiomes and emphasizes the need for further research on the functional implications of microbial diversity in the context of changing environmental and agricultural conditions.

fungal diversity↗

RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins

Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.

3D visualization↗

PyZebrascope: An Open-Source Platform for Brain-Wide Neural Activity Imaging in Zebrafish

Understanding how neurons interact across the brain to control animal behaviors is one of the central goals in neuroscience. Recent developments in fluorescent microscopy and genetically-encoded calcium indicators led to the establishment of whole-brain imaging methods in zebrafish, which record neural activity across a brain-wide volume with single-cell resolution. Pioneering studies of whole-brain imaging used custom light-sheet microscopes, and their operation relied on commercially developed and maintained software not available globally. Hence it has been challenging to disseminate and develop the technology in the research community. Here, we present PyZebrascope, an open-source Python platform designed for neural activity imaging in zebrafish using light-sheet microscopy. PyZebrascope has intuitive user interfaces and supports essential features for whole-brain imaging, such as two orthogonal excitation beams and eye damage prevention. Its camera module can handle image data throughput of up to 800 MB/s from camera acquisition to file writing while maintaining stable CPU and memory usage. Its modular architecture allows the inclusion of advanced algorithms for microscope control and image processing. As a proof of concept, we implemented a novel automatic algorithm for maximizing the image resolution in the brain by precisely aligning the excitation beams to the image focal plane. PyZebrascope enables whole-brain neural activity imaging in fish behaving in a virtual reality environment. Thus, PyZebrascope will help disseminate and develop light-sheet microscopy techniques in the neuroscience community and advance our understanding of whole-brain neural dynamics during animal behaviors.

59 BASIC BIOLOGICAL SCIENCES↗

Radiation Oncology in the Land of the Pyramids: How Sudan Continues to Push the Frontiers of Cancer Care in Eastern Africa

When faced with illness, Sudanese patients have traditionally relied primarily on folklore healers. In the recent past, Sudan increased its health care spending and placed ever-greater importance on medical education. Although traditional remedies still play an important role, Sudanese patients increasingly consult conventional medicine. Not only infectious diseases but also a rising burden of noncommunicable conditions, including cancer, represent major health care challenges. Therefore, Sudan will need to make the best out of the limited resources available and further increase investment in health care to confront these trends successfully. Sudan was one of the first African countries to recognize the importance of radiation oncology in multidisciplinary cancer care and began investing in it in the 1960s. Today, there are 4 comprehensive cancer centers in the country, which offer radiation therapy and employ 10 radiation therapy machines for a population of about 45 million people. This proportion is an indication that Sudan still has an underfunded health care system with a lack of infrastructure and human resources. The present manuscript intends to provide a well-rounded overview of radiation oncology in Sudan today.

62 RADIOLOGY AND NUCLEAR MEDICINE↗

Direct Optical Lithography of Colloidal Metal Oxide Nanomaterials for Diffractive Optical Elements with 2π Phase Control

Spatially patterned dielectric materials are ubiquitous in electronic, photonic, and optoelectronic devices. These patterns are typically made by subtractive or additive approaches utilizing vapor-phase reagents. On the other hand, recent advances in solution-phase synthesis of oxide nanomaterials have unlocked a materials library with greater compositional, microstructural, and interfacial tunability. However, methods to pattern and integrate these nanomaterials in real-world devices are less established. In this work, we directly optically pattern oxide nanoparticles (NPs) by mixing them with photosensitive diazo-2-naphthol-4-sulfonic acid and irradiating with widely available 405 nm light. We demonstrate the direct optical lithography of ZrO 2 , TiO 2 , HfO 2 , and ITO NPs and investigate the chemical and physical changes responsible for this photoinduced decrease in solubility. Micron-thick layers of amorphous ZrO 2 NPs were patterned with micron resolution and shown to allow 2 pi phase control of visible light. We also show multilayer patterning and use it to fabricate features with different thicknesses and distinct structural colors. Upon annealing at 400 degrees C, the deposited ZrO 2 structures have excellent optical transparency across a wide wavelength range (0.3-10 mu m), a high refractive index (n = 1.84 at 633 nm), and are optically smooth. We then fabricate diffractive optical elements, such as binary phase diffraction gratings, that show efficient diffractive behavior and good thermal stability. Different oxide NPs can also be mixed prior to patterning, providing a high level of material tunability. This work demonstrates a general patterning approach that harnesses the processability and diversity of colloidal oxide nanomaterials for use in photonic applications.

2𝜋 phase shift↗

Toward first principles-based simulations of dense hydrogen

Accurate knowledge of the properties of hydrogen at high compression is crucial for astrophysics (e.g., planetary and stellar interiors, brown dwarfs, atmosphere of compact stars) and laboratory experiments, including inertial confinement fusion. There exists experimental data for the equation of state, conductivity, and Thomson scattering spectra. However, the analysis of the measurements at extreme pressures and temperatures typically involves additional model assumptions, which makes it difficult to assess the accuracy of the experimental data rigorously. On the other hand, theory and modeling have produced extensive collections of data. They originate from a very large variety of models and simulations including path integral Monte Carlo (PIMC) simulations, density functional theory (DFT), chemical models, machine-learned models, and combinations thereof. At the same time, each of these methods has fundamental limitations (fermion sign problem in PIMC, approximate exchange–correlation functionals of DFT, inconsistent interaction energy contributions in chemical models, etc.), so for some parameter ranges accurate predictions are difficult. Recently, a number of breakthroughs in first principles PIMC as well as in DFT simulations were achieved which are discussed in this review. Here we use these results to benchmark different simulation methods. We present an update of the hydrogen phase diagram at high pressures, the expected phase transitions, and thermodynamic properties including the equation of state and momentum distribution. Furthermore, we discuss available dynamic results for warm dense hydrogen, including the conductivity, dynamic structure factor, plasmon dispersion, imaginary-time structure, and density response functions. We conclude by outlining strategies to combine different simulations to achieve accurate theoretical predictions that are based on first principles.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Disentangling the physics of the attractive Hubbard model as a fully interacting model of fermions via the accessible and symmetry-resolved entanglement entropies

The complicated ways in which electrons interact in many-body systems such as molecules and materials have long been viewed through the lens of local electron correlation and associated correlation functions. However, quantum information science has demonstrated that more global diagnostics of quantum states like the entanglement entropy can provide a complementary and clarifying lens on electronic behavior. One particularly useful measure that can be used to distinguish between quantum and classical sources of entanglement is the accessible entanglement, the entanglement available as a quantum resource for systems subject to conservation laws, such as fixed particle number, due to superselection rules. In this work, we introduce an algorithm and demonstrate how to compute accessible and symmetry-resolved entanglements for interacting fermion systems. This is accomplished by combining an incremental version of the swap algorithm with a recursive auxiliary field quantum Monte Carlo algorithm recently developed by the authors. We apply these tools to study the pairing and charge density waves exhibited in the paradigmatic attractive Hubbard model via entanglement. We find that the particle and spin symmetry-resolved entanglements and their related full probability distribution functions show very clear—and unique—signatures of the underlying electronic behavior even when those features are less pronounced in conventional correlation functions. Altogether, this work provides a systematic means of characterizing the entanglement within quantum systems that can grant a deeper understanding of the complicated electronic behavior that underlies quantum phase transitions and crossovers in many-body systems.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Atomic-Scale Surface Studies of Bulk Metallic Glasses. Final Report

Bulk metallic glasses (BMGs) are of both scientific and technological interest because the absence of periodic atomic arrangements provides them with unique physical, chemical, and mechanical properties. Their high strength, superior elasticity, and an ability to be easily formed into virtually unlimited shapes with feature sizes from centimeters to Angstroms by blow molding and thermoplastic forming makes them an attractive choice for more and more practical applications and products. Due to their complex internal structure, however, experiments that yield insight into their exact atomic arrangements have been scarce. As a result, glass physics is one of the last remaining unexplored fields of materials science despite the scientific and technological importance of glasses in our daily lives, and the question how to characterize and control matter away from equilibrium, as glasses are, was listed as one of five Grand Challenges in a recent DoE report. The main reason for the slow progress in glass physics is the lack of experimental tools that enable access to atomic-scale structural and behavioral information for disordered materials. Such atomic-scale knowledge is mandatory to establish structure-property relationships that ultimately could allow to custom-design alloys featuring specific desired characteristics. With no such relationships available, theory development in glass remains basic and the few that exist are often untested. The aim of this research was to enable progress in our understanding of BMGs by developing a new approach that will allow a meaningful application of local surface science methods to specially prepared BMG samples to obtain a wealth of quantitative information on their atomic arrangements. Key was the availability of specially prepared samples whose surfaces feature large atomically flat terraces despite being entirely amorphous, which we have produced from a Pt 57.5 Cu 14.7 Ni 5.3 P 22.5 alloy (‘Pt-BMG’) both under ambient conditions as well as in ultrahigh vacuum using a unique setup that has been specially developed within this grant. Our approach starts with the in-situ preparation of oxide crystals that are terminated by large terraces, from which exact mirror images out of BMG will be produced using thermoplastic forming (TPF); for the research within this grant, we have successfully used (001)-oriented SrTiO 3 single crystal surfaces as well as (100)-, (110)-, and (111)-oriented single crystals made from LaAlO 3 . Since the resulting BMG replicas display all features of the original crystal with sub-Angstrom fidelity, thereby mimicking the original crystal’s termination by atomically flat terraces without being crystalline themselves, they are ideally suited for further investigation. The following atomic-scale local studies were then carried within this proposal: (i) high-resolution surface imaging and local spectroscopy using scanning probe microscopy, which showed disordered atom-like features and revealed changes in the gradient of the local surface potential on a 1-2 nm length scale; (ii) characterization of atomic-scale plastic flow with affected volumes as low as 1000 atoms, which showed local hardness near or above the theoretically predicted maximum and, once plastic deformation was initiated, homogeneous flow of the atoms involved; (iii) characterization of surface relaxation processes and the onset of crystallization induced by annealing, which showed that upon heating over the material’s glass transition temperature, the surface rearranges and relaxes towards a more stable, denser packed glass, which increases on-terrace surface roughness, while surface tension smoothens step edges; and (iv) studies that investigate the dependence of the material’s mechanical properties and structure on processing parameters, revealing that relaxed glasses get denser, harder, and more elastic. In combination, this information allows to combine structural models with mechanical properties and preparation history, thereby facilitating the development of preparation-structure-property relationships for metallic glasses. With the availability of such information, bulk metallic glasses can be further optimized to be used in more and more applications in industry.

36 MATERIALS SCIENCE↗

Optimized cryogenic setup for microwave loss characterization of superconducting coaxial cables

As superconducting quantum systems scale up to enable applications like large-scale quantum computing, challenges such as fabrication yield, wiring complexity, and microwave crosstalk drive the need for high-fidelity, low-loss, modular interconnects. In recent experiments, the performance of these interconnects is often limited by cable loss, a factor that becomes even more critical as we aim for higher fidelity operations and connect increasingly coherent modules. In this talk, we present our cryogenic microwave loss characterization setup, carefully designed to minimize losses external to the coaxial cables under test. We also share results for several commercially-available superconducting cables measured with this setup and briefly discuss our ongoing efforts to develop custom coaxial cables capable of achieving state-of-the-art performance.

Vallières, André [Northwestern U.]↗

Optimized cryogenic setup for microwave loss characterization of superconducting coaxial cables

As superconducting quantum systems scale up to enable applications like large-scale quantum computing, challenges such as fabrication yield, wiring complexity, and microwave crosstalk drive the need for high-fidelity, low-loss, modular interconnects. In recent experiments, the performance of these interconnects is often limited by cable loss, a factor that becomes even more critical as we aim for higher fidelity operations and connect increasingly coherent modules. In this talk, we present our cryogenic microwave loss characterization setup, carefully designed to minimize losses external to the coaxial cables under test. We also share results for several commercially-available superconducting cables measured with this setup and briefly discuss our ongoing efforts to develop custom coaxial cables capable of achieving state-of-the-art performance.

Vallières, André [Northwestern U.]↗

Single Carrier Modulation Resource Allocation for Massive MIMO with Virtual Antennas

Today’s Massive MIMO cellular operation is dominated by orthogonal frequency division multiplexing (OFDM) modulation. One of the advantages of OFDM is the flexibility to carve up the available spectrum into resource blocks (RBs) that can operate adjacent to one another. Massive MIMO adds spatial multiplexing layers on top of the RBs, enabling the simultaneous operation of dozens of UEs. Cyclic prefixed single carrier modulation (CP-SCM) is an alternative to OFDM that also benefits from massive MIMO and is useful as an OFDM alternative in specific scenarios. However, until recently, no resource allocation method has been proposed for CP-SCM. In this paper, we present a CP-SCM resource allocation scheme using virtual antennas in a massive MIMO time domain duplexed scenario. By creating several virtual antennas for each physical antenna, the benefits of massive MIMO are achieved with a smaller physical antenna count. Resources are quantized into data streams, and each user can be assigned a variable number of simultaneous streams. This paper presents a detailed development and analysis of multi-stream processing (MSP) for both uplink detection and downlink precoding. We also introduce heterogeneous MSP, where CP-SCM and OFDM signals can be processed in the same MSP framework.

5G and beyond communications↗

Policies and Practices to Improve the Chemistry Graduate Student Experience: Implications of the ACS Survey of Graduate Students

STEM graduate education is vitally important in producing the talent needed to fuel our economy and provide solutions for the challenges we face in emerging diseases and climate change. Yet recent research indicates that women and students who identify as members of minority groups traditionally underrepresented in STEM face extraordinary challenges in their graduate careers. This commentary describes ways in which chemistry graduate education could become more supportive and inclusive through changes by graduate students, faculty, departments, funding agencies, and professional organizations. As a result the scientific workforce could utilize the full range of available talent and become more productive.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An Intercomparison of Large‐Eddy Simulations of a Convection Cloud Chamber Using Haze‐Capable Bin and Lagrangian Cloud Microphysics Schemes

Abstract Recent in situ observations show that haze particles exist in a convection cloud chamber. The microphysics schemes previously used for large‐eddy simulations of the cloud chamber could not fully resolve haze particles and the associated processes, including their activation and deactivation. Specifically, cloud droplet activation was modeled based on Twomey‐type parameterizations, wherein cloud droplets were formed when a critical supersaturation for the available cloud condensation nuclei (CCN) was exceeded and haze particles were not explicitly resolved. Here, we develop and adapt haze‐capable bin and Lagrangian microphysics schemes to properly resolve the activation and deactivation processes. Results are compared with the Twomey‐type CCN‐based bin microphysics scheme in which haze particles are not fully resolved. We find that results from the haze‐capable bin microphysics scheme agree well with those from the Lagrangian microphysics scheme. However, both schemes significantly differ from those from a CCN‐based bin microphysics scheme unless CCN recycling is considered. Haze particles from the recycling of deactivated cloud droplets can strongly enhance cloud droplet number concentration due to a positive feedback in haze‐cloud interactions in the cloud chamber. Haze particle size distributions are more realistic when considering solute and curvature effects that enable representing the complete physics of the activation process. Our study suggests that haze particles and their interactions with cloud droplets may have a strong impact on cloud properties when supersaturation fluctuations are comparable to mean supersaturation, as is the case in the cloud chamber and likely is the case in the atmosphere, especially in polluted conditions.

54 ENVIRONMENTAL SCIENCES↗

The 2021 update of the EPA’s adverse outcome pathway database

The EPA developed the Adverse Outcome Pathway Database (AOP-DB) to better characterize adverse outcomes of toxicological interest that are relevant to human health and the environment. Here we present the most recent version of the EPA Adverse Outcome Pathway Database (AOP-DB), version 2. AOP-DB v.2 introduces several substantial updates, which include automated data pulls from the AOP-Wiki 2.0, the integration of tissue-gene network data, and human AOP-gene data by population, semantic mapping and SPARQL endpoint creation, in addition to the presentation of the first publicly available AOP-DB web user interface. Potential users of the data may investigate specific molecular targets of an AOP, the relation of those gene/protein targets to other AOPs, cross-species, pathway, or disease-AOP relationships, or frequencies of AOP-related functional variants in particular populations, for example. Version updates described herein help inform new testable hypotheses about the etiology and mechanisms underlying adverse outcomes of environmental and toxicological concern.

59 BASIC BIOLOGICAL SCIENCES↗